From f803a19e1fead7e7c749b59e5737ebbe66d1d5bd Mon Sep 17 00:00:00 2001 From: Heinz-Alexander Fuetterer Date: Sat, 3 Aug 2024 15:45:39 +0200 Subject: [PATCH 1/6] chore: convert json files in data directory to yaml --- fuji_server/data/README.md | 23 +- fuji_server/data/access_rights.json | 171 - fuji_server/data/access_rights.yaml | 121 + fuji_server/data/file_formats.json | 2326 - fuji_server/data/file_formats.yaml | 1665 + .../data/identifiers_org_resolver_data.json | 36272 --------- .../data/identifiers_org_resolver_data.yaml | 30750 ++++++++ fuji_server/data/jsonldcontext.json | 7988 -- fuji_server/data/jsonldcontext.yaml | 5377 ++ fuji_server/data/licenses.json | 5539 -- fuji_server/data/licenses.yaml | 4211 ++ fuji_server/data/linked_vocab.json | 6284 -- fuji_server/data/linked_vocab.yaml | 4190 ++ .../linked_vocabs/bioportal_ontologies.json | 9224 --- .../linked_vocabs/bioportal_ontologies.yaml | 6717 ++ .../data/linked_vocabs/bioregistry.json | 61916 ---------------- .../data/linked_vocabs/bioregistry.yaml | 52384 +++++++++++++ .../linked_vocabs/bioregistry_ontologies.json | 46201 ------------ .../linked_vocabs/bioregistry_ontologies.yaml | 39101 ++++++++++ .../data/linked_vocabs/cessda_ontologies.json | 538 - .../data/linked_vocabs/cessda_ontologies.yaml | 465 + .../data/linked_vocabs/fhir_ontologies.json | 38 - .../data/linked_vocabs/fhir_ontologies.yaml | 28 + .../data/linked_vocabs/fuji_ontologies.json | 76 - .../data/linked_vocabs/fuji_ontologies.yaml | 60 + .../data/linked_vocabs/gesis_ontologies.json | 38 - .../data/linked_vocabs/gesis_ontologies.yaml | 30 + .../data/linked_vocabs/iso_ontologies.json | 1065 - .../data/linked_vocabs/iso_ontologies.yaml | 909 + .../data/linked_vocabs/lov_ontologies.json | 9672 --- .../data/linked_vocabs/lov_ontologies.yaml | 9332 +++ ..._ontologies.json => mmisw_ontologies.yaml} | 0 .../data/linked_vocabs/sdn_ontologies.json | 4160 -- .../data/linked_vocabs/sdn_ontologies.yaml | 3577 + .../data/linked_vocabs/sweet_ontologies.json | 2477 - .../data/linked_vocabs/sweet_ontologies.yaml | 2025 + fuji_server/data/longterm_formats.json | 119 - fuji_server/data/metadata_standards.json | 6287 -- fuji_server/data/metadata_standards.yaml | 4010 + fuji_server/data/metadata_standards_uris.json | 40040 ---------- fuji_server/data/metadata_standards_uris.yaml | 23639 ++++++ fuji_server/data/open_formats.json | 78 - fuji_server/data/software_file.json | 69 - fuji_server/data/software_file.yaml | 46 + fuji_server/data/standard_uri_protocols.json | 50 - fuji_server/data/standard_uri_protocols.yaml | 32 + fuji_server/harvester/github_harvester.py | 10 +- fuji_server/helper/linked_vocab_helper.py | 24 +- fuji_server/helper/preprocessor.py | 88 +- tests/conftest.py | 4 + tests/harvester/test_github_harvester.py | 15 + tests/helper/test_linked_vocab_helper.py | 15 + tests/helper/test_preprocessor.py | 129 +- 53 files changed, 188864 insertions(+), 240741 deletions(-) delete mode 100644 fuji_server/data/access_rights.json create mode 100644 fuji_server/data/access_rights.yaml delete mode 100644 fuji_server/data/file_formats.json create mode 100644 fuji_server/data/file_formats.yaml delete mode 100644 fuji_server/data/identifiers_org_resolver_data.json create mode 100644 fuji_server/data/identifiers_org_resolver_data.yaml delete mode 100644 fuji_server/data/jsonldcontext.json create mode 100644 fuji_server/data/jsonldcontext.yaml delete mode 100644 fuji_server/data/licenses.json create mode 100644 fuji_server/data/licenses.yaml delete mode 100644 fuji_server/data/linked_vocab.json create mode 100644 fuji_server/data/linked_vocab.yaml delete mode 100644 fuji_server/data/linked_vocabs/bioportal_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/bioportal_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/bioregistry.json create mode 100644 fuji_server/data/linked_vocabs/bioregistry.yaml delete mode 100644 fuji_server/data/linked_vocabs/bioregistry_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/bioregistry_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/cessda_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/cessda_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/fhir_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/fhir_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/fuji_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/fuji_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/gesis_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/gesis_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/iso_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/iso_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/lov_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/lov_ontologies.yaml rename fuji_server/data/linked_vocabs/{mmisw_ontologies.json => mmisw_ontologies.yaml} (100%) delete mode 100644 fuji_server/data/linked_vocabs/sdn_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/sdn_ontologies.yaml delete mode 100644 fuji_server/data/linked_vocabs/sweet_ontologies.json create mode 100644 fuji_server/data/linked_vocabs/sweet_ontologies.yaml delete mode 100644 fuji_server/data/longterm_formats.json delete mode 100644 fuji_server/data/metadata_standards.json create mode 100644 fuji_server/data/metadata_standards.yaml delete mode 100644 fuji_server/data/metadata_standards_uris.json create mode 100644 fuji_server/data/metadata_standards_uris.yaml delete mode 100644 fuji_server/data/open_formats.json delete mode 100644 fuji_server/data/software_file.json create mode 100644 fuji_server/data/software_file.yaml delete mode 100644 fuji_server/data/standard_uri_protocols.json create mode 100644 fuji_server/data/standard_uri_protocols.yaml create mode 100644 tests/harvester/test_github_harvester.py create mode 100644 tests/helper/test_linked_vocab_helper.py diff --git a/fuji_server/data/README.md b/fuji_server/data/README.md index 60c2ccea..a1309a33 100644 --- a/fuji_server/data/README.md +++ b/fuji_server/data/README.md @@ -1,21 +1,18 @@ # Data files - -- [`linked_vocabs/*_ontologies.json`](./linked_vocabs) -- [`access_rights.json`](./access_rights.json): Lists COAR, EPRINTS, EU, OPENAIRE access rights. Used for evaluation of the data access level, FsF-A1-01M, which looks for metadata item `access_level`. +- [`linked_vocabs/*_ontologies.yaml`](./linked_vocabs) +- [`access_rights.yaml`](./access_rights.yaml): Lists COAR, EPRINTS, EU, OPENAIRE access rights. Used for evaluation of the data access level, FsF-A1-01M, which looks for metadata item `access_level`. - [`bioschemastypes.txt`](./bioschemastypes.txt) - [`creativeworktypes.txt`](./creativeworktypes.txt) - [`default_namespaces.txt`](./default_namespaces.txt): Excluded during evaluation of the semantic vocabulary, FsF-I2-01M. -- [`file_formats.json`](./file_formats.json): Dictionary of scientific file formats. Used in evaluation of R1.3-02D to check the file format of the data. +- [`file_formats.yaml`](./file_formats.yaml): Dictionary of scientific file formats. Used in evaluation of R1.3-02D to check the file format of the data. - [`google_cache.db`](./google_cache.db): Used for evaluating FsF-F4-01M (searchability in major catalogues like DataCite registry, Google Dataset, Mendeley, ...). Google Data search is queried for a PID in column `google_links`. It's a dataset with metadata about datasets that have a DOI or persistent identifier from `identifer.org`. -- [`identifiers_org_resolver_data.json`](./identifiers_org_resolver_data.json): Used in [`IdentifierHelper`](fuji_server/helper/identifier_helper.py). -- [`jsonldcontext.json`](./jsonldcontext.json) -- [`licenses.json`](./licenses.json): Used to populate `Preprocessor.license_names`, a list of SPDX licences. Used in evaluation of licenses, FsF-R1.1-01M. -- [`linked_vocab.json`](./linked_vocab.json) -- [`longterm_formats.json`](./longterm_formats.json): This isn't used any more (code is commented out). Instead, the info should be pulled from [`file_formats.json`](./file_formats.json). -- [`metadata_standards_uris.json`](./metadata_standards_uris.json) -- [`metadata_standards.json`](./metadata_standards.json): Used in evaluation of community metadata, FsF-R1.3-01M. -- [`open_formats.json`](./open_formats.json): This isn't used any more (code is commented out). Instead, the info should be pulled from [`file_formats.json`](./file_formats.json). +- [`identifiers_org_resolver_data.yaml`](./identifiers_org_resolver_data.yaml): Used in [`IdentifierHelper`](fuji_server/helper/identifier_helper.py). +- [`jsonldcontext.yaml`](./jsonldcontext.yaml) +- [`licenses.yaml`](./licenses.yaml): Used to populate `Preprocessor.license_names`, a list of SPDX licences. Used in evaluation of licenses, FsF-R1.1-01M. +- [`linked_vocab.yaml`](./linked_vocab.yaml) +- [`metadata_standards_uris.yaml`](./metadata_standards_uris.yaml) +- [`metadata_standards.yaml`](./metadata_standards.yaml): Used in evaluation of community metadata, FsF-R1.3-01M. - [`repodois.yaml`](./repodois.yaml): DOIs from re3data (Datacite). - [`ResourceTypes.txt`](./ResourceTypes.txt) -- [`standard_uri_protocols.json`](./standard_uri_protocols.json): Used for evaluating access through standardised protocols (FsF-A1-03D). Mapping of acronym to long name (e.g. FTP, SFTP, HTTP etc.) +- [`standard_uri_protocols.yaml`](./standard_uri_protocols.yaml): Used for evaluating access through standardised protocols (FsF-A1-03D). Mapping of acronym to long name (e.g. FTP, SFTP, HTTP etc.) diff --git a/fuji_server/data/access_rights.json b/fuji_server/data/access_rights.json deleted file mode 100644 index 9cd1aab8..00000000 --- a/fuji_server/data/access_rights.json +++ /dev/null @@ -1,171 +0,0 @@ -{ - "COAR_access_right": { - "id": "COAR_access_rights", - "identifier": { - "type": "namespace", - "value": "https://vocabularies.coar-repositories.org/access_rights" - }, - "label": "COAR access rights", - "members": [ - { - "access_condition": "embargoed", - "id": "c_f1cf", - "label": "embargoed access", - "source": "coar-repositories.org", - "uri": "http://purl.org/coar/access_right/c_f1cf" - }, - { - "access_condition": "metadataonly", - "id": "c_14cb", - "label": "metadata only access", - "source": "coar-repositories.org", - "uri": "http://purl.org/coar/access_right/c_14cb" - }, - { - "access_condition": "restricted", - "id": "c_16ec", - "label": "restricted access", - "source": "coar-repositories.org", - "uri": "http://purl.org/coar/access_right/c_16ec" - }, - { - "access_condition": "public", - "id": "c_abf2", - "label": "open access", - "source": "coar-repositories.org", - "uri": "http://purl.org/coar/access_right/c_abf2" - } - ], - "source": "coar-repositories.org" - }, - "EPRINTS_access_rights": { - "id": "EPRINTS_access_rights", - "identifier": { - "type": "namespace", - "value": "http://purl.org/eprint/accessRights/" - }, - "label": "ePrints access rights vocabulary", - "members": [ - { - "access_condition": "public", - "id": "OpenAccess", - "label": "Open Access", - "source": "ukoln.ac.uk", - "uri": "http://purl.org/eprint/accessRights/OpenAccess" - }, - { - "access_condition": "restricted", - "id": "RestrictedAccess", - "label": "Restricted Access", - "source": "ukoln.ac.uk", - "uri": "http://purl.org/eprint/accessRights/RestrictedAccess" - }, - { - "access_condition": "closed", - "id": "ClosedAccess", - "label": "Closed Access", - "source": "ukoln.ac.uk", - "uri": "http://purl.org/eprint/accessRights/ClosedAccess" - } - ], - "source": "ukoln.ac.uk" - }, - "EU_access_rights": { - "id": "EU_access_rights", - "identifier": { - "type": "namespace", - "value": "http://publications.europa.eu/resource/authority/access-right/" - }, - "label": "EU publications office access-right authority table", - "members": [ - { - "access_condition": "restricted", - "id": "NON_PUBLIC", - "label": "non-public", - "source": "publications.europa.eu", - "uri": "http://publications.europa.eu/resource/authority/access-right/NON_PUBLIC" - }, - { - "access_condition": "embargoed", - "id": "OP_DATPRO", - "label": "Provisional data", - "source": "publications.europa.eu", - "uri": "http://publications.europa.eu/resource/authority/access-right/OP_DATPRO" - }, - { - "access_condition": "public", - "id": "PUBLIC", - "label": "public", - "source": "publications.europa.eu", - "uri": "http://publications.europa.eu/resource/authority/access-right/PUBLIC" - }, - { - "access_condition": "restricted", - "id": "RESTRICTED", - "label": "restricted", - "source": "publications.europa.eu", - "uri": "http://publications.europa.eu/resource/authority/access-right/RESTRICTED" - }, - { - "access_condition": "restricted", - "id": "SENSITIVE", - "label": "sensitive", - "source": "publications.europa.eu", - "uri": "http://publications.europa.eu/resource/authority/access-right/SENSITIVE" - }, - { - "access_condition": "restricted", - "id": "CONFIDENTIAL", - "label": "confidential", - "source": "publications.europa.eu", - "uri": "http://publications.europa.eu/resource/authority/access-right/CONFIDENTIAL" - }, - { - "access_condition": "public", - "id": "NORMAL", - "label": "normal", - "source": "publications.europa.eu", - "uri": "http://publications.europa.eu/resource/authority/access-right/NORMAL" - } - ], - "source": "publications.europa.eu" - }, - "OPENAIRE_access_rights": { - "id": "OPENAIRE_access_rights", - "identifier": { - "value": "info:eu-repo/semantics/" - }, - "label": "OpenAire access rights list", - "members": [ - { - "access_condition": "closed", - "id": "closedAccess", - "label": "closed Access", - "source": "openaire.eu", - "uri": "info:eu-repo/semantics/closedAccess" - }, - { - "access_condition": "embargoed", - "id": "embargoedAccess", - "label": "embargoed Access", - "source": "openaire.eu", - "uri": "info:eu-repo/semantics/embargoedAccess" - }, - { - "access_condition": "restricted", - "id": "restrictedAccess", - "label": "restricted Access", - "source": "openaire.eu", - "uri": "info:eu-repo/semantics/restrictedAccess" - }, - { - "access_condition": "public", - "id": "openAccess", - "label": "open Access", - "source": "openaire.eu", - "uri": "info:eu-repo/semantics/openAccess" - } - ], - "source": "openaire.eu" - } -} diff --git a/fuji_server/data/access_rights.yaml b/fuji_server/data/access_rights.yaml new file mode 100644 index 00000000..df2aee15 --- /dev/null +++ b/fuji_server/data/access_rights.yaml @@ -0,0 +1,121 @@ +COAR_access_right: + id: COAR_access_rights + identifier: + type: namespace + value: https://vocabularies.coar-repositories.org/access_rights + label: COAR access rights + members: + - access_condition: embargoed + id: c_f1cf + label: embargoed access + source: coar-repositories.org + uri: http://purl.org/coar/access_right/c_f1cf + - access_condition: metadataonly + id: c_14cb + label: metadata only access + source: coar-repositories.org + uri: http://purl.org/coar/access_right/c_14cb + - access_condition: restricted + id: c_16ec + label: restricted access + source: coar-repositories.org + uri: http://purl.org/coar/access_right/c_16ec + - access_condition: public + id: c_abf2 + label: open access + source: coar-repositories.org + uri: http://purl.org/coar/access_right/c_abf2 + source: coar-repositories.org +EPRINTS_access_rights: + id: EPRINTS_access_rights + identifier: + type: namespace + value: http://purl.org/eprint/accessRights/ + label: ePrints access rights vocabulary + members: + - access_condition: public + id: OpenAccess + label: Open Access + source: ukoln.ac.uk + uri: http://purl.org/eprint/accessRights/OpenAccess + - access_condition: restricted + id: RestrictedAccess + label: Restricted Access + source: ukoln.ac.uk + uri: http://purl.org/eprint/accessRights/RestrictedAccess + - access_condition: closed + id: ClosedAccess + label: Closed Access + source: ukoln.ac.uk + uri: http://purl.org/eprint/accessRights/ClosedAccess + source: ukoln.ac.uk +EU_access_rights: + id: EU_access_rights + identifier: + type: namespace + value: http://publications.europa.eu/resource/authority/access-right/ + label: EU publications office access-right authority table + members: + - access_condition: restricted + id: NON_PUBLIC + label: non-public + source: publications.europa.eu + uri: http://publications.europa.eu/resource/authority/access-right/NON_PUBLIC + - access_condition: embargoed + id: OP_DATPRO + label: Provisional data + source: publications.europa.eu + uri: http://publications.europa.eu/resource/authority/access-right/OP_DATPRO + - access_condition: public + id: PUBLIC + label: public + source: publications.europa.eu + uri: http://publications.europa.eu/resource/authority/access-right/PUBLIC + - access_condition: restricted + id: RESTRICTED + label: restricted + source: publications.europa.eu + uri: http://publications.europa.eu/resource/authority/access-right/RESTRICTED + - access_condition: restricted + id: SENSITIVE + label: sensitive + source: publications.europa.eu + uri: http://publications.europa.eu/resource/authority/access-right/SENSITIVE + - access_condition: restricted + id: CONFIDENTIAL + label: confidential + source: publications.europa.eu + uri: http://publications.europa.eu/resource/authority/access-right/CONFIDENTIAL + - access_condition: public + id: NORMAL + label: normal + source: publications.europa.eu + uri: http://publications.europa.eu/resource/authority/access-right/NORMAL + source: publications.europa.eu +OPENAIRE_access_rights: + id: OPENAIRE_access_rights + identifier: + value: info:eu-repo/semantics/ + label: OpenAire access rights list + members: + - access_condition: closed + id: closedAccess + label: closed Access + source: openaire.eu + uri: info:eu-repo/semantics/closedAccess + - access_condition: embargoed + id: embargoedAccess + label: embargoed Access + source: openaire.eu + uri: info:eu-repo/semantics/embargoedAccess + - access_condition: restricted + id: restrictedAccess + label: restricted Access + source: openaire.eu + uri: info:eu-repo/semantics/restrictedAccess + - access_condition: public + id: openAccess + label: open Access + source: openaire.eu + uri: info:eu-repo/semantics/openAccess + source: openaire.eu diff --git a/fuji_server/data/file_formats.json b/fuji_server/data/file_formats.json deleted file mode 100644 index a5816049..00000000 --- a/fuji_server/data/file_formats.json +++ /dev/null @@ -1,2326 +0,0 @@ -{ - "3d_studio_format": { - "ext": [ - "*.3ds" - ], - "mime": [ - "image/x-3ds", - "application/x-3ds" - ], - "name": "3D Studio format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "aac_advanced_audio_coding_file_format": { - "ext": [ - "*.aac" - ], - "mime": [ - "audio/x-aac", - "audio/aac" - ], - "name": "AAC (Advanced Audio Coding) File Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "adobe_digital_negative_dng_": { - "ext": [ - "*.dng" - ], - "mime": [ - "image/x-adobe-dng" - ], - "name": "Adobe Digital Negative (DNG)", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "aiff_audio_interchange_file_format_": { - "ext": [ - "*.aiff", - "*.aff", - "*.aifc", - "*.aif", - "*.ief" - ], - "mime": [ - "audio/x-midi", - "sound/aiff", - "audio/aiff", - "audio/x-rmf", - "audio/x-pn-aiff", - "audio/x-gsm", - "audio/x-aiff", - "audio/rmf", - "audio/vnd.qcelp" - ], - "name": "AIFF (Audio Interchange File Format)", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "apple_lossless_audio_codec_alac_": { - "ext": [ - "*.m4a" - ], - "mime": [ - "audio/mp4" - ], - "name": "Apple Lossless Audio Codec (ALAC)", - "reason": [ - "open format" - ], - "source": [ - "various" - ] - }, - "apple_numbers": { - "ext": [ - "*.numbers", - "*.numbers.zip" - ], - "mime": [ - "application/vnd.apple.numbers" - ], - "name": "Apple Numbers", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "av1_image_file_format_avif_": { - "ext": [ - "*.avifs", - "*.avif" - ], - "mime": [ - "image/avif-sequence", - "image/avif" - ], - "name": "AV1 Image File Format\u00a0(AVIF)", - "reason": [ - "open format" - ], - "source": [ - "various" - ] - }, - "avi_audio_video_interleaved_file_format": { - "ext": [ - "*.avi" - ], - "mime": [ - "application/x-troff-msvideo", - "audio/avi", - "video/x-msvideo", - "video/msvideo", - "video/vnd.avi", - "video/avi" - ], - "name": "AVI (Audio Video Interleaved) File Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "avi_audio_video_interleaved_video_file_format": { - "ext": [ - "*.gvi" - ], - "mime": [ - "video/avi" - ], - "name": "AVI (Audio Video Interleaved) Video File Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "bed_browser_extensible_data_": { - "ext": [ - "*.bed" - ], - "mime": [ - "text/x-bed" - ], - "name": "BED (Browser Extensible Data)", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "beilstein_crossfire_file": { - "ext": [ - "*.bsd" - ], - "mime": [ - "chemical/x-crossfire" - ], - "name": "Beilstein Crossfire file", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "c_source_code_file": { - "ext": [ - "*.c" - ], - "mime": [ - "text/x-c" - ], - "name": "C Source Code File", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "cactvs_format": { - "ext": [ - "*.cascii", - "*.ctx" - ], - "mime": [ - "chemical/x-cactvs", - "chemical/x-cactvs-binary", - "chemical/x-cactvs-ascii", - "chemical/x-cactus", - "chemical/x-cactus-ascii" - ], - "name": "CACTVS format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "ccdc_isostar_library": { - "ext": [ - "*.istr" - ], - "mime": [ - "chemical/x-isostar" - ], - "name": "CCDC IsoStar Library", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "ccp4_file_format": { - "ext": [ - "*.ccp4" - ], - "mime": [ - "application/CCP4-mtz", - "application/CCP4-mtz-phases", - "application/CCP4-mtz-freerflag", - "application/CCP4-mtz-observed", - "application/CCP4-unmerged-experimental", - "application/CCP4-mtz-map" - ], - "name": "CCP4 file format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "cd_audio_cd_audio_track_shortcut": { - "ext": [ - "*.cda" - ], - "mime": [ - "audio/audiocd", - "application/x-cda" - ], - "name": "CD Audio CD Audio track shortcut", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "cfd_general_notation_system": { - "ext": [ - "*.cgns" - ], - "mime": [ - "application/cgns" - ], - "name": "CFD General Notation System, ADF (Advanced Data Format)", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "chem3d_format": { - "ext": [ - "*.c3d" - ], - "mime": [ - "chemical/x-chem3d" - ], - "name": "Chem3D Format", - "reason": [ - "scientific format" - ], - 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] - }, - "mpeg_4_media_file": { - "ext": [ - "*.f4v" - ], - "mime": [ - "application/mp4", - "video/mp4" - ], - "name": "MPEG-4 Media File", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "mpeg_file_format": { - "ext": [ - "*.mp3", - "*.mpg", - "*.mpeg", - "*.mpa", - "*.m1v", - "*.m1a", - "*.mpv" - ], - "mime": [ - "video/mpeg", - "video/x-mpeg", - "video/mpg", - "video/x-mpg", - "video/mpv", - "video/mp1s", - "audio/mpeg", - "application/x-pn-mpg" - ], - "name": "MPEG File Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "ms_works_file": { - "ext": [ - "*.wdb", - "*.wps", - "*.xlr", - "*.wks", - "*.wcm" - ], - "mime": [ - "application/vnd.ms-works", - "application/x-tika-msworks-spreadsheet" - ], - "name": "MS Works File", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "msi_alchemy_format": { - "ext": [ - "*.alc" - ], - "mime": [ - "chemical/x-alchemy" - ], - "name": "MSI Alchemy format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "msi_cerius2_datafile": { - "ext": [ - "*.c3d" - ], - "mime": [ - "chemical/x-cerius" - ], - "name": "MSI Cerius2 Datafile", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "multiple_image_network_graphics": { - "ext": [ - "*.mng" - ], - "mime": [ - "video/x-mng" - ], - "name": "Multiple-Image Network Graphics", - "reason": [ - "open format" - ], - "source": [ - "various" - ] - }, - "nasa_common_data_format_cdf_": { - "ext": [ - "*.cdf" - ], - "mime": [ - "application/x-cdf" - ], - "name": "NASA common data format (.cdf)", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "netcdf": { - "ext": [ - "*.nc", - "*.cdf", - "*.cf" - ], - "mime": [ - "application/x-netcdf", - "application/netcdf" - ], - "name": "NetCDF", - "reason": [ - "scientific format", - "open format" - ], - "source": [ - "various" - ] - }, - "newick_format": { - "ext": [ - "*.tree" - ], - "mime": [ - "text/x-nh" - ], - "name": "Newick format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "nsdstat_format": { - "ext": [ - "*.nsdstat" - ], - "mime": [ - "application/x-nsdstat" - ], - "name": "NSDstat Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "nucleotide_sequence_format": { - "ext": [ - "*.gcg" - ], - "mime": [ - "chemical/x-gcg8-sequence" - ], - "name": "Nucleotide Sequence Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "ogg_multimedia_container_format": { - "ext": [ - "*.ogm", - "*.ogx", - "*.ogg", - "*.oga", - "*.opus", - "*.ogv" - ], - "mime": [ - "video/daala", - "video/x-oggrgb", - "audio/x-ogg-flac", - "audio/ogg", - "audio/x-ogg-pcm", - "video/x-ogm", - "video/theora", - "application/x-ogg", - "video/x-theora", - "video/x-ogg-uvs", - "application/ogg", - "video/x-ogg-yuv", - "video/x-ogguvs", - "video/x-daala", - "video/ogg", - "audio/opus", - "audio/speex", - "video/x-oggyuv", - "video/x-ogg-rgb", - "audio/x-ogg" - ], - "name": "Ogg Multimedia Container Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "ogg_packaged_dirac_video": { - "ext": [ - "*.drc" - ], - "mime": [ - "video/x-dirac" - ], - "name": "Ogg Packaged Dirac Video", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "ogg_speex_codec_multimedia_file": { - "ext": [ - "*.spx" - ], - "mime": [ - "application/x-speex", - "audio/x-speex", - "audio/speex" - ], - "name": "Ogg Speex Codec Multimedia File", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "opendocument_spreadsheet": { - "ext": [ - "*.fods", - "*.ots", - "*.ods" - ], - "mime": [ - "application/vnd.oasis.opendocument.spreadsheet-template", - "application/vnd.oasis.opendocument.spreadsheet" - ], - "name": "OpenDocument Spreadsheet", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "openexr_file_format": { - "ext": [ - "*.exr" - ], - "mime": [ - "image/x-exr" - ], - "name": "OpenEXR File Format", - "reason": [ - "open format" - ], - "source": [ - "various" - ] - }, - "openoffice_org_xml": { - "ext": [ - "*.sxg", - "*.sxc", - "*.sxd", - "*.stc", - "*.std", - "*.sxm" - ], - "mime": [ - "application/vnd.sun.xml.calc", - "application/vnd.sun.xml.calc.template" - ], - "name": "OpenOffice.org XML", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "openraster_image_format": { - "ext": [ - "*.ora" - ], - "mime": [ - "image/openraster" - ], - "name": "OpenRaster Image Format", - "reason": [ - "open format" - ], - "source": [ - "various" - ] - }, - "pcma": { - "ext": [ - "*.wav" - ], - "mime": [ - "audio/pcma-wb", - "audio/pcma" - ], - "name": "PCMA", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "pcmu": { - "ext": [ - "*.wav" - ], - "mime": [ - "audio/pcmu-wb", - "audio/pcmu" - ], - "name": "PCMU", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "portable_document_format": { - "ext": [ - "*.pdfxml", - "*.pdf", - "*.mars" - ], - "mime": [ - "application/vnd.adobe.pdfxml", - "text/x-pdf", - "application/x-pdf", - "text/pdf", - "application/pdf", - "application/vnd.adobe.x-mars", - "application/vnd.pdf" - ], - "name": "Portable Document Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "portable_network_graphics": { - "ext": [ - "*.png", - "*.apng" - ], - "mime": [ - "image/png", - "image/vnd.mozilla.apng" - ], - "name": "Portable Network Graphics", - "reason": [ - "long term format", - "open format" - ], - "source": [ - "ISO/TR 22299", - "various" - ] - }, - "protein_data_bank_format": { - "ext": [ - "*.pdb" - ], - "mime": [ - "chemical/x-pdb" - ], - "name": "Protein Data Bank format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "python_file": { - "ext": [ - "*.py" - ], - "mime": [ - "text/x-python", - "text/x-python-script" - ], - "name": "Python File", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "quattro_pro_format": { - "ext": [ - "*.qpw", - "*.wq2", - "*.wq1", - "*.wb3", - "*.wb2", - "*.wb1" - ], - "mime": [ - "application/x-quattro-pro" - ], - "name": "Quattro Pro Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "r_file_format": { - "ext": [ - "*.r", - "*.R" - ], - "mime": [ - "application/x-rlang-transport", - "text/x-r-source", - "type/x-r-syntax", - "application/x-R-2" - ], - "name": "R File Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "root": { - "ext": [ - "*.root" - ], - "mime": [ - "application/x-root" - ], - "name": "CERN ROOT file", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "sas_file_format": { - "ext": [ - "*.sas" - ], - "mime": [ - "application/x-sas-log", - "application/x-sas-data", - "application/x-sas-catalog", - "application/x-sas-system", - "application/x-sas-output", - "text/x-sas-syntax", - "application/x-sas-transport", - "application/x-sas", - "application/x-sas-syntax" - ], - "name": "SAS File Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "scalable_vector_graphics": { - "ext": [ - "*.svgz", - "*.svg" - ], - "mime": [ - "image/svg+xml", - "image/svg-xml" - ], - "name": "Scalable Vector Graphics", - "reason": [ - "long term format", - "open format" - ], - "source": [ - "ISO/TR 22299", - "various" - ] - }, - "sff_molecular_biology_format": { - "ext": [ - "*.sff" - ], - "mime": [ - "chemical/seq-na-sff" - ], - "name": "SFF molecular biology format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "silo_3d_model": { - "ext": [ - "*.sia", - "*.silo", - "*.sib" - ], - "mime": [ - "model/mesh" - ], - "name": "Silo 3D model", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "smiles_chemical_format": { - "ext": [ - "*.smi" - ], - "mime": [ - "chemical/x-daylight-smiles" - ], - "name": "SMILES chemical format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "spc_format_for_spectral_and_chromatographic_data_b_": { - "ext": [ - "*.spc" - ], - "mime": [ - "chemical/x-galactic-spc" - ], - "name": "SPC format for spectral and chromatographic data (B)", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "spss_file_format": { - "ext": [ - "*.zip", - "*.sav", - "*.sps", - "*.por" - ], - "mime": [ - "application/x-dvn-csvspss-zip", - "text/x-spss-syntax", - "application/x-spss-syntax", - "application/x-spss-portable", - "application/x-spss-sav", - "application/x-spss-por", - "application/x-spss-sps" - ], - "name": "SPSS File Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "staroffice_calc_format": { - "ext": [ - "*stc", - "*.sdc" - ], - "mime": [ - "application/x-starcalc", - "application/vnd.stardivision.calc", - "application/vnd.sun.xml.calc.template" - ], - "name": "StarOffice Calc Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "stata_data_file_format": { - "ext": [ - "*.do", - "*.dta" - ], - "mime": [ - "application/x-stata", - "application/x-stata-6", - "application/x-stata-dta", - "application/x-stata-smcl", - "application/x-stata-syntax", - "application/x-stata-ado", - "application/x-stata-do", - "application/x-stata-14", - "application/x-stata-13", - "application/x-stata-15" - ], - "name": "Stata Data File Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "step_file_iso_10303_21": { - "ext": [ - "*.21", - "*.p21", - "*.step", - "*.stpnc", - "*.stp" - ], - "mime": [ - "model/step", - "model/step+xml", - "model/step+zip", - "model/step-xml+zip" - ], - "name": "STEP-file, ISO 10303-21", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "stl_stereolithography_format": { - "ext": [ - "*.sla", - "*.stl" - ], - "mime": [ - "application/sla", - "model/stl", - "model/x.stl-ascii", - "model/x.stl-binary" - ], - "name": "STL Stereolithography format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "stockholm_format": { - "ext": [ - "*.sto" - ], - "mime": [ - "text/x-stockholm-alignment" - ], - "name": "Stockholm format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "swissprot_sequence_format": { - "ext": [ - "*.sw" - ], - "mime": [ - "chemical/x-swissprot" - ], - "name": "SwissProt sequence format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "systems_biology_markup_language_sbml_": { - "ext": [ - "*.sbml" - ], - "mime": [ - "application/sbml+xml" - ], - "name": "Systems Biology Markup Language (SBML)", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "tab_ddi_format": { - "description": "A zipped tab (tsv) file together with a DDI XML metadata, informal type defined by Dataverse", - "ext": [ - "*.zip" - ], - "mime": [ - "application/x-dvn-tabddi-zip" - ], - "name": "TAB DDI Format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "tagged_image_file_format": { - "ext": [ - "*.tif", - "*.tfx", - "*.tfw", - "*.tiff" - ], - "mime": [ - "image/tiff" - ], - "name": "Tagged Image File Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "tripos_molecule_structure_format_": { - "ext": [ - "*.mol2" - ], - "mime": [ - "chemical/x-mol2" - ], - "name": "Tripos molecule structure format ", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "video_object_file_vob_": { - "ext": [ - "*.vob" - ], - "mime": [ - "video/x-ms-vob" - ], - "name": "Video Object File (VOB)", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "vorbis_encoded_audio": { - "ext": [ - "*.wav" - ], - "mime": [ - "audio/vorbis-config", - "audio/vorbis" - ], - "name": "Vorbis encoded audio", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "wave_audio_file_format": { - "ext": [ - "*.wave", - "*.wav" - ], - "mime": [ - "audio/x-wav", - "audio/vnd.wave", - "audio/wave", - "audio/x-pn-wav", - "audio/wav" - ], - "name": "WAVE Audio File Format", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "webp_format": { - "ext": [ - "*.webp" - ], - "mime": [ - "image/webp" - ], - "name": "WebP Format", - "reason": [ - "open format" - ], - "source": [ - "various" - ] - }, - "windows_bitmap_image_file_bmp_": { - "ext": [ - "*.bmp" - ], - "mime": [ - "image/x-ms-bmp", - "image/bmp" - ], - "name": "Windows Bitmap Image File (BMP)", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "windows_media_video": { - "ext": [ - "*.asf", - "*.wmv" - ], - "mime": [ - "video/x-ms-asf", - "video/x-ms-wmv" - ], - "name": "Windows Media Video", - "reason": [ - "long term format" - ], - "source": [ - "ISO/TR 22299" - ] - }, - "wolfram_computable_document_format_cdf_": { - "ext": [ - "*.cdf" - ], - "mime": [ - "application/vnd.wolfram.cdf.text", - "application/vnd.wolfram.cdf" - ], - "name": "Wolfram Computable Document Format (CDF)", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - }, - "x_pixmap_xpm_": { - "ext": [ - "*.xpm", - "*.pm" - ], - "mime": [ - "image/x-xpixmap" - ], - "name": "X PixMap\u00a0(XPM)", - "reason": [ - "open format" - ], - "source": [ - "various" - ] - }, - "xtelplot_file_format": { - "ext": [ - "*.xtel" - ], - "mime": [ - "chemical/x-xtel" - ], - "name": "Xtelplot file format", - "reason": [ - "scientific format" - ], - "source": [ - "various" - ] - } -} diff --git a/fuji_server/data/file_formats.yaml b/fuji_server/data/file_formats.yaml new file mode 100644 index 00000000..b2af6bf4 --- /dev/null +++ b/fuji_server/data/file_formats.yaml @@ -0,0 +1,1665 @@ +3d_studio_format: + ext: + - '*.3ds' + mime: + - image/x-3ds + - application/x-3ds + name: 3D Studio format + reason: + - scientific format + source: + - various +aac_advanced_audio_coding_file_format: + ext: + - '*.aac' + mime: + - audio/x-aac + - audio/aac + name: AAC (Advanced Audio Coding) File Format + reason: + - long term format + source: + - ISO/TR 22299 +adobe_digital_negative_dng_: + ext: + - '*.dng' + mime: + - image/x-adobe-dng + name: Adobe Digital Negative (DNG) + reason: + - long term format + source: + - ISO/TR 22299 +aiff_audio_interchange_file_format_: + ext: + - '*.aiff' + - '*.aff' + - '*.aifc' + - '*.aif' + - '*.ief' + mime: + - audio/x-midi + - sound/aiff + - audio/aiff + - audio/x-rmf + - audio/x-pn-aiff + - audio/x-gsm + - audio/x-aiff + - audio/rmf + - audio/vnd.qcelp + name: AIFF (Audio Interchange File Format) + reason: + - long term format + source: + - ISO/TR 22299 +apple_lossless_audio_codec_alac_: + ext: + - '*.m4a' + mime: + - audio/mp4 + name: Apple Lossless Audio Codec (ALAC) + reason: + - open format + source: + - various +apple_numbers: + ext: + - '*.numbers' + - '*.numbers.zip' + mime: + - application/vnd.apple.numbers + name: Apple Numbers + reason: + - scientific format + source: + - various +av1_image_file_format_avif_: + ext: + - '*.avifs' + - '*.avif' + mime: + - image/avif-sequence + - image/avif + name: AV1 Image File Format (AVIF) + reason: + - open format + source: + - various +avi_audio_video_interleaved_file_format: + ext: + - '*.avi' + mime: + - application/x-troff-msvideo + - audio/avi + - video/x-msvideo + - video/msvideo + - video/vnd.avi + - video/avi + name: AVI (Audio Video Interleaved) File Format + reason: + - long term format + source: + - ISO/TR 22299 +avi_audio_video_interleaved_video_file_format: + ext: + - '*.gvi' + mime: + - video/avi + name: AVI (Audio Video Interleaved) Video File Format + reason: + - long term format + source: + - ISO/TR 22299 +bed_browser_extensible_data_: + ext: + - '*.bed' + mime: + - text/x-bed + name: BED (Browser Extensible Data) + reason: + - scientific format + source: + - various +beilstein_crossfire_file: + ext: + - '*.bsd' + mime: + - chemical/x-crossfire + name: Beilstein Crossfire file + reason: + - scientific format + source: + - various +c_source_code_file: + ext: + - '*.c' + mime: + - text/x-c + name: C Source Code File + reason: + - scientific format + source: + - various +cactvs_format: + ext: + - '*.cascii' + - '*.ctx' + mime: + - chemical/x-cactvs + - chemical/x-cactvs-binary + - chemical/x-cactvs-ascii + - chemical/x-cactus + - chemical/x-cactus-ascii + name: CACTVS format + reason: + - scientific format + source: + - various +ccdc_isostar_library: + ext: + - '*.istr' + mime: + - chemical/x-isostar + name: CCDC IsoStar Library + reason: + - scientific format + source: + - various +ccp4_file_format: + ext: + - '*.ccp4' + mime: + - application/CCP4-mtz + - application/CCP4-mtz-phases + - application/CCP4-mtz-freerflag + - application/CCP4-mtz-observed + - application/CCP4-unmerged-experimental + - application/CCP4-mtz-map + name: CCP4 file format + reason: + - scientific format + source: + - various +cd_audio_cd_audio_track_shortcut: + ext: + - '*.cda' + mime: + - audio/audiocd + - application/x-cda + name: CD Audio CD Audio track shortcut + reason: + - long term format + source: + - ISO/TR 22299 +cfd_general_notation_system: + ext: + - '*.cgns' + mime: + - application/cgns + name: CFD General Notation System, ADF (Advanced Data Format) + reason: + - scientific format + source: + - various +chem3d_format: + ext: + - '*.c3d' + mime: + - chemical/x-chem3d + name: Chem3D Format + reason: + - scientific format + source: + - various +chemdraw_exchange_file: + ext: + - '*.cdx' + mime: + - chemical/x-cdxml + - chemical/x-cdx + name: ChemDraw eXchange file + reason: + - scientific format + source: + - various +chemical_markup_language: + ext: + - '*.cml' + mime: + - chemical/x-cml + name: Chemical Markup Language + reason: + - scientific format + source: + - various +collada_digital_asset_exchange_format: + ext: + - '*.dae' + mime: + - model/vnd.collada+xml + name: COLLADA digital asset exchange format + reason: + - scientific format + source: + - various +computer_graphics_metafile: + ext: + - '*.cgm' + mime: + - image/cgm + name: Computer Graphics Metafile + reason: + - long term format + source: + - ISO/TR 22299 +crystallographic_information_file: + ext: + - '*.mif' + - '*.cif' + mime: + - chemical/x-cif + name: Crystallographic Information File + reason: + - scientific format + source: + - various +crystalmaker_file: + ext: + - '*.cmdf' + mime: + - chemical/x-cmdf + name: Crystalmaker File + reason: + - scientific format + source: + - various +daylight_smiles_string: + ext: + - '*.smi' + mime: + - chemical/x-daylight-smiles + name: Daylight SMILES string + reason: + - scientific format + source: + - various +dbase_table_for_esri_shapefile: + ext: + - '*.dbf' + - '*.dbase' + mime: + - application/dbase + - application/dbf + name: dBASE Table for ESRI Shapefile + reason: + - scientific format + source: + - various +device_independent_bitmap_dib_: + ext: + - '*.dib' + mime: + - image/dib + name: Device-Independent bitmap (DIB) + reason: + - long term format + source: + - ISO/TR 22299 +dicom: + ext: + - '*.dic' + - '*.dcm' + mime: + - application/dicom + - image/dicom-rle + name: DICOM + reason: + - scientific format + source: + - various +dolby_heaac: + ext: + - '*.wav' + mime: + - audio/vnd.dolby.heaac.1 + name: Dolby HEAAC + reason: + - long term format + source: + - ISO/TR 22299 +embl_nucleotide_sequence_format: + ext: + - '*.emb' + mime: + - chemical/x-embl-dl-nucleotide + name: EMBL nucleotide sequence format + reason: + - scientific format + source: + - various +esri_shapefile: + ext: + - '*.prj' + - '*.shx' + - '*.shp' + mime: + - application/prj + - application/zipped-shapefile + - application/x-esri-shape + - application/shx + - application/shp + - application/x-shapefile + name: ESRI Shapefile + reason: + - scientific format + source: + - various +esri_spatial_index: + ext: + - '*.sbn' + - '*.sbx' + mime: + - application/sbx + - application/sbn + name: ESRI Spatial Index + reason: + - scientific format + source: + - various +extensible_3d_x3d_file_format_family: + ext: + - '*.x3db' + - '*.x3dbz' + - '*.x3dz' + - '*.x3dv' + - '*.x3d' + - '*.x3dvz' + mime: + - model/x3d+xml + - model/x3d+binary + - model/x3d+fastinfoset + - model/x3d+vrml + - model/x3d-vrml + name: Extensible 3D (X3D) File Format Family + reason: + - long term format + source: + - ISO/TR 22299 +fasta: + ext: + - '*.fasta' + - '*.frn' + - '*.faa' + - '*.fna' + mime: + - chemical/seq-aa-fasta + - chemical/seq-na-fasta + - text/x-fasta + name: FASTA + reason: + - scientific format + source: + - various +fastq: + ext: + - '*.fq' + - '*.fastq' + - '*.fa' + mime: + - chemical/seq-na-fastq + name: FASTQ + reason: + - scientific format + source: + - various +fhir_file_format: + description: FHIR is a standard for health care data exchange, published by HL7 + ext: [] + mime: + - application/fhir+xml + - application/fhir+json + - application/fhir+turtle + - application/xml+fhir + - application/json+fhir + - application/turtle+fhir + name: FHIR + reason: + - scientific format + source: + - various +flexible_image_transport_system_fits_: + ext: + - '*.fits' + - '*.fts' + - '*.fit' + mime: + - application/fits + - image/fits + name: Flexible Image Transport System (FITS) + reason: + - scientific format + source: + - various +free_lossless_image_format_flif_: + ext: + - '*.flif' + mime: + - image/flif + name: Free Lossless Image Format (FLIF) + reason: + - open format + source: + - various +gamess_us_ab_initio_input_file: + ext: + - '*.inp' + mime: + - chemical/x-gamess-input + name: GAMESS(US) Ab initio Input File + reason: + - scientific format + source: + - various +gaussian_checkpoint_file: + ext: + - '*.fch' + - '*.fchk' + mime: + - chemical/x-gaussian-checkpoint + name: Gaussian Checkpoint file + reason: + - scientific format + source: + - various +gaussian_cube_file: + ext: + - '*.cub' + mime: + - chemical/x-cube + - chemical/x-gaussian-cube + name: Gaussian Cube file + reason: + - scientific format + source: + - various +gaussian_log_file: + ext: + - '*.gal' + mime: + - chemical/x-gaussian-log + name: Gaussian log file + reason: + - scientific format + source: + - various +genbank_molecular_biology_format: + ext: + - '*.gbk' + - '*.gb' + mime: + - chemical/seq-na-genbank + name: GenBank molecular biology format + reason: + - scientific format + source: + - various +general_feature_format: + ext: + - '*.gff' + mime: + - text/x-gff3 + name: General feature format + reason: + - scientific format + source: + - various +geographic_tagged_image_file_format_geotiff_: + ext: + - '*.tif' + mime: + - image/geotiff + name: Geographic Tagged Image File Format (GeoTIFF) + reason: + - long term format + source: + - ISO/TR 22299 +geojson_a_geographic_data_format_based_on_json: + ext: + - '*.geojson' + mime: + - application/geo+json + name: GeoJSON a geographic data format based on JSON + reason: + - scientific format + source: + - various +gerber_format: + ext: + - '*.gpt' + - '*.gbo' + - '*.gtl' + - '*.gbp' + - '*.gtp' + - '*.gbs' + - '*.gpb' + - '*.gml' + - '*.gbr' + - '*.gto' + - '*.gbl' + - '*.gts' + - '*.gko' + mime: + - application/vnd.gerber + name: Gerber format + reason: + - open format + source: + - various +gnumeric_spreadsheet: + ext: + - '*.gnm' + - '*.gnumeric' + mime: + - application/x-gnumeric + name: Gnumeric spreadsheet + reason: + - scientific format + source: + - various +graphics_interchange_format: + ext: + - '*.gif' + mime: + - image/gif + name: Graphics Interchange Format + reason: + - long term format + - open format + source: + - ISO/TR 22299 + - various +grib: + ext: + - '*.grb1' + - '*.grb2' + - '*.grb' + mime: + - application/x-grib + - application/wmo-grib2 + name: GRIB + reason: + - scientific format + source: + - various +hdf: + ext: + - '*.hdf' + - '*.hdf5' + - '*.h5' + mime: + - application/x-hdf5 + - application/x-hdf + name: HDF + reason: + - scientific format + source: + - various +hyperchen_hin_data_format: + ext: + - '*.hin' + mime: + - chemical/x-hin + name: HyperChen HIN data format + reason: + - scientific format + source: + - various +iso14976_spectroscopic_format: + ext: + - '*.vms' + mime: + - chemical/x-vamas-iso14976 + name: ISO14976 Spectroscopic format + reason: + - scientific format + source: + - various +jcamp_dx_a_chemical_spectroscopy_format: + ext: + - '*.jdx' + mime: + - chemical/x-jcamp-dx + name: JCAMP-DX a chemical spectroscopy format + reason: + - scientific format + source: + - various +jpeg_2000_file_format: + ext: + - '*.jpf' + - '*.jpx' + - '*.jpg' + - '*.jp2' + - '*.mj2' + - '*.jpm' + mime: + - image/jpx + - image/jpeg2000 + - image/x-jpeg2000-image + - image/jp2 + - image/jpm + - image/jpeg2000-image + name: JPEG 2000 File Format + reason: + - long term format + - open format + source: + - ISO/TR 22299 + - various +jpg_joint_photographic_experts_group_file_format: + ext: + - '*.jpf' + - '*.jfif' + - '*.jls' + - '*.jif' + - '*.jmh' + - '*.jpg' + - '*.jp2' + - '*.jpeg' + - '*.jpe' + - '*.j' + - '*.jfi' + - '*.spf' + mime: + - image/jpeg + - application/jpg + - image/jpm + - image/jpg + name: JPG (Joint Photographic Experts Group) File Format + reason: + - long term format + source: + - ISO/TR 22299 +jt_3d_visualization_format: + ext: + - '*.jt' + mime: + - model/jt + name: JT 3D visualization format + reason: + - long term format + source: + - ISO/TR 22299 +jupyter_notebook_file: + ext: + - '*.ipynb' + mime: + - application/x-ipynb+json + name: Jupyter Notebook File + reason: + - scientific format + source: + - various +kinetic_protein_structure_images: + ext: + - '*.kin' + mime: + - chemical/x-kinemage + name: Kinetic (Protein Structure) Images + reason: + - scientific format + source: + - various +lotus_1_2_3_format: + ext: + - '*.wk3' + - '*.wk4' + - '*.wk1' + - '*.wks' + - '*.wk2' + - '*.wk*' + mime: + - application/vnd.lotus-1-2-3 + name: Lotus 1-2-3 Format + reason: + - scientific format + source: + - various +macmolecule_file_format: + ext: + - '*.mcm' + mime: + - chemical/x-macmolecule + name: MacMolecule File Format + reason: + - scientific format + source: + - various +macromodel_molecular_mechanics: + ext: + - '*.mmod' + - '*.mmd' + mime: + - chemical/x-macromodel-input + name: MacroModel Molecular Mechanics + reason: + - scientific format + source: + - various +material_exchange_format_mxf_: + ext: + - '*.mxf' + mime: + - application/mxf + name: Material Exchange Format (MXF) + reason: + - long term format + source: + - ISO/TR 22299 +mathematica_format: + ext: + - '*.wl' + - '*.m' + - '*.ma' + - '*.nb' + mime: + - application/vnd.wolfram.mathematica + - application/mathematica + - application/vnd.wolfram.mathematica.package + - text/x-mathematica + name: Mathematica Format + reason: + - scientific format + source: + - various +mathml_math_content_format: + ext: + - '*.mml' + mime: + - text/mathml + - application/mathml+xml + name: MathML math content format + reason: + - scientific format + source: + - various +matlab_format: + ext: + - '*.m' + - '*.mat' + mime: + - application/matlab-mat + - text/x-matlab + - application/x-matlab-figure + - application/x-matlab-workspace + - application/x-matlab-data + name: Matlab Format + reason: + - scientific format + source: + - various +mdl_mol_molecular_models_and_drawings_format: + ext: + - '*.mol' + mime: + - chemical/x-mdl-molfile + name: MDL MOL molecular models and drawings format + reason: + - scientific format + source: + - various +mdl_reaction_data_file: + ext: + - '*.rd' + mime: + - chemical/x-mdl-rdfile + name: MDL Reaction-data file + reason: + - scientific format + source: + - various +mdl_reaction_format: + ext: + - '*.rxn' + mime: + - chemical/x-mdl-rxnfile + name: MDL Reaction format + reason: + - scientific format + source: + - various +mdl_structure_data_file: + ext: + - '*.sd' + mime: + - chemical/x-mdl-sdfile + name: MDL Structure-data file + reason: + - scientific format + source: + - various +mdl_transportable_graphics_file: + ext: + - '*.rd' + mime: + - chemical/x-mdl-tgf + name: MDL Transportable Graphics file + reason: + - scientific format + source: + - various +microsoft_excel_file: + ext: + - '*.xlc' + - '*.xld' + - '*.xlt' + - '*.xlsm' + - '*.xls' + - '*.xlsb' + - '*.xlw' + - '*.xll' + - '*.xlm' + - '*.xla' + mime: + - application/vnd.ms-excel.addin.macroenabled.12 + - application/vnd.ms-excel.template.macroenabled.12 + - application/vnd.ms-excel.sheet.binary.macroenabled.12 + - application/vnd.openxmlformats-officedocument.spreadsheetml.template + - application/vnd.ms-excel.sheet.4 + - application/msexcel + - application/vnd.ms-excel.workspace.3 + - application/vnd.openxmlformats-officedocument.spreadsheetml.sheet + - application/x-tika-old-excel + - application/vnd.ms-excel.sheet.3 + - application/vnd.ms-excel.sheet.2 + - application/vnd.ms-excel.workspace.4 + - application/vnd.ms-excel + - application/vnd.ms-excel.sheet.macroenabled.12 + name: Microsoft Excel File + reason: + - scientific format + source: + - various +miniseed_format: + ext: + - '*.mseed' + mime: + - application/vnd.fdsn.mseed + name: miniSEED Format + reason: + - scientific format + source: + - various +mmcif_3d_molecular_model_format: + ext: + - '*.mmcif' + mime: + - chemical/x-mmcif + name: MMCIF 3D molecular model format + reason: + - scientific format + source: + - various +molconn_z_format: + ext: + - '*.b' + mime: + - chemical/x-molconn-Z + name: Molconn-Z Format + reason: + - scientific format + source: + - various +motion_jpeg_2000_file_format: + ext: + - '*.jpf' + - '*.jpgm' + - '*.jpx' + - '*.mjp2' + - '*.mp1' + - '*.jp2' + - '*.mj2' + - '*.mp2' + - '*.jpm' + mime: + - video/jpm + - video/mj2 + - video/mpeg + name: Motion JPEG 2000 File Format + reason: + - long term format + - open format + source: + - ISO/TR 22299 + - various +mp3_file_format: + ext: + - '*.mp3' + mime: + - audio/x-mpegaudio + - audio/x-mpg + - audio/mp3 + - audio/mpeg + - audio/mpg + - audio/mpeg3 + - audio/x-mpeg3 + - audio/x-mp3 + name: MP3 File Format + reason: + - long term format + source: + - ISO/TR 22299 +mpeg_2_file_format: + ext: + - '*.m2v' + - '*.mpeg' + - '*.m2a' + - '*.ts' + - '*.mpg' + - '*.m2ts' + mime: + - video/mpeg + - video/mp2p + - video/x-mpeg2a + - video/mpeg2 + - video/mp2t + - application/x-pn-mpg + name: MPEG-2 File Format + reason: + - long term format + source: + - ISO/TR 22299 +mpeg_4_file_format: + ext: + - '*.m4a' + - '*.mpg' + - '*.m4v' + - '*.mp4' + mime: + - application/mp4 + - video/mp4v-es + - application/mpeg4-iod-xmt + - video/mpeg4-generic + - audio/mp4 + - application/mpeg4-iod + - video/mp4 + - application/mpeg4-generic + name: MPEG-4 File Format + reason: + - long term format + source: + - ISO/TR 22299 +mpeg_4_media_file: + ext: + - '*.f4v' + mime: + - application/mp4 + - video/mp4 + name: MPEG-4 Media File + reason: + - long term format + source: + - ISO/TR 22299 +mpeg_file_format: + ext: + - '*.mp3' + - '*.mpg' + - '*.mpeg' + - '*.mpa' + - '*.m1v' + - '*.m1a' + - '*.mpv' + mime: + - video/mpeg + - video/x-mpeg + - video/mpg + - video/x-mpg + - video/mpv + - video/mp1s + - audio/mpeg + - application/x-pn-mpg + name: MPEG File Format + reason: + - long term format + source: + - ISO/TR 22299 +ms_works_file: + ext: + - '*.wdb' + - '*.wps' + - '*.xlr' + - '*.wks' + - '*.wcm' + mime: + - application/vnd.ms-works + - application/x-tika-msworks-spreadsheet + name: MS Works File + reason: + - scientific format + source: + - various +msi_alchemy_format: + ext: + - '*.alc' + mime: + - chemical/x-alchemy + name: MSI Alchemy format + reason: + - scientific format + source: + - various +msi_cerius2_datafile: + ext: + - '*.c3d' + mime: + - chemical/x-cerius + name: MSI Cerius2 Datafile + reason: + - scientific format + source: + - various +multiple_image_network_graphics: + ext: + - '*.mng' + mime: + - video/x-mng + name: Multiple-Image Network Graphics + reason: + - open format + source: + - various +nasa_common_data_format_cdf_: + ext: + - '*.cdf' + mime: + - application/x-cdf + name: NASA common data format (.cdf) + reason: + - scientific format + source: + - various +netcdf: + ext: + - '*.nc' + - '*.cdf' + - '*.cf' + mime: + - application/x-netcdf + - application/netcdf + name: NetCDF + reason: + - scientific format + - open format + source: + - various +newick_format: + ext: + - '*.tree' + mime: + - text/x-nh + name: Newick format + reason: + - scientific format + source: + - various +nsdstat_format: + ext: + - '*.nsdstat' + mime: + - application/x-nsdstat + name: NSDstat Format + reason: + - scientific format + source: + - various +nucleotide_sequence_format: + ext: + - '*.gcg' + mime: + - chemical/x-gcg8-sequence + name: Nucleotide Sequence Format + reason: + - scientific format + source: + - various +ogg_multimedia_container_format: + ext: + - '*.ogm' + - '*.ogx' + - '*.ogg' + - '*.oga' + - '*.opus' + - '*.ogv' + mime: + - video/daala + - video/x-oggrgb + - audio/x-ogg-flac + - audio/ogg + - audio/x-ogg-pcm + - video/x-ogm + - video/theora + - application/x-ogg + - video/x-theora + - video/x-ogg-uvs + - application/ogg + - video/x-ogg-yuv + - video/x-ogguvs + - video/x-daala + - video/ogg + - audio/opus + - audio/speex + - video/x-oggyuv + - video/x-ogg-rgb + - audio/x-ogg + name: Ogg Multimedia Container Format + reason: + - long term format + source: + - ISO/TR 22299 +ogg_packaged_dirac_video: + ext: + - '*.drc' + mime: + - video/x-dirac + name: Ogg Packaged Dirac Video + reason: + - long term format + source: + - ISO/TR 22299 +ogg_speex_codec_multimedia_file: + ext: + - '*.spx' + mime: + - application/x-speex + - audio/x-speex + - audio/speex + name: Ogg Speex Codec Multimedia File + reason: + - long term format + source: + - ISO/TR 22299 +opendocument_spreadsheet: + ext: + - '*.fods' + - '*.ots' + - '*.ods' + mime: + - application/vnd.oasis.opendocument.spreadsheet-template + - application/vnd.oasis.opendocument.spreadsheet + name: OpenDocument Spreadsheet + reason: + - scientific format + source: + - various +openexr_file_format: + ext: + - '*.exr' + mime: + - image/x-exr + name: OpenEXR File Format + reason: + - open format + source: + - various +openoffice_org_xml: + ext: + - '*.sxg' + - '*.sxc' + - '*.sxd' + - '*.stc' + - '*.std' + - '*.sxm' + mime: + - application/vnd.sun.xml.calc + - application/vnd.sun.xml.calc.template + name: OpenOffice.org XML + reason: + - scientific format + source: + - various +openraster_image_format: + ext: + - '*.ora' + mime: + - image/openraster + name: OpenRaster Image Format + reason: + - open format + source: + - various +pcma: + ext: + - '*.wav' + mime: + - audio/pcma-wb + - audio/pcma + name: PCMA + reason: + - long term format + source: + - ISO/TR 22299 +pcmu: + ext: + - '*.wav' + mime: + - audio/pcmu-wb + - audio/pcmu + name: PCMU + reason: + - long term format + source: + - ISO/TR 22299 +portable_document_format: + ext: + - '*.pdfxml' + - '*.pdf' + - '*.mars' + mime: + - application/vnd.adobe.pdfxml + - text/x-pdf + - application/x-pdf + - text/pdf + - application/pdf + - application/vnd.adobe.x-mars + - application/vnd.pdf + name: Portable Document Format + reason: + - long term format + source: + - ISO/TR 22299 +portable_network_graphics: + ext: + - '*.png' + - '*.apng' + mime: + - image/png + - image/vnd.mozilla.apng + name: Portable Network Graphics + reason: + - long term format + - open format + source: + - ISO/TR 22299 + - various +protein_data_bank_format: + ext: + - '*.pdb' + mime: + - chemical/x-pdb + name: Protein Data Bank format + reason: + - scientific format + source: + - various +python_file: + ext: + - '*.py' + mime: + - text/x-python + - text/x-python-script + name: Python File + reason: + - scientific format + source: + - various +quattro_pro_format: + ext: + - '*.qpw' + - '*.wq2' + - '*.wq1' + - '*.wb3' + - '*.wb2' + - '*.wb1' + mime: + - application/x-quattro-pro + name: Quattro Pro Format + reason: + - scientific format + source: + - various +r_file_format: + ext: + - '*.r' + - '*.R' + mime: + - application/x-rlang-transport + - text/x-r-source + - type/x-r-syntax + - application/x-R-2 + name: R File Format + reason: + - scientific format + source: + - various +root: + ext: + - '*.root' + mime: + - application/x-root + name: CERN ROOT file + reason: + - scientific format + source: + - various +sas_file_format: + ext: + - '*.sas' + mime: + - application/x-sas-log + - application/x-sas-data + - application/x-sas-catalog + - application/x-sas-system + - application/x-sas-output + - text/x-sas-syntax + - application/x-sas-transport + - application/x-sas + - application/x-sas-syntax + name: SAS File Format + reason: + - scientific format + source: + - various +scalable_vector_graphics: + ext: + - '*.svgz' + - '*.svg' + mime: + - image/svg+xml + - image/svg-xml + name: Scalable Vector Graphics + reason: + - long term format + - open format + source: + - ISO/TR 22299 + - various +sff_molecular_biology_format: + ext: + - '*.sff' + mime: + - chemical/seq-na-sff + name: SFF molecular biology format + reason: + - scientific format + source: + - various +silo_3d_model: + ext: + - '*.sia' + - '*.silo' + - '*.sib' + mime: + - model/mesh + name: Silo 3D model + reason: + - scientific format + source: + - various +smiles_chemical_format: + ext: + - '*.smi' + mime: + - chemical/x-daylight-smiles + name: SMILES chemical format + reason: + - scientific format + source: + - various +spc_format_for_spectral_and_chromatographic_data_b_: + ext: + - '*.spc' + mime: + - chemical/x-galactic-spc + name: SPC format for spectral and chromatographic data (B) + reason: + - scientific format + source: + - various +spss_file_format: + ext: + - '*.zip' + - '*.sav' + - '*.sps' + - '*.por' + mime: + - application/x-dvn-csvspss-zip + - text/x-spss-syntax + - application/x-spss-syntax + - application/x-spss-portable + - application/x-spss-sav + - application/x-spss-por + - application/x-spss-sps + name: SPSS File Format + reason: + - scientific format + source: + - various +staroffice_calc_format: + ext: + - '*stc' + - '*.sdc' + mime: + - application/x-starcalc + - application/vnd.stardivision.calc + - application/vnd.sun.xml.calc.template + name: StarOffice Calc Format + reason: + - scientific format + source: + - various +stata_data_file_format: + ext: + - '*.do' + - '*.dta' + mime: + - application/x-stata + - application/x-stata-6 + - application/x-stata-dta + - application/x-stata-smcl + - application/x-stata-syntax + - application/x-stata-ado + - application/x-stata-do + - application/x-stata-14 + - application/x-stata-13 + - application/x-stata-15 + name: Stata Data File Format + reason: + - scientific format + source: + - various +step_file_iso_10303_21: + ext: + - '*.21' + - '*.p21' + - '*.step' + - '*.stpnc' + - '*.stp' + mime: + - model/step + - model/step+xml + - model/step+zip + - model/step-xml+zip + name: STEP-file, ISO 10303-21 + reason: + - long term format + source: + - ISO/TR 22299 +stl_stereolithography_format: + ext: + - '*.sla' + - '*.stl' + mime: + - application/sla + - model/stl + - model/x.stl-ascii + - model/x.stl-binary + name: STL Stereolithography format + reason: + - scientific format + source: + - various +stockholm_format: + ext: + - '*.sto' + mime: + - text/x-stockholm-alignment + name: Stockholm format + reason: + - scientific format + source: + - various +swissprot_sequence_format: + ext: + - '*.sw' + mime: + - chemical/x-swissprot + name: SwissProt sequence format + reason: + - scientific format + source: + - various +systems_biology_markup_language_sbml_: + ext: + - '*.sbml' + mime: + - application/sbml+xml + name: Systems Biology Markup Language (SBML) + reason: + - scientific format + source: + - various +tab_ddi_format: + description: A zipped tab (tsv) file together with a DDI XML metadata, informal type defined by Dataverse + ext: + - '*.zip' + mime: + - application/x-dvn-tabddi-zip + name: TAB DDI Format + reason: + - scientific format + source: + - various +tagged_image_file_format: + ext: + - '*.tif' + - '*.tfx' + - '*.tfw' + - '*.tiff' + mime: + - image/tiff + name: Tagged Image File Format + reason: + - long term format + source: + - ISO/TR 22299 +tripos_molecule_structure_format_: + ext: + - '*.mol2' + mime: + - chemical/x-mol2 + name: 'Tripos molecule structure format ' + reason: + - scientific format + source: + - various +video_object_file_vob_: + ext: + - '*.vob' + mime: + - video/x-ms-vob + name: Video Object File (VOB) + reason: + - long term format + source: + - ISO/TR 22299 +vorbis_encoded_audio: + ext: + - '*.wav' + mime: + - audio/vorbis-config + - audio/vorbis + name: Vorbis encoded audio + reason: + - long term format + source: + - ISO/TR 22299 +wave_audio_file_format: + ext: + - '*.wave' + - '*.wav' + mime: + - audio/x-wav + - audio/vnd.wave + - audio/wave + - audio/x-pn-wav + - audio/wav + name: WAVE Audio File Format + reason: + - long term format + source: + - ISO/TR 22299 +webp_format: + ext: + - '*.webp' + mime: + - image/webp + name: WebP Format + reason: + - open format + source: + - various +windows_bitmap_image_file_bmp_: + ext: + - '*.bmp' + mime: + - image/x-ms-bmp + - image/bmp + name: Windows Bitmap Image File (BMP) + reason: + - long term format + source: + - ISO/TR 22299 +windows_media_video: + ext: + - '*.asf' + - '*.wmv' + mime: + - video/x-ms-asf + - video/x-ms-wmv + name: Windows Media Video + reason: + - long term format + source: + - ISO/TR 22299 +wolfram_computable_document_format_cdf_: + ext: + - '*.cdf' + mime: + - application/vnd.wolfram.cdf.text + - application/vnd.wolfram.cdf + name: Wolfram Computable Document Format (CDF) + reason: + - scientific format + source: + - various +x_pixmap_xpm_: + ext: + - 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It can be searched by keyword or CAS indetifier.", - "id": 1312, - "mirId": "MIR:00000458", - "modified": "2019-06-11T14:17:25.144+0000", - "name": "Molbase", - "namespaceEmbeddedInLui": false, - "pattern": "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$", - "prefix": "molbase", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Molbase at Chinese Academy of Sciences", - "id": 1314, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1313, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "name": "Chinese Academy of Sciences, Xuhui District Shanghai", - "rorId": null - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "mirId": "MIR:00100593", - "name": "Molbase at Chinese Academy of Sciences", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.molbase.com/", - "sampleId": "128796-39-4", - "urlPattern": "http://www.molbase.com/en/index.php?app=search&search_keyword={$id}" - } - ], - "sampleId": "128796-39-4" - }, - { - "created": "2019-06-11T14:17:25.397+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.", - "id": 1315, - "mirId": "MIR:00000459", - "modified": "2019-06-11T14:17:25.397+0000", - "name": "YRC PDR", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "yrcpdr", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "YRC PDR at University of Washington", - "id": 1317, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1316, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Department of Biochemistry, University of Washington, Seattle", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100594", - "name": "YRC PDR at University of Washington", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.yeastrc.org/pdr/", - "sampleId": "2673500", - "urlPattern": "http://yeastrc.org/pdr/viewProtein.do?id={$id}" - } - ], - "sampleId": "2673500" - }, - { - "created": "2019-06-11T14:17:25.610+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].", - "id": 1318, - "mirId": "MIR:00000460", - "modified": "2019-06-11T14:17:25.610+0000", - "name": "Yeast Intron Database v3", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z0-9]+$", - "prefix": "yid", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Yeast Intron Database version 3 at Baskin School of Engineering", - "id": 1320, - "institution": { - "description": "UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n", - "homeUrl": "https://www.ucsc.edu", - "id": 1319, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "University of California, Santa Cruz", - "rorId": "https://ror.org/03s65by71" - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100595", - "name": "Yeast Intron Database version 3 at Baskin School of Engineering", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://compbio.soe.ucsc.edu/yeast_introns.html", - "sampleId": "SNR17A", - "urlPattern": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName={$id}" - } - ], - "sampleId": "SNR17A" - }, - { - "created": "2019-06-11T14:17:25.854+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.", - "id": 1321, - "mirId": "MIR:00000461", - "modified": "2019-06-11T14:17:25.854+0000", - "name": "FuncBase Fly", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "funcbase.fly", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "FuncBase Fly at Harvard Medical School", - "id": 1323, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1322, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Harvard Medical School, Boston, Massachusetts", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100596", - "name": "FuncBase Fly at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://func.mshri.on.ca/fly", - "sampleId": "10194", - "urlPattern": "http://func.mshri.on.ca/fly/genes/list_functional_scores/{$id}" - } - ], - "sampleId": "10194" - }, - { - "created": "2019-06-11T14:17:26.074+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. 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This collection references human data.", - "id": 1324, - "mirId": "MIR:00000462", - "modified": "2019-06-11T14:17:26.074+0000", - "name": "FuncBase Human", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "funcbase.human", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "FuncBase Human at Harvard Medical School", - "id": 1325, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1322, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Harvard Medical School, Boston, Massachusetts", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100597", - "name": "FuncBase Human at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://func.mshri.on.ca/human/", - "sampleId": "119514", - "urlPattern": "http://func.mshri.on.ca/human/genes/list_functional_scores/{$id}" - } - ], - "sampleId": "119514" - }, - { - "created": "2019-06-11T14:17:26.285+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.", - "id": 1326, - "mirId": "MIR:00000463", - "modified": "2019-06-11T14:17:26.285+0000", - "name": "FuncBase Mouse", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "funcbase.mouse", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "FuncBase Mouse at Harvard Medical School", - "id": 1327, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1322, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Harvard Medical School, Boston, Massachusetts", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100598", - "name": "FuncBase Mouse at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://func.mshri.on.ca/mouse/", - "sampleId": "1351341", - "urlPattern": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/{$id}" - } - ], - "sampleId": "1351341" - }, - { - "created": "2019-06-11T14:18:18.874+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.", - "id": 1881, - "mirId": "MIR:00000679", - "modified": "2019-06-11T14:18:18.874+0000", - "name": "The cBioPortal for Cancer Genomics", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9\\_]+$", - "prefix": "cbioportal", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "The cBioPortal for Cancer Genomics", - "id": 1883, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1882, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Memorial Sloan Kettering Cancer Center", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100909", - "name": "The cBioPortal for Cancer Genomics", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.cbioportal.org", - "sampleId": "laml_tcga_pub", - "urlPattern": "http://www.cbioportal.org/study?id={$id}#summary" - } - ], - "sampleId": "laml_tcga_pub" - }, - { - "created": "2019-06-11T14:17:26.470+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.", - "id": 1328, - "mirId": "MIR:00000464", - "modified": "2019-06-11T14:17:26.470+0000", - "name": "FuncBase Yeast", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "funcbase.yeast", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "FuncBase Yeast at Harvard Medical School", - "id": 1329, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1322, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Harvard Medical School, Boston, Massachusetts", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100599", - "name": "FuncBase Yeast at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://func.mshri.on.ca/yeast", - "sampleId": "2701", - "urlPattern": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/{$id}" - } - ], - "sampleId": "2701" - }, - { - "created": "2019-06-11T14:17:26.654+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.", - "id": 1330, - "mirId": "MIR:00000465", - "modified": "2019-06-11T14:17:26.654+0000", - "name": "YDPM", - "namespaceEmbeddedInLui": false, - "pattern": "^Y[A-Z]{2}\\d+[CW]$", - "prefix": "ydpm", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "YDPM at Stanford University School of Medicine", - "id": 1332, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1331, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Stanford University School of Medicine, Stanford, California", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100600", - "name": "YDPM at Stanford University School of Medicine", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www-deletion.stanford.edu/YDPM/", - "sampleId": "YAL001C", - "urlPattern": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id}" - } - ], - "sampleId": "YAL001C" - }, - { - "created": "2019-06-11T14:17:26.886+0000", - "deprecated": false, - "deprecationDate": null, - "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.", - "id": 1333, - "mirId": "MIR:00000466", - "modified": "2019-06-11T14:17:26.886+0000", - "name": "WormBase RNAi", - "namespaceEmbeddedInLui": false, - "pattern": "^WBRNAi\\d{8}$", - "prefix": "wb.rnai", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "WormBase RNAi", - "id": 1334, - "institution": { - "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100601", - "name": "WormBase RNAi", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://www.wormbase.org/", - "sampleId": "WBRNAi00086878", - "urlPattern": "https://www.wormbase.org/species/c_elegans/rnai/{$id}" - } - ], - "sampleId": "WBRNAi00086878" - }, - { - "created": "2019-06-11T14:17:27.086+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", - "id": 1335, - "mirId": "MIR:00000468", - "modified": "2019-06-11T14:17:27.086+0000", - "name": "PASS2", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pass2", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "PASS2 at National centre for Biological Sciences (India)", - "id": 1337, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1336, - "location": { - "countryCode": "IN", - "countryName": "India" - }, - "name": "National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka", - "rorId": null - }, - "location": { - "countryCode": "IN", - "countryName": "India" - }, - "mirId": "MIR:00100603", - "name": "PASS2 at National centre for Biological Sciences (India)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://caps.ncbs.res.in/pass2/", - "sampleId": "46977", - "urlPattern": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id={$id}" - } - ], - "sampleId": "46977" - }, - { - "created": "2019-06-11T14:17:27.338+0000", - "deprecated": false, - "deprecationDate": null, - "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.", - "id": 1338, - "mirId": "MIR:00000469", - "modified": "2019-06-11T14:17:27.338+0000", - "name": "ICEberg element", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "iceberg.element", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "ICEberg element at Shanghai Jiaotong University", - "id": 1340, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1339, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "name": "State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai", - "rorId": null - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "mirId": "MIR:00100604", - "name": "ICEberg element at Shanghai Jiaotong University", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://db-mml.sjtu.edu.cn/ICEberg/", - "sampleId": "100", - "urlPattern": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id={$id}" - } - ], - "sampleId": "100" - }, - { - "created": "2019-06-11T14:17:27.601+0000", - "deprecated": false, - "deprecationDate": null, - "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. 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This collection references projects.", - "id": 1453, - "mirId": "MIR:00000515", - "modified": "2019-06-11T14:17:38.030+0000", - "name": "PRIDE Project", - "namespaceEmbeddedInLui": false, - "pattern": "^P(X|R)D\\d{6}$", - "prefix": "pride.project", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "PRIDE Project at EBI", - "id": 1454, - "institution": { - "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100662", - "name": "PRIDE Project at EBI", - "official": true, - "providerCode": "ebi", - "resourceHomeUrl": "https://www.ebi.ac.uk/pride/", - "sampleId": "PXD000440", - "urlPattern": "https://www.ebi.ac.uk/pride/archive/projects/{$id}" - }, - { - "deprecated": false, - "deprecationDate": null, - "description": "PRIDE Project through OmicsDI", - "id": 1455, - "institution": { - "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100858", - "name": "PRIDE Project through OmicsDI", - "official": false, - "providerCode": "omicsdi", - "resourceHomeUrl": "https://www.omicsdi.org/", - "sampleId": "PXD000440", - "urlPattern": "https://www.omicsdi.org/dataset/pride/{$id}" - } - ], - "sampleId": "PXD000440" - }, - { - "created": "2019-06-11T14:17:38.379+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.", - "id": 1456, - "mirId": "MIR:00000516", - "modified": "2019-06-11T14:17:38.379+0000", - "name": "Antibody Registry", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{6}$", - "prefix": "antibodyregistry", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Antibody Registry at University of California", - "id": 1458, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1457, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Neuroscience Information Framework, University of California, San Diego, California", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100664", - "name": "Antibody Registry at University of California", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://antibodyregistry.org/", - "sampleId": "493771", - "urlPattern": "http://antibodyregistry.org/AB_{$id}" - } - ], - "sampleId": "493771" - }, - { - "created": "2019-06-11T14:17:38.625+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", - "id": 1459, - "mirId": "MIR:00000517", - "modified": "2019-06-11T14:17:38.625+0000", - "name": "Mathematical Modelling Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^MAMO_\\d{7}$", - "prefix": "mamo", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "MAMO through BioPortal", - "id": 1460, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 5, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "National Center for Biomedical Ontology, Stanford", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100665", - "name": "MAMO through BioPortal", - "official": false, - "providerCode": "bptl", - "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/MAMO", - "sampleId": "MAMO_0000026", - "urlPattern": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/{$id}" - }, - { - "deprecated": false, - "deprecationDate": null, - "description": "MaMO through OLS", - "id": 1461, - "institution": { - "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100758", - "name": "MaMO through OLS", - "official": false, - "providerCode": "ols", - "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/mamo", - "sampleId": "MAMO_0000026", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form={$id}" - } - ], - "sampleId": "MAMO_0000026" - }, - { - "created": "2019-06-11T14:17:38.985+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", - "id": 1462, - "mirId": "MIR:00000518", - "modified": "2019-06-11T14:17:38.985+0000", - "name": "Plant Environment Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^(P)?EO\\:\\d{7}$", - "prefix": "eo", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Plant Environment Ontology through Gramene", - "id": 1463, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 556, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Cold Spring Harbor Laboratory, New York", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100667", - "name": "Plant Environment Ontology through Gramene", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://archive.gramene.org/db/ontology/search_term?id=EO:0007359", - "sampleId": "0007404", - "urlPattern": "http://archive.gramene.org/db/ontology/search?query=EO:{$id}" - }, - { - "deprecated": false, - "deprecationDate": null, - "description": "Plant Environment Ontology through BioPortal", - "id": 1464, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 5, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "National Center for Biomedical Ontology, Stanford", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100668", - "name": "Plant Environment Ontology through BioPortal", - "official": false, - "providerCode": "bptl", - "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/PECO", - "sampleId": "0007404", - "urlPattern": "http://purl.bioontology.org/ontology/PECO/EO:{$id}" - }, - { - "deprecated": false, - "deprecationDate": null, - "description": "Plant Environment Ontology through OLS", - "id": 1465, - "institution": { - "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100669", - "name": "Plant Environment Ontology through OLS", - "official": false, - "providerCode": "ols", - "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/eo", - "sampleId": "0007404", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=EO:{$id}" - } - ], - "sampleId": "0007404" - }, - { - "created": "2019-06-11T14:17:39.487+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", - "id": 1466, - "mirId": "MIR:00000519", - "modified": "2019-06-11T14:17:39.487+0000", - "name": "Identifiers.org Terms", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z]+$", - "prefix": "idot", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "IdoT via biomodels.net", - "id": 1467, - "institution": { - "description": "At EMBL-EBI, we make the world\u2019s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "homeUrl": "https://www.ebi.ac.uk", - "id": 2, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "name": "European Bioinformatics Institute", - "rorId": "https://ror.org/02catss52" - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "mirId": "MIR:00100670", - "name": "IdoT via biomodels.net", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://identifiers.org/", - "sampleId": "identifierPattern", - "urlPattern": "https://biomodels.net/vocab/idot.rdf#{$id}" - } - ], - "sampleId": "identifierPattern" - }, - { - "created": "2019-06-11T14:17:39.906+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].", - "id": 1470, - "mirId": "MIR:00000521", - "modified": "2019-06-11T14:17:39.906+0000", - "name": "Yeast Intron Database v4.3", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z0-9]+$", - "prefix": "yeastintron", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Yeast Intron Database version 4.3 at Baskin School of Engineering", - "id": 1471, - "institution": { - "description": "UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n", - "homeUrl": "https://www.ucsc.edu", - "id": 1319, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "University of California, Santa Cruz", - "rorId": "https://ror.org/03s65by71" - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100673", - "name": "Yeast Intron Database version 4.3 at Baskin School of Engineering", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://intron.ucsc.edu/yeast4.3/", - "sampleId": "SNR17A", - "urlPattern": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName={$id}" - } - ], - "sampleId": "SNR17A" - }, - { - "created": "2019-06-11T14:17:40.104+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.", - "id": 1472, - "mirId": "MIR:00000522", - "modified": "2019-06-11T14:17:40.104+0000", - "name": "Antibiotic Resistance Genes Database", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z_]{3}[0-9]{4,}$", - "prefix": "ardb", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "ARDB at University of Maryland", - "id": 1474, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1473, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "name": "Center for Bioinformatics and Computational Biology, University of Maryland, Maryland", - "rorId": null - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "mirId": "MIR:00100678", - "name": "ARDB at University of Maryland", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://ardb.cbcb.umd.edu/", - "sampleId": "CAE46076", - "urlPattern": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term={$id}" - } - ], - "sampleId": "CAE46076" - }, - { - "created": "2019-06-11T14:17:40.344+0000", - "deprecated": false, - "deprecationDate": null, - "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.", - "id": 1475, - "mirId": "MIR:00000524", - "modified": "2019-06-11T14:17:40.344+0000", - "name": "ProteomicsDB Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "proteomicsdb.protein", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Proteomics DB Protein at Center for Integrated Protein Science", - "id": 1477, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1476, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "name": "Center for Integrated Protein Science, Munich,", - "rorId": null - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "mirId": "MIR:00100680", - "name": "Proteomics DB Protein at Center for Integrated Protein Science", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://www.proteomicsdb.org/#human", - "sampleId": "53504", - "urlPattern": "https://www.proteomicsdb.org/#human/proteinDetails/{$id}/summary" - } - ], - "sampleId": "53504" - }, - { - "created": "2019-06-11T14:17:40.583+0000", - "deprecated": false, - "deprecationDate": null, - "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.", - "id": 1478, - "mirId": "MIR:00000525", - "modified": "2019-06-11T14:17:40.583+0000", - "name": "ProteomicsDB Peptide", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "proteomicsdb.peptide", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Proteomics DB Peptide at Center for Integrated Protein Science", - "id": 1480, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1479, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "name": "Center for Integrated Protein Science, Munich", - "rorId": null - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "mirId": "MIR:00100681", - "name": "Proteomics DB Peptide at Center for Integrated Protein Science", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://www.proteomicsdb.org/#peptideSearch", - "sampleId": "53504", - "urlPattern": "https://www.proteomicsdb.org/#human/proteinDetails/{$id}/peptides/" - } - ], - "sampleId": "53504" - }, - { - "created": "2019-06-11T14:17:40.825+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.", - "id": 1481, - "mirId": "MIR:00000526", - "modified": "2019-06-11T14:17:40.825+0000", - "name": "Human Proteome Map Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "hpm.protein", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)", - "id": 1482, - "institution": { - "description": "CURATOR_REVIEW", - "homeUrl": "CURATOR_REVIEW", - "id": 1087, - "location": { - "countryCode": "IN", - "countryName": "India" - }, - "name": "Institute of Bioinformatics, International Tech Park, Bangalore", - "rorId": null - }, - "location": { - "countryCode": "IN", - "countryName": "India" - }, - "mirId": "MIR:00100682", - "name": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "http://www.humanproteomemap.org/index.php", - "sampleId": "1968", - "urlPattern": "http://www.humanproteomemap.org/protein.php?hpm_id={$id}" - } - ], - "sampleId": "1968" - }, - { - "created": "2019-06-11T14:17:41.032+0000", - "deprecated": false, - "deprecationDate": null, - "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. 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Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs.", - "id": 1666, - "mirId": "MIR:00000600", - "modified": "2020-11-25T15:01:33.103+0000", - "name": "Progenetix", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$", - "prefix": "pgx", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Progenetix", - "id": 1668, - "institution": { - "description": "No description available", - "homeUrl": "https://www.uzh.ch/en.html", - "id": 1667, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "name": "University of Zurich", - "rorId": "https://ror.org/02crff812" - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "mirId": "MIR:00100801", - "name": "Progenetix", - "official": false, - "providerCode": "CURATOR_REVIEW", - "resourceHomeUrl": "https://progenetix.org/", - "sampleId": "pgxbs-kftva5zv", - "urlPattern": "https://progenetix.org/services/ids/{$id}" - } - ], - "sampleId": "pgxbs-kftva5zv" - }, - { - "created": "2020-12-14T12:49:56.333+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.", - "id": 2477, - "mirId": "MIR:00000789", - "modified": "2020-12-14T12:49:56.333+0000", - "name": "SARS-CoV-2", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+_COVID19_[-\\w]+$", - "prefix": "covid19", - "resources": [ - { - "deprecated": false, - "deprecationDate": null, - "description": "Elixir@UiT is the local branch of ELIXIR-NO node based at UiT.", - "id": 2478, - "institution": { - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/00wge5k78' with Wikidata IDs [Q279724], and ISNI IDs [0000000122595234]", - "homeUrl": "https://uit.no/startsida", - "id": 2476, - "location": { - "countryCode": "NO", - "countryName": "Norway" - }, - "name": "University of Troms\u00f8 - The Arctic University of Norway", - "rorId": null - }, - "location": { - "countryCode": "NO", - "countryName": "Norway" - }, - "mirId": "MIR:00000787", - "name": "Elixir@UiT", - "official": true, - "providerCode": "sfb", - "resourceHomeUrl": "https://covid19.sfb.uit.no", - "sampleId": "SFB_COVID19_MW286762", - "urlPattern": "https://covid19.sfb.uit.no/api/records/{$id}" - } - ], - "sampleId": "SFB_COVID19_MW286762" - }, - { - "created": "2020-12-14T12:57:54.560+0000", - "deprecated": false, - "deprecationDate": null, - "description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. 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Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. + homeUrl: https://bio2rdf.org + id: 33 + location: + countryCode: US + countryName: United States + name: Bio2RDF.org + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100693 + name: Bio2RDF + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ncbigene.bio2rdf.org/fct + sampleId: '100010' + urlPattern: http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:{$id} + sampleId: '100010' + - created: 2019-06-11T14:15:51.781+0000 + deprecated: false + deprecationDate: + description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. + id: 242 + mirId: MIR:00000070 + modified: 2019-06-11T14:15:51.781+0000 + name: KEGG Genes + namespaceEmbeddedInLui: false + pattern: ^\w+:[\w\d\.-]*$ + prefix: kegg.genes + resources: + - deprecated: false + deprecationDate: + description: KEGG GENES Database + id: 243 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 15 + location: + countryCode: JP + countryName: Japan + name: Kyoto University Bioinformatics Center + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100100 + name: KEGG GENES Database + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genome.jp/kegg/genes.html + sampleId: syn:ssr3451 + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: syn:ssr3451 + - created: 2019-06-11T14:15:51.985+0000 + deprecated: false + deprecationDate: + description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. + id: 244 + mirId: MIR:00000071 + modified: 2019-06-11T14:15:51.985+0000 + name: BRENDA + namespaceEmbeddedInLui: false + pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ + prefix: brenda + resources: + - deprecated: false + deprecationDate: + description: Brenda enzyme database + id: 246 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 245 + location: + countryCode: DE + countryName: Germany + name: Technical University Braunschweig, Institute for Bioinformatics and Biochemistry + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100101 + name: Brenda enzyme database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.brenda-enzymes.org/ + sampleId: 1.1.1.1 + urlPattern: https://www.brenda-enzymes.org/php/result_flat.php4?ecno={$id} + sampleId: 1.1.1.1 + - created: 2019-06-11T14:15:52.227+0000 + deprecated: false + deprecationDate: + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. + id: 247 + mirId: MIR:00000072 + modified: 2019-06-11T14:15:52.227+0000 + name: PubChem-bioassay + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubchem.bioassay + resources: + - deprecated: false + deprecationDate: + description: PubChem Bioassay at NCBI + id: 248 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100102 + name: PubChem Bioassay at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay + sampleId: '1018' + urlPattern: https://pubchem.ncbi.nlm.nih.gov/bioassay/{$id} + sampleId: '1018' + - created: 2019-06-11T14:17:58.671+0000 + deprecated: false + deprecationDate: + description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. + id: 1659 + mirId: MIR:00000597 + modified: 2019-06-11T14:17:58.671+0000 + name: BioAssay Ontology + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: bao + resources: + - deprecated: false + deprecationDate: + description: BioAssay Ontology through BioPortal + id: 1660 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100797 + name: BioAssay Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/BAO/ + sampleId: '0002989' + urlPattern: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_{$id} + - deprecated: false + deprecationDate: + description: BioAssay Ontology through OLS + id: 1661 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100798 + name: BioAssay Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://bioportal.bioontology.org/ontologies/BAO/ + sampleId: '0002989' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/bao/terms?obo_id=BAO:{$id} + sampleId: '0002989' + - created: 2019-06-11T14:15:52.436+0000 + deprecated: false + deprecationDate: + description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. + id: 249 + mirId: MIR:00000073 + modified: 2019-06-11T14:15:52.436+0000 + name: Pathway Commons + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pathwaycommons + resources: + - deprecated: false + deprecationDate: + description: Pathway Commons + id: 251 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 250 + location: + countryCode: US + countryName: United States + name: Memorial Sloan-Kettering Cancer Center + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100103 + name: Pathway Commons + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pathwaycommons.org/pc/ + sampleId: '485991' + urlPattern: http://www.pathwaycommons.org/pc/record2.do?id={$id} + sampleId: '485991' + - created: 2019-06-11T14:15:52.667+0000 + deprecated: false + deprecationDate: + description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. + id: 252 + mirId: MIR:00000074 + modified: 2019-06-11T14:15:52.667+0000 + name: HOVERGEN + namespaceEmbeddedInLui: false + pattern: ^HBG\d+$ + prefix: hovergen + resources: + - deprecated: false + deprecationDate: + description: Hovergen + id: 254 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 253 + location: + countryCode: FR + countryName: France + name: Laboratoire de Biométrie, Génétique et Biologie des Populations + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100104 + name: Hovergen + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pbil.univ-lyon1.fr/databases/hovergen.php + sampleId: HBG004341 + urlPattern: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query={$id}&db=HOVERGEN + sampleId: HBG004341 + - created: 2019-06-11T14:15:52.916+0000 + deprecated: false + deprecationDate: + description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. + id: 255 + mirId: MIR:00000075 + modified: 2019-06-11T14:15:52.916+0000 + name: Melanoma Molecular Map Project Biomaps + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mmmp:biomaps + resources: + - deprecated: false + deprecationDate: + description: main webpage + id: 257 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 256 + location: + countryCode: FR + countryName: France + name: Melanoma Molecular Map Project + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100105 + name: main webpage + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp + sampleId: '37' + urlPattern: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id={$id} + sampleId: '37' + - created: 2019-06-11T14:15:53.125+0000 + deprecated: false + deprecationDate: + description: "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.\r\nAll content is under the Creative Commons Attribution 3.0 Unported license." + id: 258 + mirId: MIR:00000076 + modified: 2019-06-11T14:15:53.125+0000 + name: WikiPathways + namespaceEmbeddedInLui: false + pattern: WP\d{1,5}(\_r\d+)?$ + prefix: wikipathways + resources: + - deprecated: false + deprecationDate: + description: WikiPathways + id: 260 + institution: + description: >- + Maastricht University (UM) is the most international university in + the Netherlands and, with 18,000 students and 4,400 employees, is + still growing. The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: US + countryName: United States + mirId: MIR:00100106 + name: WikiPathways + official: true + providerCode: um + resourceHomeUrl: http://www.wikipathways.org/ + sampleId: WP100 + urlPattern: http://www.wikipathways.org/instance/{$id} + - deprecated: false + deprecationDate: + description: > + Scholia is a service that creates visual scholarly profiles for + topic, people, organizations, species, chemicals, etc using + bibliographic and other information in Wikidata. + id: 2316 + institution: + description: >- + Maastricht University (UM) is the most international university in + the Netherlands and, with 18,000 students and 4,400 employees, is + still growing. The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00000696 + name: Scholia + official: false + providerCode: scholia + resourceHomeUrl: https://scholia.toolforge.org/ + sampleId: WP111 + urlPattern: https://scholia.toolforge.org/wikipathways/{$id} + sampleId: WP100 + - created: 2019-06-11T14:15:53.388+0000 + deprecated: false + deprecationDate: + description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. + id: 261 + mirId: MIR:00000077 + modified: 2019-06-11T14:15:53.388+0000 + name: MACiE + namespaceEmbeddedInLui: false + pattern: ^M\d{4}$ + prefix: macie + resources: + - deprecated: false + deprecationDate: + description: MACiE database of mechanisms, annotation and classification in enzymes + id: 262 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100108 + name: MACiE database of mechanisms, annotation and classification in enzymes + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html + sampleId: M0001 + urlPattern: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id={$id} + sampleId: M0001 + - created: 2019-06-11T14:15:53.607+0000 + deprecated: false + deprecationDate: + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). + id: 263 + mirId: MIR:00000078 + modified: 2019-06-11T14:15:53.607+0000 + name: miRBase Sequence + namespaceEmbeddedInLui: false + pattern: MI\d{7} + prefix: mirbase + resources: + - deprecated: false + deprecationDate: + description: miRBase Sequence Database + id: 265 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 264 + location: + countryCode: GB + countryName: United Kingdom + name: Faculty of Life Sciences, University of Manchester + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100135 + name: miRBase Sequence Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mirbase.org/ + sampleId: MI0000001 + urlPattern: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc={$id} + sampleId: MI0000001 + - created: 2019-06-11T14:15:53.859+0000 + deprecated: false + deprecationDate: + description: ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN. + id: 266 + mirId: MIR:00000079 + modified: 2019-06-11T14:15:53.859+0000 + name: ZFIN Bioentity + namespaceEmbeddedInLui: false + pattern: ^ZDB\-\w+\-\d+\-\d+$ + prefix: zfin + resources: + - deprecated: false + deprecationDate: + description: ZFIN at University of Oregon + id: 268 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 267 + location: + countryCode: US + countryName: United States + name: Zebrafish Information Network, University of Oregon + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100110 + name: ZFIN at University of Oregon + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://zfin.org + sampleId: ZDB-GENE-041118-11 + urlPattern: http://zfin.org/{$id} + - deprecated: false + deprecationDate: + description: ZFIN through BioEntity Link + id: 269 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 101 + location: + countryCode: US + countryName: United States + name: InSilico Inc, in Eugene, Oregon + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100891 + name: ZFIN through BioEntity Link + official: false + providerCode: bioentitylink + resourceHomeUrl: https://bioentity.link/ + sampleId: ZDB-GENE-041118-11 + urlPattern: https://bioentity.link/#/lexicon/public/{$id} + - deprecated: false + deprecationDate: + description: ZFIN through the Alliance of Genome Resources + id: 270 + institution: + description: The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease. + homeUrl: https://www.alliancegenome.org + id: 103 + location: + countryCode: US + countryName: United States + name: Alliance of Genome Resources + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100902 + name: ZFIN through the Alliance of Genome Resources + official: false + providerCode: agr + resourceHomeUrl: https://www.alliancegenome.org + sampleId: ZDB-GENE-041118-11 + urlPattern: https://test.alliancegenome.org/gene/ZFIN:{$id} + sampleId: ZDB-GENE-041118-11 + - created: 2019-06-11T14:15:54.375+0000 + deprecated: false + deprecationDate: + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. + id: 271 + mirId: MIR:00000080 + modified: 2019-06-11T14:15:54.375+0000 + name: HGNC + namespaceEmbeddedInLui: false + pattern: ^((HGNC|hgnc):)?\d{1,5}$ + prefix: hgnc + resources: + - deprecated: false + deprecationDate: + description: HUGO Genome Nomenclature Committee + id: 272 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100111 + name: HUGO Genome Nomenclature Committee + official: true + providerCode: ebi + resourceHomeUrl: https://www.genenames.org + sampleId: '2674' + urlPattern: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/{$id} + sampleId: '2674' + - created: 2019-06-11T14:15:54.604+0000 + deprecated: false + deprecationDate: + description: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. + id: 273 + mirId: MIR:00000081 + modified: 2019-06-11T14:15:54.604+0000 + name: Sequence Ontology + namespaceEmbeddedInLui: true + pattern: ^SO:\d{7}$ + prefix: so + resources: + - deprecated: false + deprecationDate: + description: Sequence Ontology + id: 275 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 274 + location: + countryCode: US + countryName: United States + name: Department of Molecular and Cellular Biology, University of California, Berkeley + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100112 + name: Sequence Ontology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.sequenceontology.org/ + sampleId: '0000704' + urlPattern: http://www.sequenceontology.org/miso/current_release/term/SO:{$id} + - deprecated: false + deprecationDate: + description: Sequence Ontology through BioPortal + id: 276 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100241 + name: Sequence Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/SO + sampleId: '0000704' + urlPattern: http://purl.bioontology.org/ontology/SO/SO:{$id} + - deprecated: false + deprecationDate: + description: Sequence Ontology through Ontology Lookup Service (OLS) + id: 277 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100628 + name: Sequence Ontology through Ontology Lookup Service (OLS) + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/so + sampleId: '0000704' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=SO:{$id} + sampleId: '0000704' + - created: 2019-06-11T14:15:55.126+0000 + deprecated: false + deprecationDate: + description: Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed "spontaneous". + id: 278 + mirId: MIR:00000082 + modified: 2019-06-11T14:15:55.126+0000 + name: Rhea + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: rhea + resources: + - deprecated: false + deprecationDate: + description: Rhea + id: 280 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 279 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute and Swiss Institute of Bioinformatics + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100113 + name: Rhea + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.rhea-db.org/ + sampleId: '12345' + urlPattern: https://www.rhea-db.org/reaction?id={$id} + sampleId: '12345' + - created: 2019-06-11T14:15:55.368+0000 + deprecated: false + deprecationDate: + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + id: 281 + mirId: MIR:00000084 + modified: 2019-06-11T14:15:55.368+0000 + name: ChEMBL compound + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl.compound + resources: + - deprecated: false + deprecationDate: + description: ChEMBL compound database at EBI + id: 282 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100115 + name: ChEMBL compound database at EBI + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/chembldb/ + sampleId: CHEMBL308052 + urlPattern: https://www.ebi.ac.uk/chembl/compound/inspect/{$id} + - deprecated: false + deprecationDate: + description: ChEMBL compound RDF + id: 284 + institution: + description: >- + Maastricht University (UM) is the most international university in + the Netherlands and, with 18,000 students and 4,400 employees, is + still growing. The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100484 + name: ChEMBL compound RDF + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://github.com/egonw/chembl.rdf + sampleId: CHEMBL308052 + urlPattern: http://linkedchemistry.info/chembl/chemblid/{$id} + - deprecated: false + deprecationDate: + description: ChEMBL compound RDF through EBI RDF Platform + id: 285 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100744 + name: ChEMBL compound RDF through EBI RDF Platform + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.ebi.ac.uk/rdf/services/chembl/ + sampleId: CHEMBL308052 + urlPattern: https://rdf.ebi.ac.uk/resource/chembl/molecule/{$id} + sampleId: CHEMBL308052 + - created: 2019-06-11T14:15:55.880+0000 + deprecated: false + deprecationDate: + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + id: 286 + mirId: MIR:00000085 + modified: 2019-06-11T14:15:55.880+0000 + name: ChEMBL target + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl.target + resources: + - deprecated: false + deprecationDate: + description: ChEMBL targets database at EBI + id: 287 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100116 + name: ChEMBL targets database at EBI + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/chembldb/ + sampleId: CHEMBL3467 + urlPattern: https://www.ebi.ac.uk/chembl/target/inspect/{$id} + - deprecated: false + deprecationDate: + description: ChEMBL target RDF + id: 288 + institution: + description: >- + Maastricht University (UM) is the most international university in + the Netherlands and, with 18,000 students and 4,400 employees, is + still growing. The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100485 + name: ChEMBL target RDF + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://github.com/egonw/chembl.rdf + sampleId: CHEMBL3467 + urlPattern: http://linkedchemistry.info/chembl/chemblid/{$id} + - deprecated: false + deprecationDate: + description: ChEMBL target RDF through EBI RDF Platform + id: 289 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100743 + name: ChEMBL target RDF through EBI RDF Platform + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://rdf.ebi.ac.uk/resource/chembl/ + sampleId: CHEMBL3467 + urlPattern: https://rdf.ebi.ac.uk/resource/chembl/target/{$id} + sampleId: CHEMBL3467 + - created: 2019-06-11T14:15:56.334+0000 + deprecated: false + deprecationDate: + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. + id: 290 + mirId: MIR:00000086 + modified: 2019-06-11T14:15:56.334+0000 + name: SABIO-RK Kinetic Record + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sabiork.kineticrecord + resources: + - deprecated: false + deprecationDate: + description: SABIO-RK Reaction Kinetics Database - Kinetic Dataset + id: 291 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 151 + location: + countryCode: DE + countryName: Germany + name: Heidelberg Institute for Theoretical Studies (HITS gGmbH) + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100117 + name: SABIO-RK Reaction Kinetics Database - Kinetic Dataset + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://sabiork.h-its.org/ + sampleId: '5046' + urlPattern: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid={$id} + sampleId: '5046' + - created: 2019-06-11T14:15:56.548+0000 + deprecated: false + deprecationDate: + description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. + id: 292 + mirId: MIR:00000087 + modified: 2019-06-11T14:15:56.548+0000 + name: Ligand-Gated Ion Channel database + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: lgic + resources: + - deprecated: false + deprecationDate: + description: Ligand-Gated Ion Channel database at EBI + id: 293 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100118 + name: Ligand-Gated Ion Channel database at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php + sampleId: 5HT3Arano + urlPattern: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/{$id}.php + sampleId: 5HT3Arano + - created: 2019-06-11T14:15:56.747+0000 + deprecated: false + deprecationDate: + description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. + id: 294 + mirId: MIR:00000088 + modified: 2019-06-11T14:15:56.747+0000 + name: Anatomical Therapeutic Chemical + namespaceEmbeddedInLui: false + pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ + prefix: atc + resources: + - deprecated: false + deprecationDate: + description: Anatomical Therapeutic Chemical Index at WHO + id: 296 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 295 + location: + countryCode: CH + countryName: Switzerland + name: World Health Organisation + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100119 + name: Anatomical Therapeutic Chemical Index at WHO + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.whocc.no/atc_ddd_index/ + sampleId: A10BA02 + urlPattern: http://www.whocc.no/atc_ddd_index/?code={$id} + sampleId: A10BA02 + - created: 2019-06-11T14:15:57.006+0000 + deprecated: false + deprecationDate: + description: "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies." + id: 297 + mirId: MIR:00000089 + modified: 2019-06-11T14:15:57.006+0000 + name: PharmGKB Pathways + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.pathways + resources: + - deprecated: false + deprecationDate: + description: PharmGKB at Stanford + id: 299 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 298 + location: + countryCode: US + countryName: United States + name: Department of Genetics, School of Medicine, Stanford University, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100120 + name: PharmGKB at Stanford + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pharmgkb.org/ + sampleId: PA146123006 + urlPattern: http://www.pharmgkb.org/pathway/{$id} + sampleId: PA146123006 + - created: 2019-06-11T14:15:57.258+0000 + deprecated: false + deprecationDate: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + id: 300 + mirId: MIR:00000090 + modified: 2019-06-11T14:15:57.258+0000 + name: PharmGKB Disease + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.disease + resources: + - deprecated: false + deprecationDate: + description: PharmGKB Disease at Stanford + id: 301 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 298 + location: + countryCode: US + countryName: United States + name: Department of Genetics, School of Medicine, Stanford University, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100121 + name: PharmGKB Disease at Stanford + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pharmgkb.org/ + sampleId: PA447218 + urlPattern: http://www.pharmgkb.org/disease/{$id} + sampleId: PA447218 + - created: 2019-06-11T14:15:57.451+0000 + deprecated: false + deprecationDate: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + id: 302 + mirId: MIR:00000091 + modified: 2019-06-11T14:15:57.451+0000 + name: PharmGKB Drug + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.drug + resources: + - deprecated: false + deprecationDate: + description: PharmGKB Drug at Stanford + id: 303 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 298 + location: + countryCode: US + countryName: United States + name: Department of Genetics, School of Medicine, Stanford University, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100122 + name: PharmGKB Drug at Stanford + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pharmgkb.org/ + sampleId: PA448710 + urlPattern: http://www.pharmgkb.org/drug/{$id} + sampleId: PA448710 + - created: 2019-06-11T14:15:57.654+0000 + deprecated: false + deprecationDate: + description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. + id: 304 + mirId: MIR:00000092 + modified: 2019-06-11T14:15:57.654+0000 + name: TTD Drug + namespaceEmbeddedInLui: false + pattern: ^DAP\d+$ + prefix: ttd.drug + resources: + - deprecated: false + deprecationDate: + description: Therapeutic Target Database Drug + id: 306 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 305 + location: + countryCode: SG + countryName: Singapore + name: Computational Science Department, National University of Singapore + rorId: + location: + countryCode: SG + countryName: Singapore + mirId: MIR:00100123 + name: Therapeutic Target Database Drug + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bidd.nus.edu.sg/group/ttd/ttd.asp + sampleId: DAP000773 + urlPattern: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID={$id} + sampleId: DAP000773 + - created: 2019-06-11T14:15:57.896+0000 + deprecated: false + deprecationDate: + description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. + id: 307 + mirId: MIR:00000093 + modified: 2019-06-11T14:15:57.896+0000 + name: TTD Target + namespaceEmbeddedInLui: false + pattern: ^TTDS\d+$ + prefix: ttd.target + resources: + - deprecated: false + deprecationDate: + description: Therapeutic Target Database Target + id: 308 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 305 + location: + countryCode: SG + countryName: Singapore + name: Computational Science Department, National University of Singapore + rorId: + location: + countryCode: SG + countryName: Singapore + mirId: MIR:00100124 + name: Therapeutic Target Database Target + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bidd.nus.edu.sg/group/ttd/ttd.asp + sampleId: TTDS00056 + urlPattern: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID={$id} + sampleId: TTDS00056 + - created: 2019-06-11T14:15:58.106+0000 + deprecated: false + deprecationDate: + description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' + id: 309 + mirId: MIR:00000094 + modified: 2019-06-11T14:15:58.106+0000 + name: NeuronDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: neurondb + resources: + - deprecated: false + deprecationDate: + description: NeuronDB at SenseLab + id: 311 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 310 + location: + countryCode: US + countryName: United States + name: Yale University School of Medicine + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100125 + name: NeuronDB at SenseLab + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://senselab.med.yale.edu/NeuronDB/ + sampleId: '265' + urlPattern: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id={$id} + sampleId: '265' + - created: 2019-06-11T14:15:58.342+0000 + deprecated: false + deprecationDate: + description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. + id: 312 + mirId: MIR:00000095 + modified: 2019-06-11T14:15:58.342+0000 + name: NeuroMorpho + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: neuromorpho + resources: + - deprecated: false + deprecationDate: + description: NeuroMorpho + id: 314 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 313 + location: + countryCode: US + countryName: United States + name: Krasnow Institute, Virginia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100126 + name: NeuroMorpho + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://neuromorpho.org/index.jsp + sampleId: Rosa2 + urlPattern: http://neuromorpho.org/neuron_info.jsp?neuron_name={$id} + sampleId: Rosa2 + - created: 2019-06-11T14:15:58.577+0000 + deprecated: false + deprecationDate: + description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. + id: 315 + mirId: MIR:00000096 + modified: 2019-06-11T14:15:58.577+0000 + name: ChemIDplus + namespaceEmbeddedInLui: false + pattern: ^\d+\-\d+\-\d+$ + prefix: chemidplus + resources: + - deprecated: false + deprecationDate: + description: ChemIDplus at National Library of Medicine + id: 317 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 316 + location: + countryCode: US + countryName: United States + name: National Library of Medicine, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100127 + name: ChemIDplus at National Library of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp + sampleId: 57-27-2 + urlPattern: https://chem.nlm.nih.gov/chemidplus/rn/{$id} + sampleId: 57-27-2 + - created: 2019-06-11T14:15:58.906+0000 + deprecated: false + deprecationDate: + description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. + id: 318 + mirId: MIR:00000097 + modified: 2019-06-11T14:15:58.906+0000 + name: BioSystems + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biosystems + resources: + - deprecated: false + deprecationDate: + description: BioSystems database at NCBI + id: 319 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100128 + name: BioSystems database at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/biosystems/ + sampleId: '001' + urlPattern: https://www.ncbi.nlm.nih.gov/biosystems/{$id} + sampleId: '001' + - created: 2019-06-11T14:15:59.108+0000 + deprecated: false + deprecationDate: + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + id: 320 + mirId: MIR:00000098 + modified: 2019-06-11T14:15:59.108+0000 + name: CTD Chemical + namespaceEmbeddedInLui: false + pattern: ^[CD]\d+$ + prefix: ctd.chemical + resources: + - deprecated: false + deprecationDate: + description: Comparative Toxicogenomics Database (Chemical) + id: 322 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 321 + location: + countryCode: US + countryName: United States + name: The Mount Desert Island Biological Laboratory + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100129 + name: Comparative Toxicogenomics Database (Chemical) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ctdbase.org/ + sampleId: D001151 + urlPattern: http://ctdbase.org/detail.go?type=chem&acc={$id} + sampleId: D001151 + - created: 2019-06-11T14:15:59.348+0000 + deprecated: false + deprecationDate: + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + id: 323 + mirId: MIR:00000099 + modified: 2019-06-11T14:15:59.348+0000 + name: CTD Disease + namespaceEmbeddedInLui: false + pattern: ^D\d+$ + prefix: ctd.disease + resources: + - deprecated: false + deprecationDate: + description: Comparative Toxicogenomics Database (Disease) + id: 324 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 321 + location: + countryCode: US + countryName: United States + name: The Mount Desert Island Biological Laboratory + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100130 + name: Comparative Toxicogenomics Database (Disease) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ctdbase.org/ + sampleId: D053716 + urlPattern: http://ctdbase.org/detail.go?type=disease&db=MESH&acc={$id} + sampleId: D053716 + - created: 2019-06-11T14:15:59.547+0000 + deprecated: false + deprecationDate: + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + id: 325 + mirId: MIR:00000100 + modified: 2019-06-11T14:15:59.547+0000 + name: CTD Gene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ctd.gene + resources: + - deprecated: false + deprecationDate: + description: Comparative Toxicogenomics Database (Gene) + id: 326 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 321 + location: + countryCode: US + countryName: United States + name: The Mount Desert Island Biological Laboratory + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100131 + name: Comparative Toxicogenomics Database (Gene) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ctdbase.org/ + sampleId: '101' + urlPattern: http://ctdbase.org/detail.go?type=gene&acc={$id} + sampleId: '101' + - created: 2019-06-11T14:15:59.756+0000 + deprecated: false + deprecationDate: + description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. + id: 327 + mirId: MIR:00000101 + modified: 2019-06-11T14:15:59.756+0000 + name: BioNumbers + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bionumbers + resources: + - deprecated: false + deprecationDate: + description: BioNumbers database + id: 329 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 328 + location: + countryCode: IL + countryName: Israel + name: Weizmann Institute + rorId: + location: + countryCode: IL + countryName: Israel + mirId: MIR:00100132 + name: BioNumbers database + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://bionumbers.hms.harvard.edu + sampleId: '104674' + urlPattern: https://bionumbers.hms.harvard.edu/bionumber.aspx?id={$id} + sampleId: '104674' + - created: 2019-06-11T14:16:00.005+0000 + deprecated: false + deprecationDate: + description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. + id: 330 + mirId: MIR:00000102 + modified: 2019-06-11T14:16:00.005+0000 + name: DrugBank + namespaceEmbeddedInLui: false + pattern: ^DB\d{5}$ + prefix: drugbank + resources: + - deprecated: false + deprecationDate: + description: DrugBank drug information + id: 332 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 331 + location: + countryCode: CA + countryName: Canada + name: Departments of Computing Science & Biological Sciences, University of Alberta + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100133 + name: DrugBank drug information + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.drugbank.ca/ + sampleId: DB00001 + urlPattern: http://www.drugbank.ca/drugs/{$id} + sampleId: DB00001 + - created: 2019-06-11T14:16:00.251+0000 + deprecated: false + deprecationDate: + description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. + id: 333 + mirId: MIR:00000103 + modified: 2019-06-11T14:16:00.251+0000 + name: T3DB + namespaceEmbeddedInLui: false + pattern: ^T3D\d+$ + prefix: t3db + resources: + - deprecated: false + deprecationDate: + description: Toxin and Toxin Target Database + id: 335 + institution: + description: The University of Alberta in Edmonton is one of Canada's top teaching and research universities, with an international reputation for excellence across the humanities, sciences, creative arts, business, engineering and health sciences. + homeUrl: https://www.ualberta.ca + id: 334 + location: + countryCode: CA + countryName: Canada + name: University of Alberta + rorId: https://ror.org/0160cpw27 + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100136 + name: Toxin and Toxin Target Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.t3db.org/ + sampleId: T3D0001 + urlPattern: http://www.t3db.org/toxins/{$id} + sampleId: T3D0001 + - created: 2019-06-11T14:16:00.499+0000 + deprecated: false + deprecationDate: + description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. + id: 336 + mirId: MIR:00000104 + modified: 2019-06-11T14:16:00.499+0000 + name: Small Molecule Pathway Database + namespaceEmbeddedInLui: false + pattern: ^SMP\d+$ + prefix: smpdb + resources: + - deprecated: false + deprecationDate: + description: Small Molecule Pathway Database + id: 337 + institution: + description: The University of Alberta in Edmonton is one of Canada's top teaching and research universities, with an international reputation for excellence across the humanities, sciences, creative arts, business, engineering and health sciences. + homeUrl: https://www.ualberta.ca + id: 334 + location: + countryCode: CA + countryName: Canada + name: University of Alberta + rorId: https://ror.org/0160cpw27 + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100137 + name: Small Molecule Pathway Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://smpdb.ca/ + sampleId: SMP00001 + urlPattern: http://smpdb.ca/view/{$id} + sampleId: SMP00001 + - created: 2019-06-11T14:16:00.712+0000 + deprecated: false + deprecationDate: + description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. + id: 338 + mirId: MIR:00000105 + modified: 2019-06-11T14:16:00.712+0000 + name: PhosphoSite Protein + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: phosphosite.protein + resources: + - deprecated: false + deprecationDate: + description: PhosphoSite + id: 340 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 339 + location: + countryCode: US + countryName: United States + name: Cell Signaling Technology, Inc. + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100138 + name: PhosphoSite + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.phosphosite.org/homeAction.do + sampleId: '12300' + urlPattern: http://www.phosphosite.org/proteinAction.do?id={$id} + sampleId: '12300' + - created: 2019-06-11T14:16:00.951+0000 + deprecated: false + deprecationDate: + description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. + id: 341 + mirId: MIR:00000106 + modified: 2019-06-11T14:16:00.951+0000 + name: GeneDB + namespaceEmbeddedInLui: false + pattern: ^[\w\d\.-]*$ + prefix: genedb + resources: + - deprecated: false + deprecationDate: + description: GeneDB at Sanger Institute + id: 343 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 342 + location: + countryCode: GB + countryName: United Kingdom + name: Pathogen Genomics, Sanger Institute and European Bioinformatics Institute + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100139 + name: GeneDB at Sanger Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.genedb.org/ + sampleId: LinJ.20.0070 + urlPattern: https://www.genedb.org/gene/{$id} + sampleId: LinJ.20.0070 + - created: 2019-06-11T14:16:01.178+0000 + deprecated: false + deprecationDate: + description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. + id: 344 + mirId: MIR:00000107 + modified: 2019-06-11T14:16:01.178+0000 + name: TEDDY + namespaceEmbeddedInLui: false + pattern: ^TEDDY_\d{7}$ + prefix: biomodels.teddy + resources: + - deprecated: false + deprecationDate: + description: TEDDY through BioPortal + id: 345 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100140 + name: TEDDY through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://teddyontology.sourceforge.net/ + sampleId: TEDDY_0000066 + urlPattern: http://purl.bioontology.org/ontology/TEDDY/{$id} + - deprecated: false + deprecationDate: + description: TEDDY though OLS + id: 346 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100761 + name: TEDDY though OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/teddy + sampleId: TEDDY_0000066 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?short_form={$id} + sampleId: TEDDY_0000066 + - created: 2019-06-11T14:16:01.508+0000 + deprecated: false + deprecationDate: + description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. + id: 347 + mirId: MIR:00000108 + modified: 2019-06-11T14:16:01.508+0000 + name: KiSAO + namespaceEmbeddedInLui: false + pattern: ^KISAO_\d+$ + prefix: biomodels.kisao + resources: + - deprecated: false + deprecationDate: + description: KiSAO via NCBO's Bioportal + id: 348 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100141 + name: KiSAO via NCBO's Bioportal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/KISAO + sampleId: KISAO_0000057 + urlPattern: http://purl.bioontology.org/ontology/KISAO/kisao:{$id} + - deprecated: false + deprecationDate: + description: KiSAO through OLS + id: 349 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100757 + name: KiSAO through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/kisao + sampleId: KISAO_0000057 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/kisao/terms?short_form={$id} + sampleId: KISAO_0000057 + - created: 2019-06-11T14:16:02.066+0000 + deprecated: false + deprecationDate: + description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. + id: 352 + mirId: MIR:00000110 + modified: 2019-06-11T14:16:02.066+0000 + name: Cell Type Ontology + namespaceEmbeddedInLui: true + pattern: ^CL:\d{7}$ + prefix: cl + resources: + - deprecated: false + deprecationDate: + description: Cell Type Ontology through OLS + id: 353 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100143 + name: Cell Type Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/cl + sampleId: '0000232' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:{$id} + - deprecated: false + deprecationDate: + description: Cell Type Ontology through BioPortal + id: 354 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100234 + name: Cell Type Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/CL + sampleId: '0000232' + urlPattern: http://purl.bioontology.org/ontology/CL/CL:{$id} + sampleId: '0000232' + - created: 2019-06-11T14:16:02.399+0000 + deprecated: false + deprecationDate: + description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. + id: 355 + mirId: MIR:00000111 + modified: 2019-06-11T14:16:02.399+0000 + name: Brenda Tissue Ontology + namespaceEmbeddedInLui: true + pattern: ^BTO:\d{7}$ + prefix: bto + resources: + - deprecated: false + deprecationDate: + description: Brenda Tissue Ontology through OLS + id: 356 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100144 + name: Brenda Tissue Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/bto + sampleId: '0000146' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:{$id} + - deprecated: false + deprecationDate: + description: Brenda Tissue Ontology through BioPortal + id: 357 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100233 + name: Brenda Tissue Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/BTO + sampleId: '0000146' + urlPattern: http://purl.bioontology.org/ontology/BTO/BTO:{$id} + sampleId: '0000146' + - created: 2019-06-11T14:16:02.730+0000 + deprecated: false + deprecationDate: + description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. + id: 358 + mirId: MIR:00000112 + modified: 2019-06-11T14:16:02.730+0000 + name: PATO + namespaceEmbeddedInLui: true + pattern: ^PATO:\d{7}$ + prefix: pato + resources: + - deprecated: false + deprecationDate: + description: PATO through OLS + id: 359 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100145 + name: PATO through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/pato + sampleId: '0001998' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:{$id} + - deprecated: false + deprecationDate: + description: PATO through BioPortal + id: 360 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100238 + name: PATO through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/PATO + sampleId: '0001998' + urlPattern: http://purl.bioontology.org/ontology/PATO/PATO:{$id} + sampleId: '0001998' + - created: 2019-06-11T14:16:03.054+0000 + deprecated: false + deprecationDate: + description: The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. + id: 361 + mirId: MIR:00000113 + modified: 2019-06-11T14:16:03.054+0000 + name: Chemical Component Dictionary + namespaceEmbeddedInLui: false + pattern: ^\w{3}$ + prefix: pdb-ccd + resources: + - deprecated: false + deprecationDate: + description: Protein Data Bank Chemical Component Dictionary at EBI + id: 362 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100146 + name: Protein Data Bank Chemical Component Dictionary at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ + sampleId: AB0 + urlPattern: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/{$id} + sampleId: AB0 + - created: 2019-06-11T14:16:03.253+0000 + deprecated: false + deprecationDate: + description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. + id: 363 + mirId: MIR:00000114 + modified: 2019-06-11T14:16:03.253+0000 + name: GlycomeDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: glycomedb + resources: + - deprecated: false + deprecationDate: + description: GlycomeDB carbohydrate structure database + id: 365 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 364 + location: + countryCode: DE + countryName: Germany + name: German Cancer Research Center, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100147 + name: GlycomeDB carbohydrate structure database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://glytoucan.org/ + sampleId: G77500AY + urlPattern: https://glytoucan.org/Structures/Glycans/{$id} + sampleId: G77500AY + - created: 2019-06-11T14:16:03.490+0000 + deprecated: false + deprecationDate: + description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. + id: 366 + mirId: MIR:00000115 + modified: 2019-06-11T14:16:03.490+0000 + name: LipidBank + namespaceEmbeddedInLui: false + pattern: ^\w+\d+$ + prefix: lipidbank + resources: + - deprecated: false + deprecationDate: + description: LipidBank the Lipid database + id: 368 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 367 + location: + countryCode: JP + countryName: Japan + name: Department of Computational Biology, University of Tokyo, Tokyo + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100148 + name: LipidBank the Lipid database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://lipidbank.jp/index.html + sampleId: BBA0001 + urlPattern: http://lipidbank.jp/cgi-bin/detail.cgi?id={$id} + sampleId: BBA0001 + - created: 2019-06-11T14:16:03.735+0000 + deprecated: false + deprecationDate: + description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. + id: 369 + mirId: MIR:00000116 + modified: 2019-06-11T14:16:03.735+0000 + name: KEGG Orthology + namespaceEmbeddedInLui: false + pattern: ^K\d+$ + prefix: kegg.orthology + resources: + - deprecated: false + deprecationDate: + description: KEGG Orthology Database + id: 370 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 367 + location: + countryCode: JP + countryName: Japan + name: Department of Computational Biology, University of Tokyo, Tokyo + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100149 + name: KEGG Orthology Database + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genome.jp/kegg/ko.html + sampleId: K00001 + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: K00001 + - created: 2019-06-11T14:16:03.923+0000 + deprecated: false + deprecationDate: + description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. + id: 371 + mirId: MIR:00000117 + modified: 2019-06-11T14:16:03.923+0000 + name: ProDom + namespaceEmbeddedInLui: false + pattern: ^PD\d+$ + prefix: prodom + resources: + - deprecated: false + deprecationDate: + description: ProDom Protein Domain Database + id: 373 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 372 + location: + countryCode: FR + countryName: France + name: Laboratoire des Interactions Plantes-Microorganismes, INRA/CNRS + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100150 + name: ProDom Protein Domain Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://prodom.prabi.fr/prodom/current/html/home.php + sampleId: PD10000 + urlPattern: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query={$id} + sampleId: PD10000 + - created: 2019-06-11T14:16:04.151+0000 + deprecated: false + deprecationDate: + description: The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. + id: 374 + mirId: MIR:00000118 + modified: 2019-06-11T14:16:04.151+0000 + name: SMART + namespaceEmbeddedInLui: false + pattern: ^SM\d{5}$ + prefix: smart + resources: + - deprecated: false + deprecationDate: + description: SMART (Simple Modular Architecture Research Tool) + id: 376 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 375 + location: + countryCode: DE + countryName: Germany + name: EMBL, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100151 + name: SMART (Simple Modular Architecture Research Tool) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://smart.embl-heidelberg.de/ + sampleId: SM00015 + urlPattern: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN={$id} + sampleId: SM00015 + - created: 2019-06-11T14:16:04.400+0000 + deprecated: false + deprecationDate: + description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. + id: 377 + mirId: MIR:00000119 + modified: 2019-06-11T14:16:04.400+0000 + name: Conserved Domain Database + namespaceEmbeddedInLui: false + pattern: ^(cd)?\d{5}$ + prefix: cdd + resources: + - deprecated: false + deprecationDate: + description: Conserved Domain Database at NCBI + id: 379 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 378 + location: + countryCode: US + countryName: United States + name: National Library of Medicine, National Institutes of Health, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100152 + name: Conserved Domain Database at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd + sampleId: cd00400 + urlPattern: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid={$id} + sampleId: cd00400 + - created: 2019-06-11T14:16:04.654+0000 + deprecated: false + deprecationDate: + description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. + id: 380 + mirId: MIR:00000120 + modified: 2019-06-11T14:16:04.654+0000 + name: Relation Ontology + namespaceEmbeddedInLui: false + pattern: ^RO_\d{7}$ + prefix: ro + resources: + - deprecated: false + deprecationDate: + description: OBO Relation Ontology through OntoBee + id: 382 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 381 + location: + countryCode: US + countryName: United States + name: University of Michigan Medical School (MI), Lawrence Berkeley National Laboratory (CA) and Science Commons (MA) + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100764 + name: OBO Relation Ontology through OntoBee + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://obofoundry.org/ontology/ro.html + sampleId: RO_0002533 + urlPattern: http://purl.obolibrary.org/obo/{$id} + - deprecated: false + deprecationDate: + description: OBO Relation Ontology through OLS + id: 383 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100767 + name: OBO Relation Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/ro + sampleId: RO_0002533 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/ro/terms?short_form={$id} + sampleId: RO_0002533 + - created: 2019-06-11T14:16:05.062+0000 + deprecated: false + deprecationDate: + description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. + id: 384 + mirId: MIR:00000121 + modified: 2019-06-11T14:16:05.062+0000 + name: Molecular Modeling Database + namespaceEmbeddedInLui: false + pattern: ^\d{1,5}$ + prefix: mmdb + resources: + - deprecated: false + deprecationDate: + description: MMDB at NCBI + id: 385 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 378 + location: + countryCode: US + countryName: United States + name: National Library of Medicine, National Institutes of Health, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100154 + name: MMDB at NCBI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure + sampleId: '50885' + urlPattern: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid={$id} + sampleId: '50885' + - created: 2019-06-11T14:16:05.272+0000 + deprecated: false + deprecationDate: + description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. + id: 386 + mirId: MIR:00000122 + modified: 2019-06-11T14:16:05.272+0000 + name: IMEx + namespaceEmbeddedInLui: false + pattern: ^IM-\d+(-?)(\d+?)$ + prefix: imex + resources: + - deprecated: false + deprecationDate: + description: IMEx Consortium running at EBI + id: 387 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100155 + name: IMEx Consortium running at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.imexconsortium.org/ + sampleId: IM-19210-3 + urlPattern: https://www.ebi.ac.uk/intact/imex/main.xhtml?query={$id} + - deprecated: false + deprecationDate: + description: IMEx Consortium though Intact + id: 388 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100663 + name: IMEx Consortium though Intact + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.ebi.ac.uk/intact/ + sampleId: IM-19210-3 + urlPattern: https://imexcentral.org/icentral/imex/rec/{$id} + sampleId: IM-19210-3 + - created: 2019-06-11T14:16:05.614+0000 + deprecated: false + deprecationDate: + description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' + id: 389 + mirId: MIR:00000123 + modified: 2019-06-11T14:16:05.614+0000 + name: iRefWeb + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: irefweb + resources: + - deprecated: false + deprecationDate: + description: iRefWeb Protein Interaction Reference Index + id: 391 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 390 + location: + countryCode: CA + countryName: Canada + name: Wodak Lab, Hospital for Sick Children, Toronto + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100156 + name: iRefWeb Protein Interaction Reference Index + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://wodaklab.org/iRefWeb/ + sampleId: '617102' + urlPattern: http://wodaklab.org/iRefWeb/interaction/show/{$id} + sampleId: '617102' + - created: 2019-06-11T14:16:05.849+0000 + deprecated: false + deprecationDate: + description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. + id: 392 + mirId: MIR:00000124 + modified: 2019-06-11T14:16:05.849+0000 + name: Microbial Protein Interaction Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mpid + resources: + - deprecated: false + deprecationDate: + description: Microbial Protein Interaction Database + id: 394 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 393 + location: + countryCode: US + countryName: United States + name: J. Craig Venter Institute, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100157 + name: Microbial Protein Interaction Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.jcvi.org/mpidb/about.php + sampleId: '172' + urlPattern: http://www.jcvi.org/mpidb/experiment.php?interaction_id={$id} + - deprecated: false + deprecationDate: + description: Microbial Protein Interaction Database subset through IntAct + id: 395 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100655 + name: Microbial Protein Interaction Database subset through IntAct + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/intact/ + sampleId: '1776' + urlPattern: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-{$id} + sampleId: '172' + - created: 2019-06-11T14:16:06.208+0000 + deprecated: false + deprecationDate: + description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. + id: 396 + mirId: MIR:00000125 + modified: 2019-06-11T14:16:06.208+0000 + name: PhosphoSite Residue + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: phosphosite.residue + resources: + - deprecated: false + deprecationDate: + description: PhosphoSite Residue + id: 397 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 339 + location: + countryCode: US + countryName: United States + name: Cell Signaling Technology, Inc. + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100159 + name: PhosphoSite Residue + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.phosphosite.org/homeAction.do + sampleId: '2842' + urlPattern: http://www.phosphosite.org/siteAction.do?id={$id} + sampleId: '2842' + - created: 2019-06-11T14:16:06.417+0000 + deprecated: false + deprecationDate: + description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). + id: 398 + mirId: MIR:00000126 + modified: 2019-06-11T14:16:06.417+0000 + name: NeuroLex + namespaceEmbeddedInLui: false + pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$ + prefix: neurolex + resources: + - deprecated: false + deprecationDate: + description: NeuroLex Neuroscience Lexicon + id: 400 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 399 + location: + countryCode: US + countryName: United States + name: Department of Neuroscience, University of California, San Diego + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100160 + name: NeuroLex Neuroscience Lexicon + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.neurolex.org/wiki/Main_Page + sampleId: Birnlex_721 + urlPattern: http://www.neurolex.org/wiki/{$id} + - deprecated: false + deprecationDate: + description: NeuroLex through NCBO's BioPortal + id: 401 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100183 + name: NeuroLex through NCBO's BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/BIRNLEX + sampleId: birnlex_1672 + urlPattern: http://purl.bioontology.org/ontology/BIRNLEX/{$id} + sampleId: Birnlex_721 + - created: 2019-06-11T14:16:06.780+0000 + deprecated: false + deprecationDate: + description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). + id: 402 + mirId: MIR:00000127 + modified: 2019-06-11T14:16:06.780+0000 + name: Ontology for Biomedical Investigations + namespaceEmbeddedInLui: false + pattern: (^OBI:\d{7}$)|(^OBI_\d{7}$) + prefix: obi + resources: + - deprecated: false + deprecationDate: + description: OBI through Ontobee + id: 404 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 403 + location: + countryCode: US + countryName: United States + name: University of Michigan Medical School (MI), awrence Berkeley National Laboratory (CA) and Science Commons (MA) + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100162 + name: OBI through Ontobee + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ontobee.org/ + sampleId: OBI_0000070 + urlPattern: http://purl.obolibrary.org/obo/{$id} + - deprecated: false + deprecationDate: + description: Ontology for Biomedical Investigations through Bioportal + id: 405 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100177 + name: Ontology for Biomedical Investigations through Bioportal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/OBI + sampleId: OBI:0000070 + urlPattern: http://purl.bioontology.org/ontology/OBI/{$id} + - deprecated: false + deprecationDate: + description: OBI through OLS + id: 406 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100760 + name: OBI through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/obi + sampleId: OBI:0000070 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/obi/terms?obo_id={$id} + sampleId: OBI_0000070 + - created: 2019-06-11T14:16:44.568+0000 + deprecated: false + deprecationDate: + description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. + id: 831 + mirId: MIR:00000283 + modified: 2019-06-11T14:16:44.568+0000 + name: ASAP + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+$ + prefix: asap + resources: + - deprecated: false + deprecationDate: + description: ASAP at University of Wisconsin + id: 833 + institution: + description: >- + The University of Wisconsin–Madison is a public research + university in Madison, Wisconsin. Founded when Wisconsin achieved + statehood in 1848, UW–Madison is the official state university of + Wisconsin, and the flagship campus of the University of Wisconsin + System. + + It was the first public university established in Wisconsin and remains the oldest and largest public university in the state. It became a land-grant institution in 1866. + + The 933-acre (378 ha) main campus, located on the shores of Lake Mendota, includes four National Historic Landmarks. + + The University also owns and operates a historic 1,200-acre (486 ha) arboretum established in 1932, located 4 miles (6.4 km) south of the main campus. + homeUrl: https://www.wisc.edu/ + id: 2054 + location: + countryCode: US + countryName: United States + name: University of Wisconsin-Madison + rorId: https://ror.org/01y2jtd41 + location: + countryCode: US + countryName: United States + mirId: MIR:00100364 + name: ASAP at University of Wisconsin + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://asap.ahabs.wisc.edu/asap/home.php + sampleId: ABE-0009634 + urlPattern: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID={$id} + sampleId: ABE-0009634 + - created: 2019-06-11T14:16:07.366+0000 + deprecated: false + deprecationDate: + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. + id: 407 + mirId: MIR:00000128 + modified: 2019-06-11T14:16:07.366+0000 + name: SABIO-RK EC Record + namespaceEmbeddedInLui: false + pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ + prefix: sabiork.ec + resources: + - deprecated: false + deprecationDate: + description: SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC) + id: 409 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 408 + location: + countryCode: DE + countryName: Germany + name: Heidelberg Institute for Theoretical Studies (HITS gGmbH) + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100163 + name: SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://sabiork.h-its.org/ + sampleId: 2.7.1.1 + urlPattern: http://sabiork.h-its.org/newSearch?q=ecnumber:{$id} + sampleId: 2.7.1.1 + - created: 2019-06-11T14:16:07.624+0000 + deprecated: false + deprecationDate: + description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. + id: 410 + mirId: MIR:00000129 + modified: 2019-06-11T14:16:07.624+0000 + name: Ontology of Physics for Biology + namespaceEmbeddedInLui: false + pattern: ^OPB_\d+$ + prefix: opb + resources: + - deprecated: false + deprecationDate: + description: Ontology of Physics for Biology through Bioportal + id: 411 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100167 + name: Ontology of Physics for Biology through Bioportal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/OPB + sampleId: OPB_00573 + urlPattern: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23{$id} + sampleId: OPB_00573 + - created: 2019-06-11T14:16:07.820+0000 + deprecated: false + deprecationDate: + description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. + id: 412 + mirId: MIR:00000130 + modified: 2019-06-11T14:16:07.820+0000 + name: JWS Online + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: jws + resources: + - deprecated: false + deprecationDate: + description: JWS Online Model Repository at Stellenbosch + id: 414 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 413 + location: + countryCode: ZA + countryName: South Africa + name: Department of Biochemistry, Stellenbosch University + rorId: + location: + countryCode: ZA + countryName: South Africa + mirId: MIR:00100168 + name: JWS Online Model Repository at Stellenbosch + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://jjj.biochem.sun.ac.za/models/ + sampleId: curien + urlPattern: http://jjj.biochem.sun.ac.za/models/{$id}/ + - deprecated: false + deprecationDate: + description: JWS Online Model Repository at Manchester + id: 418 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 417 + location: + countryCode: GB + countryName: United Kingdom + name: Manchester Interdisciplinary Biocentre, University of Manchester + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100170 + name: JWS Online Model Repository at Manchester + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://jjj.mib.ac.uk/index.html + sampleId: curien + urlPattern: http://jjj.mib.ac.uk/models/{$id} + - deprecated: false + deprecationDate: + description: JWS Online Model Repository at Amsterdam + id: 416 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 415 + location: + countryCode: NL + countryName: Netherlands + name: University of Amsterdam + rorId: + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100169 + name: JWS Online Model Repository at Amsterdam + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://jjj.bio.vu.nl/models/ + sampleId: curien + urlPattern: http://jjj.bio.vu.nl/models/{$id}/ + sampleId: curien + - created: 2019-06-11T14:16:08.429+0000 + deprecated: false + deprecationDate: + description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. + id: 419 + mirId: MIR:00000131 + modified: 2019-06-11T14:16:08.429+0000 + name: ModelDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: modeldb + resources: + - deprecated: false + deprecationDate: + description: ModelDB at SenseLab + id: 420 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 310 + location: + countryCode: US + countryName: United States + name: Yale University School of Medicine + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100171 + name: ModelDB at SenseLab + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://senselab.med.yale.edu/ModelDB/ + sampleId: '45539' + urlPattern: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model={$id} + sampleId: '45539' + - created: 2019-06-11T14:16:08.635+0000 + deprecated: false + deprecationDate: + description: "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. 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While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: 473 + mirId: MIR:00000151 + modified: 2019-06-11T14:16:13.424+0000 + name: GiardiaDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: giardiadb + resources: + - deprecated: false + deprecationDate: + description: GiardiaDB at EuPathDB + id: 474 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 467 + location: + countryCode: US + countryName: United States + name: Center for Tropical & Emerging Global Diseases, University of Georgia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100196 + name: GiardiaDB at EuPathDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://giardiadb.org/giardiadb/ + sampleId: GL50803_102438 + urlPattern: https://giardiadb.org/giardiadb/app/record/gene/{$id} + sampleId: GL50803_102438 + - created: 2019-06-11T14:16:13.630+0000 + deprecated: false + deprecationDate: + description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: 475 + mirId: MIR:00000152 + modified: 2019-06-11T14:16:13.630+0000 + name: MicrosporidiaDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: microsporidia + resources: + - deprecated: false + deprecationDate: + description: MicrosporidiaDB at EuPathDB + id: 476 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 467 + location: + countryCode: US + countryName: United States + name: Center for Tropical & Emerging Global Diseases, University of Georgia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100197 + name: MicrosporidiaDB at EuPathDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://microsporidiadb.org/micro/ + sampleId: ECU03_0820i + urlPattern: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id} + sampleId: ECU03_0820i + - created: 2019-06-11T14:16:13.817+0000 + deprecated: false + deprecationDate: + description: ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: 477 + mirId: MIR:00000153 + modified: 2019-06-11T14:16:13.817+0000 + name: ToxoDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: toxoplasma + resources: + - deprecated: false + deprecationDate: + description: ToxoDB at EuPathDB + id: 478 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 467 + location: + countryCode: US + countryName: United States + name: Center for Tropical & Emerging Global Diseases, University of Georgia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100198 + name: ToxoDB at EuPathDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://toxodb.org/toxo/ + sampleId: TGME49_053730 + urlPattern: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id} + sampleId: TGME49_053730 + - created: 2019-06-11T14:16:14.019+0000 + deprecated: false + deprecationDate: + description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: 479 + mirId: MIR:00000154 + modified: 2019-06-11T14:16:14.019+0000 + name: TrichDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: trichdb + resources: + - deprecated: false + deprecationDate: + description: TrichDB at EuPathDB + id: 480 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 467 + location: + countryCode: US + countryName: United States + name: Center for Tropical & Emerging Global Diseases, University of Georgia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100199 + name: TrichDB at EuPathDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://trichdb.org/trichdb/ + sampleId: TVAG_386080 + urlPattern: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id} + sampleId: TVAG_386080 + - created: 2019-06-11T14:16:14.213+0000 + deprecated: false + deprecationDate: + description: TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: 481 + mirId: MIR:00000155 + modified: 2019-06-11T14:16:14.213+0000 + name: TriTrypDB + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?\w+(\.)?\w+ + prefix: tritrypdb + resources: + - deprecated: false + deprecationDate: + description: TriTrypDB at EuPathDB + id: 483 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 482 + location: + countryCode: GB + countryName: United Kingdom + name: Wellcome Trust Sanger Institute, Hinxton + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100200 + name: TriTrypDB at EuPathDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://tritrypdb.org/tritrypdb/ + sampleId: Tb927.8.620 + urlPattern: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id} + sampleId: Tb927.8.620 + - created: 2019-06-11T14:16:14.437+0000 + deprecated: false + deprecationDate: + description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. + id: 484 + mirId: MIR:00000156 + modified: 2019-06-11T14:16:14.437+0000 + name: BDGP insertion DB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: bdgp.insertion + resources: + - deprecated: false + deprecationDate: + description: BDGP Gene Disruption Project + id: 486 + institution: + description: Baylor College of Medicine is a health sciences university that creates knowledge and applies science and discoveries to further education, healthcare and community service locally and globally. + homeUrl: https://www.bcm.edu + id: 485 + location: + countryCode: US + countryName: United States + name: Baylor College of Medicine + rorId: https://ror.org/02pttbw34 + location: + countryCode: US + countryName: United States + mirId: MIR:00100201 + name: BDGP Gene Disruption Project + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://flypush.imgen.bcm.tmc.edu/pscreen/ + sampleId: KG09531 + urlPattern: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line={$id} + sampleId: KG09531 + - created: 2019-06-11T14:16:14.695+0000 + deprecated: false + deprecationDate: + description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. + id: 487 + mirId: MIR:00000157 + modified: 2019-06-11T14:16:14.695+0000 + name: BeetleBase + namespaceEmbeddedInLui: false + pattern: ^TC\d+$ + prefix: beetlebase + resources: + - deprecated: false + deprecationDate: + description: BeetleBase at Kansas State University + id: 489 + institution: + description: Kansas State University is a comprehensive, research, land-grant institution serving students and the people of Kansas, the nation, and the world. + homeUrl: https://www.k-state.edu/ + id: 488 + location: + countryCode: US + countryName: United States + name: Kansas State University + rorId: https://ror.org/05p1j8758 + location: + countryCode: US + countryName: United States + mirId: MIR:00100202 + name: BeetleBase at Kansas State University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://beetlebase.org/ + sampleId: TC010103 + urlPattern: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name={$id} + sampleId: TC010103 + - created: 2019-06-11T14:16:14.938+0000 + deprecated: false + deprecationDate: + description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. + id: 490 + mirId: MIR:00000158 + modified: 2019-06-11T14:16:14.938+0000 + name: BOLD Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bold.taxonomy + resources: + - deprecated: false + deprecationDate: + description: BOLD taxonomy browser + id: 492 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 491 + location: + countryCode: CA + countryName: Canada + name: Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100203 + name: BOLD taxonomy browser + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.boldsystems.org/ + sampleId: '27267' + urlPattern: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid={$id} + sampleId: '27267' + - created: 2019-06-11T14:16:15.166+0000 + deprecated: false + deprecationDate: + description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. + id: 493 + mirId: MIR:00000159 + modified: 2019-06-11T14:16:15.166+0000 + name: dbEST + namespaceEmbeddedInLui: false + pattern: ^([A-Z]+)?\d+(\.\d+)?$ + prefix: dbest + resources: + - deprecated: false + deprecationDate: + description: dbEST at NCBI + id: 494 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100204 + name: dbEST at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/nucest + sampleId: BP100000 + urlPattern: https://www.ncbi.nlm.nih.gov/nucest/{$id} + - deprecated: false + deprecationDate: + description: dbEST through European Nucleotide Archive (ENA) + id: 495 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100331 + name: dbEST through European Nucleotide Archive (ENA) + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/ena + sampleId: BP100000.1 + urlPattern: https://www.ebi.ac.uk/ena/data/view/{$id} + - deprecated: false + deprecationDate: + description: dbEST through DNA Data Bank of Japan (DDBJ) + id: 496 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 121 + location: + countryCode: JP + countryName: Japan + name: DNA Data Bank of Japan, Mishima, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100651 + name: dbEST through DNA Data Bank of Japan (DDBJ) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ddbj.nig.ac.jp/ + sampleId: BP100000 + urlPattern: http://getentry.ddbj.nig.ac.jp/getentry/na/{$id} + sampleId: BP100000 + - created: 2019-06-11T14:16:15.607+0000 + deprecated: false + deprecationDate: + description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. + id: 497 + mirId: MIR:00000160 + modified: 2019-06-11T14:16:15.607+0000 + name: dbProbe + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dbprobe + resources: + - deprecated: false + deprecationDate: + description: dbProbe at NCBI + id: 498 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100205 + name: dbProbe at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe + sampleId: '1000000' + urlPattern: https://www.ncbi.nlm.nih.gov/probe/?term={$id} + sampleId: '1000000' + - created: 2019-06-11T14:16:15.831+0000 + deprecated: false + deprecationDate: + description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. + id: 499 + mirId: MIR:00000161 + modified: 2019-06-11T14:16:15.831+0000 + name: dbSNP + namespaceEmbeddedInLui: false + pattern: ^rs\d+$ + prefix: dbsnp + resources: + - deprecated: false + deprecationDate: + description: dbSNP at NCBI + id: 500 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100206 + name: dbSNP at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/snp/ + sampleId: rs121909098 + urlPattern: https://www.ncbi.nlm.nih.gov/snp/{$id} + - deprecated: false + deprecationDate: + description: SNP2TFBS + id: 502 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100927 + name: SNP2TFBS + official: false + providerCode: sib + resourceHomeUrl: https://ccg.epfl.ch/snp2tfbs/ + sampleId: rs11603840 + urlPattern: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid={$id} + sampleId: rs121909098 + - created: 2019-06-11T14:16:16.225+0000 + deprecated: false + deprecationDate: + description: UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. + id: 503 + mirId: MIR:00000162 + modified: 2019-06-11T14:16:16.225+0000 + name: UniSTS + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unists + resources: + - deprecated: false + deprecationDate: + description: UniSTS at NCBI + id: 504 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100207 + name: UniSTS at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists + sampleId: '456789' + urlPattern: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid={$id} + sampleId: '456789' + - created: 2019-06-11T14:16:16.429+0000 + deprecated: false + deprecationDate: + description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. + id: 505 + mirId: MIR:00000163 + modified: 2019-06-11T14:16:16.429+0000 + name: EcoGene + namespaceEmbeddedInLui: false + pattern: ^EG\d+$ + prefix: ecogene + resources: + - deprecated: false + deprecationDate: + description: EcoGene at University of Miami + id: 507 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 506 + location: + countryCode: US + countryName: United States + name: Miller School of Medicine, University of Miami + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100208 + name: EcoGene at University of Miami + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ecogene.org/ + sampleId: EG10173 + urlPattern: http://www.ecogene.org/gene/{$id} + sampleId: EG10173 + - created: 2019-06-11T14:16:45.049+0000 + deprecated: false + deprecationDate: + description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). + id: 837 + mirId: MIR:00000285 + modified: 2019-06-11T14:16:45.049+0000 + name: BDGP EST + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?(\d+)?$ + prefix: bdgp.est + resources: + - deprecated: false + deprecationDate: + description: BDGP EST at NCBI + id: 838 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100366 + name: BDGP EST at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/dbEST/index.html + sampleId: EY223054.1 + urlPattern: https://www.ncbi.nlm.nih.gov/nucest/{$id} + sampleId: EY223054.1 + - created: 2019-06-11T14:16:16.652+0000 + deprecated: false + deprecationDate: + description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. + id: 508 + mirId: MIR:00000164 + modified: 2019-06-11T14:16:16.652+0000 + name: GABI + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gabi + resources: + - deprecated: false + deprecationDate: + description: GABI at Max Planck + id: 510 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 509 + location: + countryCode: DE + countryName: Germany + name: Max Planck Institute of Molecular Plant Physiology, Berlin + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100210 + name: GABI at Max Planck + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gabipd.org/ + sampleId: '2679240' + urlPattern: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId={$id}&Mode=ShowBioObject + sampleId: '2679240' + - created: 2019-06-11T14:16:16.885+0000 + deprecated: false + deprecationDate: + description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. + id: 511 + mirId: MIR:00000165 + modified: 2019-06-11T14:16:16.885+0000 + name: GreenGenes + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: greengenes + resources: + - deprecated: false + deprecationDate: + description: GreenGenes at Lawrence Berkeley + id: 513 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 512 + location: + countryCode: US + countryName: United States + name: Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100211 + name: GreenGenes at Lawrence Berkeley + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://greengenes.lbl.gov/ + sampleId: '100000' + urlPattern: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id={$id} + sampleId: '100000' + - created: 2019-06-11T14:16:17.150+0000 + deprecated: false + deprecationDate: + description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. + id: 514 + mirId: MIR:00000166 + modified: 2019-06-11T14:16:17.150+0000 + name: GRIN Plant Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: grin.taxonomy + resources: + - deprecated: false + deprecationDate: + description: GRIN at Maryland + id: 516 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 515 + location: + countryCode: US + countryName: United States + name: National Germplasm Resources Laboratory, Beltsville, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100212 + name: GRIN at Maryland + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en + sampleId: '19333' + urlPattern: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?{$id} + sampleId: '19333' + - created: 2019-06-11T14:16:17.382+0000 + deprecated: false + deprecationDate: + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. + id: 517 + mirId: MIR:00000167 + modified: 2019-06-11T14:16:17.382+0000 + name: H-InvDb Locus + namespaceEmbeddedInLui: false + pattern: ^HIX\d{7}(\.\d+)?$ + prefix: hinv.locus + resources: + - deprecated: false + deprecationDate: + description: H-Invitational Locus View at BIRC + id: 519 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 518 + location: + countryCode: JP + countryName: Japan + name: BIRC, Tokyo + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100213 + name: H-Invitational Locus View at BIRC + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://h-invitational.jp/hinv/ahg-db/index.jsp + sampleId: HIX0004394 + urlPattern: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id={$id} + sampleId: HIX0004394 + - created: 2019-06-11T14:16:17.622+0000 + deprecated: false + deprecationDate: + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. + id: 520 + mirId: MIR:00000168 + modified: 2019-06-11T14:16:17.622+0000 + name: H-InvDb Transcript + namespaceEmbeddedInLui: false + pattern: ^HIT\d{9}(\.\d+)?$ + prefix: hinv.transcript + resources: + - deprecated: false + deprecationDate: + description: H-Invitational Transcript View at BIRC + id: 521 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 518 + location: + countryCode: JP + countryName: Japan + name: BIRC, Tokyo + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100214 + name: H-Invitational Transcript View at BIRC + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://h-invitational.jp/hinv/ahg-db/index.jsp + sampleId: HIT000195363 + urlPattern: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id={$id} + sampleId: HIT000195363 + - created: 2019-06-11T14:16:17.817+0000 + deprecated: false + deprecationDate: + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. + id: 522 + mirId: MIR:00000169 + modified: 2019-06-11T14:16:17.817+0000 + name: H-InvDb Protein + namespaceEmbeddedInLui: false + pattern: ^HIP\d{9}(\.\d+)?$ + prefix: hinv.protein + resources: + - deprecated: false + deprecationDate: + description: H-Invitational Protein View at BIRC + id: 523 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 518 + location: + countryCode: JP + countryName: Japan + name: BIRC, Tokyo + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100215 + name: H-Invitational Protein View at BIRC + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://h-invitational.jp/hinv/ahg-db/index.jsp + sampleId: HIP000030660 + urlPattern: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id={$id} + sampleId: HIP000030660 + - created: 2019-06-11T14:16:18.019+0000 + deprecated: false + deprecationDate: + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. + id: 524 + mirId: MIR:00000170 + modified: 2019-06-11T14:16:18.019+0000 + name: HOMD Sequence Metainformation + namespaceEmbeddedInLui: false + pattern: ^SEQF\d+$ + prefix: homd.seq + resources: + - deprecated: false + deprecationDate: + description: HOMD sequence metainformation at The Forsyth Institute + id: 526 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 525 + location: + countryCode: US + countryName: United States + name: The Forsyth Institute, Boston + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100216 + name: HOMD sequence metainformation at The Forsyth Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.homd.org/index.php + sampleId: SEQF1003 + urlPattern: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid={$id} + sampleId: SEQF1003 + - created: 2019-06-11T14:16:18.268+0000 + deprecated: false + deprecationDate: + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. + id: 527 + mirId: MIR:00000171 + modified: 2019-06-11T14:16:18.268+0000 + name: HOMD Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: homd.taxon + resources: + - deprecated: false + deprecationDate: + description: HOMD taxon information at The Forsyth Institute + id: 528 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 525 + location: + countryCode: US + countryName: United States + name: The Forsyth Institute, Boston + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100217 + name: HOMD taxon information at The Forsyth Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.homd.org/index.php + sampleId: '811' + urlPattern: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid={$id}&view=dynamic + sampleId: '811' + - created: 2019-06-11T14:16:18.461+0000 + deprecated: false + deprecationDate: + description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). + id: 529 + mirId: MIR:00000172 + modified: 2019-06-11T14:16:18.461+0000 + name: IRD Segment Sequence + namespaceEmbeddedInLui: false + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: ird.segment + resources: + - deprecated: false + deprecationDate: + description: IRD at BioHealthBase + id: 531 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 530 + location: + countryCode: US + countryName: United States + name: Southwestern Medical Center, University of Texas, Dallas + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100218 + name: IRD at BioHealthBase + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.fludb.org/ + sampleId: CY077097 + urlPattern: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession={$id} + sampleId: CY077097 + - created: 2019-06-11T14:16:18.690+0000 + deprecated: false + deprecationDate: + description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. + id: 532 + mirId: MIR:00000173 + modified: 2019-06-11T14:16:18.690+0000 + name: ISFinder + namespaceEmbeddedInLui: false + pattern: ^IS\w+(\-\d)?$ + prefix: isfinder + resources: + - deprecated: false + deprecationDate: + description: IS Finder at CNRS + id: 534 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 533 + location: + countryCode: FR + countryName: France + name: Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100219 + name: IS Finder at CNRS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www-is.biotoul.fr/i + sampleId: ISA1083-2 + urlPattern: https://www-is.biotoul.fr/scripts/ficheIS.php?name={$id} + sampleId: ISA1083-2 + - created: 2019-06-11T14:16:18.921+0000 + deprecated: false + deprecationDate: + description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. + id: 535 + mirId: MIR:00000174 + modified: 2019-06-11T14:16:18.921+0000 + name: Japan Collection of Microorganisms + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jcm + resources: + - deprecated: false + deprecationDate: + description: JCM at RIKEN BioResource Center + id: 537 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 536 + location: + countryCode: JP + countryName: Japan + name: RIKEN BioResource Center, Ibaraki + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100220 + name: JCM at RIKEN BioResource Center + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.jcm.riken.go.jp/ + sampleId: '17254' + urlPattern: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM={$id} + sampleId: '17254' + - created: 2019-06-11T14:16:19.173+0000 + deprecated: false + deprecationDate: + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. + id: 538 + mirId: MIR:00000175 + modified: 2019-06-11T14:16:19.173+0000 + name: Integrated Microbial Genomes Taxon + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: img.taxon + resources: + - deprecated: false + deprecationDate: + description: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory + id: 540 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 539 + location: + countryCode: US + countryName: United States + name: Lawrence Berkeley National Laboratory, Berkeley + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100221 + name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://img.jgi.doe.gov/ + sampleId: '648028003' + urlPattern: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid={$id} + sampleId: '648028003' + - created: 2019-06-11T14:16:19.420+0000 + deprecated: false + deprecationDate: + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. + id: 541 + mirId: MIR:00000176 + modified: 2019-06-11T14:16:19.420+0000 + name: Integrated Microbial Genomes Gene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: img.gene + resources: + - deprecated: false + deprecationDate: + description: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory + id: 542 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 539 + location: + countryCode: US + countryName: United States + name: Lawrence Berkeley National Laboratory, Berkeley + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100222 + name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://img.jgi.doe.gov/ + sampleId: '638309541' + urlPattern: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid={$id} + sampleId: '638309541' + - created: 2019-06-11T14:16:19.610+0000 + deprecated: false + deprecationDate: + description: MaizeGDB is the maize research community's central repository for genetics and genomics information. + id: 543 + mirId: MIR:00000177 + modified: 2019-06-11T14:16:19.610+0000 + name: MaizeGDB Locus + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: maizegdb.locus + resources: + - deprecated: false + deprecationDate: + description: MaizeGDB at Missouri + id: 545 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 544 + location: + countryCode: US + countryName: United States + name: Division of Plant Sciences, Missouri + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100223 + name: MaizeGDB at Missouri + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.maizegdb.org/ + sampleId: '25011' + urlPattern: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id={$id} + sampleId: '25011' + - created: 2019-06-11T14:16:19.843+0000 + deprecated: false + deprecationDate: + description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. + id: 546 + mirId: MIR:00000178 + modified: 2019-06-11T14:16:19.843+0000 + name: MycoBank + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mycobank + resources: + - deprecated: false + deprecationDate: + description: MycoBank at Fungal Biodiversity Centre + id: 548 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 547 + location: + countryCode: NL + countryName: Netherlands + name: CBS-KNAW Fungal Biodiversity Centre, Utrecht + rorId: + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100224 + name: MycoBank at Fungal Biodiversity Centre + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mycobank.org/ + sampleId: '349124' + urlPattern: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_={$id} + sampleId: '349124' + - created: 2019-06-11T14:16:20.103+0000 + deprecated: false + deprecationDate: + description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. + id: 549 + mirId: MIR:00000179 + modified: 2019-06-11T14:16:20.103+0000 + name: NITE Biological Research Center Catalogue + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: nbrc + resources: + - deprecated: false + deprecationDate: + description: NBRC Catalogue at National Institute of Technology Evaluation + id: 551 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 550 + location: + countryCode: JP + countryName: Japan + name: National Institute of Technology Evaluation, Tokyo + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100225 + name: NBRC Catalogue at National Institute of Technology Evaluation + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.nbrc.nite.go.jp/e/index.html + sampleId: '00001234' + urlPattern: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT={$id} + sampleId: '00001234' + - created: 2019-06-11T14:16:20.362+0000 + deprecated: false + deprecationDate: + description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. + id: 552 + mirId: MIR:00000180 + modified: 2019-06-11T14:16:20.362+0000 + name: Pseudomonas Genome Database + namespaceEmbeddedInLui: false + pattern: ^P\w+$ + prefix: pseudomonas + resources: + - deprecated: false + deprecationDate: + description: Pseudomonas Genome Database at Simon Fraser University + id: 554 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 553 + location: + countryCode: CA + countryName: Canada + name: Simon Fraser University, British Columbia + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100226 + name: Pseudomonas Genome Database at Simon Fraser University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pseudomonas.com/ + sampleId: PSEEN0001 + urlPattern: http://www.pseudomonas.com/feature/show/?locus_tag={$id} + sampleId: PSEEN0001 + - created: 2019-06-11T14:16:20.589+0000 + deprecated: false + deprecationDate: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. + id: 555 + mirId: MIR:00000181 + modified: 2019-06-11T14:16:20.589+0000 + name: Gramene protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: gramene.protein + resources: + - deprecated: false + deprecationDate: + description: Gramene Protein at Cold Spring Harbor + id: 557 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 556 + location: + countryCode: US + countryName: United States + name: Cold Spring Harbor Laboratory, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100227 + name: Gramene Protein at Cold Spring Harbor + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gramene.org/ + sampleId: '78073' + urlPattern: http://www.gramene.org/db/protein/protein_search?protein_id={$id} + sampleId: '78073' + - created: 2019-06-11T14:16:20.812+0000 + deprecated: false + deprecationDate: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. + id: 558 + mirId: MIR:00000182 + modified: 2019-06-11T14:16:20.812+0000 + name: Gramene genes + namespaceEmbeddedInLui: false + pattern: ^GR\:\d+$ + prefix: gramene.gene + resources: + - deprecated: false + deprecationDate: + description: Gramene Genes at Cold Spring Harbor + id: 559 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 556 + location: + countryCode: US + countryName: United States + name: Cold Spring Harbor Laboratory, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100228 + name: Gramene Genes at Cold Spring Harbor + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gramene.org/ + sampleId: GR:0080039 + urlPattern: http://www.gramene.org/db/genes/search_gene?acc={$id} + sampleId: GR:0080039 + - created: 2019-06-11T14:16:21.008+0000 + deprecated: false + deprecationDate: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. + id: 560 + mirId: MIR:00000183 + modified: 2019-06-11T14:16:21.008+0000 + name: Gramene Taxonomy + namespaceEmbeddedInLui: false + pattern: ^GR\_tax\:\d+$ + prefix: gramene.taxonomy + resources: + - deprecated: false + deprecationDate: + description: Gramene Taxonomy at Cold Spring Harbor + id: 561 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 556 + location: + countryCode: US + countryName: United States + name: Cold Spring Harbor Laboratory, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100229 + name: Gramene Taxonomy at Cold Spring Harbor + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gramene.org/ + sampleId: GR_tax:013681 + urlPattern: http://www.gramene.org/db/ontology/search?id={$id} + sampleId: GR_tax:013681 + - created: 2019-06-11T14:16:21.219+0000 + deprecated: false + deprecationDate: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. + id: 562 + mirId: MIR:00000184 + modified: 2019-06-11T14:16:21.219+0000 + name: Gramene QTL + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gramene.qtl + resources: + - deprecated: false + deprecationDate: + description: Gramene Quantitative Trait Loci at Cold Spring Harbor + id: 563 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 556 + location: + countryCode: US + countryName: United States + name: Cold Spring Harbor Laboratory, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100230 + name: Gramene Quantitative Trait Loci at Cold Spring Harbor + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gramene.org/ + sampleId: CQG5 + urlPattern: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id={$id} + sampleId: CQG5 + - created: 2019-06-11T14:16:21.425+0000 + deprecated: false + deprecationDate: + description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. + id: 564 + mirId: MIR:00000185 + modified: 2019-06-11T14:16:21.425+0000 + name: Sol Genomics Network + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sgn + resources: + - deprecated: false + deprecationDate: + description: Sol Genomics Network at Boyce Thompson Institute for Plant Research + id: 566 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 565 + location: + countryCode: US + countryName: United States + name: Boyce Thompson Institute for Plant Research, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100231 + name: Sol Genomics Network at Boyce Thompson Institute for Plant Research + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://solgenomics.net/ + sampleId: '0001' + urlPattern: http://solgenomics.net/phenome/locus_display.pl?locus_id={$id} + sampleId: '0001' + - created: 2019-06-11T14:16:21.882+0000 + deprecated: false + deprecationDate: + description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. + id: 570 + mirId: MIR:00000187 + modified: 2019-06-11T14:16:21.882+0000 + name: BioPortal + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bioportal + resources: + - deprecated: false + deprecationDate: + description: BioPortal at National Center for Biomedical Ontology + id: 572 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 571 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford University + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100244 + name: BioPortal at National Center for Biomedical Ontology + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ + sampleId: '1046' + urlPattern: http://bioportal.bioontology.org/ontologies/{$id} + sampleId: '1046' + - created: 2019-06-11T14:16:22.127+0000 + deprecated: false + deprecationDate: + description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. + id: 573 + mirId: MIR:00000188 + modified: 2019-06-11T14:16:22.127+0000 + name: MIRIAM Registry resource + namespaceEmbeddedInLui: false + pattern: ^MIR:001\d{5}$ + prefix: miriam.resource + resources: + - deprecated: false + deprecationDate: + description: MIRIAM Registry (resources) + id: 574 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100245 + name: MIRIAM Registry (resources) + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/miriam/ + sampleId: MIR:00100005 + urlPattern: https://www.ebi.ac.uk/miriam/main/resources/{$id} + sampleId: MIR:00100005 + - created: 2019-06-11T14:16:22.318+0000 + deprecated: false + deprecationDate: + description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' + id: 575 + mirId: MIR:00000189 + modified: 2019-06-11T14:16:22.318+0000 + name: EDAM Ontology + namespaceEmbeddedInLui: false + pattern: ^(data|topic|operation|format)\_\d{4}$ + prefix: edam + resources: + - deprecated: false + deprecationDate: + description: EDAM through BioPortal + id: 576 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100536 + name: EDAM through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/EDAM + sampleId: data_1664 + urlPattern: http://purl.bioontology.org/ontology/EDAM/{$id} + - deprecated: false + deprecationDate: + description: EDAM through OLS + id: 577 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100762 + name: EDAM through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/edam + sampleId: data_1664 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/edam/terms?short_form={$id} + sampleId: data_1664 + - created: 2019-06-11T14:16:22.644+0000 + deprecated: false + deprecationDate: + description: The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. + id: 578 + mirId: MIR:00000190 + modified: 2019-06-11T14:16:22.644+0000 + name: Protein Model Database + namespaceEmbeddedInLui: false + pattern: ^PM\d{7} + prefix: pmdb + resources: + - deprecated: false + deprecationDate: + description: Protein Model Database at University of Rome + id: 580 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 579 + location: + countryCode: IT + countryName: Italy + name: CASPUR and Biocomputing group, Department of Biochemical Sciences, University of Rome, Rome + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00100247 + name: Protein Model Database at University of Rome + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://bioinformatics.cineca.it/PMDB/ + sampleId: PM0012345 + urlPattern: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch={$id} + sampleId: PM0012345 + - created: 2019-06-11T14:16:22.902+0000 + deprecated: false + deprecationDate: + description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. + id: 581 + mirId: MIR:00000193 + modified: 2019-06-11T14:16:22.902+0000 + name: ArachnoServer + namespaceEmbeddedInLui: false + pattern: ^AS\d{6}$ + prefix: arachnoserver + resources: + - deprecated: false + deprecationDate: + description: ArachnoServer at Brisbane + id: 583 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 582 + location: + countryCode: AU + countryName: Australia + name: Institute for Molecular Bioscience, The University of Queensland, Brisbane + rorId: + location: + countryCode: AU + countryName: Australia + mirId: MIR:00100250 + name: ArachnoServer at Brisbane + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.arachnoserver.org/ + sampleId: AS000060 + urlPattern: http://www.arachnoserver.org/toxincard.html?id={$id} + sampleId: AS000060 + - created: 2019-06-11T14:16:23.132+0000 + deprecated: false + deprecationDate: + description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. + id: 584 + mirId: MIR:00000194 + modified: 2019-06-11T14:16:23.132+0000 + name: BioCyc + namespaceEmbeddedInLui: false + pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ + prefix: biocyc + resources: + - deprecated: false + deprecationDate: + description: BioCyc at SRI International + id: 586 + institution: + description: SRI is an independent, nonprofit research center that works with clients to take the most advanced R&D from the laboratory to the marketplace. + homeUrl: https://www.sri.com/ + id: 1692 + location: + countryCode: US + countryName: United States + name: SRI International + rorId: https://ror.org/05s570m15 + location: + countryCode: US + countryName: United States + mirId: MIR:00100251 + name: BioCyc at SRI International + official: false + providerCode: sri + resourceHomeUrl: http://biocyc.org + sampleId: ECOLI:CYT-D-UBIOX-CPLX + urlPattern: http://biocyc.org/getid?id={$id} + sampleId: ECOLI:CYT-D-UBIOX-CPLX + - created: 2019-06-11T14:16:23.358+0000 + deprecated: false + deprecationDate: + description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. + id: 587 + mirId: MIR:00000195 + modified: 2019-06-11T14:16:23.358+0000 + name: CAZy + namespaceEmbeddedInLui: false + pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ + prefix: cazy + resources: + - deprecated: false + deprecationDate: + description: CAZy at CNRS + id: 589 + institution: + description: The Architecture et Fonction des Macromolécules Biologiques (AFMB) laboratory, overseen by the CNRS and AMU, is a center of structural biology localized on the Luminy campus in the South of Marseilles, France, and in partnership with INRA under contract. + homeUrl: http://www.afmb.univ-mrs.fr + id: 588 + location: + countryCode: FR + countryName: France + name: Architecture et Fonction des Macromolécules Biologiques + rorId: https://ror.org/04jm8zw14 + location: + countryCode: FR + countryName: France + mirId: MIR:00100252 + name: CAZy at CNRS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cazy.org/ + sampleId: GT10 + urlPattern: http://www.cazy.org/{$id}.html + sampleId: GT10 + - created: 2019-06-11T14:16:23.594+0000 + deprecated: false + deprecationDate: + description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. + id: 590 + mirId: MIR:00000196 + modified: 2019-06-11T14:16:23.594+0000 + name: GOA + namespaceEmbeddedInLui: false + pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ + prefix: goa + resources: + - deprecated: false + deprecationDate: + description: GOA through QuickGO + id: 591 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100253 + name: GOA through QuickGO + official: false + providerCode: quickgo + resourceHomeUrl: https://www.ebi.ac.uk/GOA/ + sampleId: P12345 + urlPattern: https://www.ebi.ac.uk/QuickGO/GProtein?ac={$id} + sampleId: P12345 + - created: 2019-06-11T14:16:23.782+0000 + deprecated: false + deprecationDate: + description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. + id: 592 + mirId: MIR:00000197 + modified: 2019-06-11T14:16:23.782+0000 + name: PaleoDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paleodb + resources: + - deprecated: false + deprecationDate: + description: PaleoDB at Macquarie University + id: 594 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 593 + location: + countryCode: AU + countryName: Australia + name: Macquarie University, Sydney + rorId: + location: + countryCode: AU + countryName: Australia + mirId: MIR:00100254 + name: PaleoDB at Macquarie University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://paleodb.org/ + sampleId: '83088' + urlPattern: http://fossilworks.org/?a=taxonInfo&taxon_no={$id} + sampleId: '83088' + - created: 2019-06-11T14:16:24.045+0000 + deprecated: false + deprecationDate: + description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. + id: 595 + mirId: MIR:00000198 + modified: 2019-06-11T14:16:24.045+0000 + name: Compulyeast + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: compulyeast + resources: + - deprecated: false + deprecationDate: + description: Compluyeast database at Universidad Complutense Madrid + id: 597 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 596 + location: + countryCode: ES + countryName: Spain + name: Department Microbiology II, Universidad Complutense Madrid, Madrid + rorId: + location: + countryCode: ES + countryName: Spain + mirId: MIR:00100257 + name: Compluyeast database at Universidad Complutense Madrid + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://compluyeast2dpage.dacya.ucm.es/ + sampleId: O08709 + urlPattern: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac={$id} + sampleId: O08709 + - created: 2019-06-11T14:16:24.496+0000 + deprecated: false + deprecationDate: + description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. + id: 601 + mirId: MIR:00000200 + modified: 2019-06-11T14:16:24.496+0000 + name: EchoBASE + namespaceEmbeddedInLui: false + pattern: ^EB\d+$ + prefix: echobase + resources: + - deprecated: false + deprecationDate: + description: EchoBASE at the University of York + id: 603 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 602 + location: + countryCode: GB + countryName: United Kingdom + name: Department of Biology (Area 10), University of York, York + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100259 + name: EchoBASE at the University of York + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.york.ac.uk/ + sampleId: EB0170 + urlPattern: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID={$id} + sampleId: EB0170 + - created: 2019-06-11T14:16:24.278+0000 + deprecated: false + deprecationDate: + description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. + id: 598 + mirId: MIR:00000199 + modified: 2021-02-17T17:15:29.025+0000 + name: DisProt + namespaceEmbeddedInLui: false + pattern: ^DP\d{5}$ + prefix: disprot + resources: + - deprecated: false + deprecationDate: + description: DisProt at University of Padua + id: 600 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1769 + location: + countryCode: IT + countryName: Italy + name: University of Padua + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00100258 + name: DisProt at University of Padua + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://disprot.org/ + sampleId: DP00003 + urlPattern: https://disprot.org/{$id} + sampleId: DP00003 + - created: 2019-06-11T14:16:24.719+0000 + deprecated: false + deprecationDate: + description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' + id: 604 + mirId: MIR:00000201 + modified: 2019-06-11T14:16:24.719+0000 + name: eggNOG + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: eggnog + resources: + - deprecated: false + deprecationDate: + description: eggNOG Version 3 at European Molecular Biology Laboratory + id: 606 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 605 + location: + countryCode: DE + countryName: Germany + name: European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100260 + name: eggNOG Version 3 at European Molecular Biology Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://eggnog.embl.de/version_3.0/ + sampleId: veNOG12876 + urlPattern: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0={$id} + sampleId: veNOG12876 + - created: 2019-06-11T14:16:24.944+0000 + deprecated: false + deprecationDate: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + id: 607 + mirId: MIR:00000202 + modified: 2019-06-11T14:16:24.944+0000 + name: Ensembl Bacteria + namespaceEmbeddedInLui: false + pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ + prefix: ensembl.bacteria + resources: + - deprecated: false + deprecationDate: + description: Ensembl Bacteria at EBI + id: 608 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100261 + name: Ensembl Bacteria at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://bacteria.ensembl.org/ + sampleId: MU9_3181 + urlPattern: https://bacteria.ensembl.org/id/{$id} + sampleId: MU9_3181 + - created: 2019-06-11T14:16:25.183+0000 + deprecated: false + deprecationDate: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. + id: 609 + mirId: MIR:00000203 + modified: 2019-06-11T14:16:25.183+0000 + name: Ensembl Protists + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: ensembl.protist + resources: + - deprecated: false + deprecationDate: + description: Ensembl Protists at EBI + id: 610 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100262 + name: Ensembl Protists at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://protists.ensembl.org + sampleId: PF3D7_1328700 + urlPattern: https://protists.ensembl.org/id/{$id} + sampleId: PF3D7_1328700 + - created: 2019-06-11T14:16:25.396+0000 + deprecated: false + deprecationDate: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. + id: 611 + mirId: MIR:00000204 + modified: 2019-06-11T14:16:25.396+0000 + name: Ensembl Metazoa + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?\d+$ + prefix: ensembl.metazoa + resources: + - deprecated: false + deprecationDate: + description: Enzembl Metazoa at EBI + id: 612 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100263 + name: Enzembl Metazoa at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://metazoa.ensembl.org/ + sampleId: FBtr0084214 + urlPattern: https://metazoa.ensembl.org/id/{$id} + sampleId: FBtr0084214 + - created: 2019-06-11T14:16:25.597+0000 + deprecated: false + deprecationDate: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. + id: 613 + mirId: MIR:00000205 + modified: 2019-06-11T14:16:25.597+0000 + name: Ensembl Plants + namespaceEmbeddedInLui: false + pattern: ^\w+(\.\d+)?(\.\d+)?$ + prefix: ensembl.plant + resources: + - deprecated: false + deprecationDate: + description: Enzembl Plants at EBI + id: 614 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100264 + name: Enzembl Plants at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://plants.ensembl.org/ + sampleId: AT1G73965 + urlPattern: https://plants.ensembl.org/id/{$id} + sampleId: AT1G73965 + - created: 2019-06-11T14:16:25.804+0000 + deprecated: false + deprecationDate: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. + id: 615 + mirId: MIR:00000206 + modified: 2019-06-11T14:16:25.804+0000 + name: Ensembl Fungi + namespaceEmbeddedInLui: false + pattern: ^[A-Z-a-z0-9]+$ + prefix: ensembl.fungi + resources: + - deprecated: false + deprecationDate: + description: Enzembl Fungi at EBI + id: 616 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100265 + name: Enzembl Fungi at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://fungi.ensembl.org/ + sampleId: CADAFLAT00006211 + urlPattern: https://fungi.ensembl.org/id/{$id} + sampleId: CADAFLAT00006211 + - created: 2019-06-11T14:16:26.018+0000 + deprecated: false + deprecationDate: + description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. + id: 617 + mirId: MIR:00000207 + modified: 2019-06-11T14:16:26.018+0000 + name: HCVDB + namespaceEmbeddedInLui: false + pattern: ^M\d{5}$ + prefix: hcvdb + resources: + - deprecated: false + deprecationDate: + description: HCVDB at CNRS + id: 619 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 618 + location: + countryCode: FR + countryName: France + name: Institut de Biologie et Chimie des Protéines, CNRS, University of Lyon , Lyon-Gerland + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100266 + name: HCVDB at CNRS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://euhcvdb.ibcp.fr/euHCVdb/ + sampleId: M58335 + urlPattern: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC={$id} + sampleId: M58335 + - created: 2019-06-11T14:16:26.301+0000 + deprecated: false + deprecationDate: + description: GenAtlas is a database containing information on human genes, markers and phenotypes. + id: 620 + mirId: MIR:00000208 + modified: 2019-06-11T14:16:26.301+0000 + name: Genatlas + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: genatlas + resources: + - deprecated: false + deprecationDate: + description: Genatlas at Paris Descartes University + id: 622 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 621 + location: + countryCode: FR + countryName: France + name: Paris Descartes University, Paris + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100267 + name: Genatlas at Paris Descartes University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://genatlas.medecine.univ-paris5.fr/ + sampleId: HBB + urlPattern: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol={$id} + sampleId: HBB + - created: 2019-06-11T14:16:26.635+0000 + deprecated: false + deprecationDate: + description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. + id: 623 + mirId: MIR:00000209 + modified: 2019-06-11T14:16:26.635+0000 + name: CATH superfamily + namespaceEmbeddedInLui: false + pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ + prefix: cath.superfamily + resources: + - deprecated: false + deprecationDate: + description: CATH superfamily at UCL + id: 625 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 624 + location: + countryCode: GB + countryName: United Kingdom + name: Institute of Structural and Molecular Biology, University College London + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100268 + name: CATH superfamily at UCL + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cathdb.info/ + sampleId: 1.10.10.200 + urlPattern: http://www.cathdb.info/cathnode/{$id} + sampleId: 1.10.10.200 + - created: 2019-06-11T14:16:26.899+0000 + deprecated: false + deprecationDate: + description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. + id: 626 + mirId: MIR:00000210 + modified: 2019-06-11T14:16:26.899+0000 + name: CATH domain + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: cath.domain + resources: + - deprecated: false + deprecationDate: + description: CATH domain at UCL + id: 627 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 624 + location: + countryCode: GB + countryName: United Kingdom + name: Institute of Structural and Molecular Biology, University College London + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100269 + name: CATH domain at UCL + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cathdb.info/ + sampleId: 1cukA01 + urlPattern: http://www.cathdb.info/domain/{$id} + sampleId: 1cukA01 + - created: 2019-06-11T14:16:27.145+0000 + deprecated: false + deprecationDate: + description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. + id: 628 + mirId: MIR:00000211 + modified: 2019-06-11T14:16:27.145+0000 + name: GeneFarm + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: genefarm + resources: + - deprecated: false + deprecationDate: + description: GeneFarm at Unité de Recherche en Génomique Végétale + id: 630 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 629 + location: + countryCode: FR + countryName: France + name: Unité de Recherche en Génomique Végétale, Evry + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100270 + name: GeneFarm at Unité de Recherche en Génomique Végétale + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://urgi.versailles.inra.fr/Genefarm/ + sampleId: '4892' + urlPattern: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID={$id} + sampleId: '4892' + - created: 2019-06-11T14:16:27.419+0000 + deprecated: false + deprecationDate: + description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. + id: 631 + mirId: MIR:00000212 + modified: 2019-06-11T14:16:27.419+0000 + name: GPCRDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gpcrdb + resources: + - deprecated: false + deprecationDate: + description: GPCRDB at Radboud University + id: 633 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 632 + location: + countryCode: NL + countryName: Netherlands + name: Radboud University Nijmegen Medical Centre, Nijmegen, + rorId: + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100271 + name: GPCRDB at Radboud University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gpcrdb.org/ + sampleId: RL3R1_HUMAN + urlPattern: http://www.gpcrdb.org/protein/{$id}/ + sampleId: RL3R1_HUMAN + - created: 2019-06-11T14:16:27.678+0000 + deprecated: false + deprecationDate: + description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. + id: 634 + mirId: MIR:00000213 + modified: 2019-06-11T14:16:27.678+0000 + name: HOGENOM + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: hogenom + resources: + - deprecated: false + deprecationDate: + description: HOGENOM at CNRS + id: 636 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 635 + location: + countryCode: FR + countryName: France + name: Laboratoire de Biométrie et Biologie Evolutive, CNRS, Lyon + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100272 + name: HOGENOM at CNRS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pbil.univ-lyon1.fr/databases/hogenom/ + sampleId: HBG284870 + urlPattern: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query={$id} + sampleId: HBG284870 + - created: 2019-06-11T14:16:27.950+0000 + deprecated: false + deprecationDate: + description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. + id: 637 + mirId: MIR:00000214 + modified: 2019-06-11T14:16:27.950+0000 + name: GeneTree + namespaceEmbeddedInLui: false + pattern: ^ENSGT\d+$ + prefix: genetree + resources: + - deprecated: false + deprecationDate: + description: GeneTree at Ensembl + id: 638 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 8 + location: + countryCode: GB + countryName: United Kingdom + name: Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100273 + name: GeneTree at Ensembl + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ensembl.org/ + sampleId: ENSGT00550000074763 + urlPattern: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt={$id} + sampleId: ENSGT00550000074763 + - created: 2019-06-11T14:16:28.184+0000 + deprecated: false + deprecationDate: + description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. + id: 639 + mirId: MIR:00000215 + modified: 2019-06-11T14:16:28.184+0000 + name: HSSP + namespaceEmbeddedInLui: false + pattern: ^\w{4}$ + prefix: hssp + resources: + - deprecated: false + deprecationDate: + description: HSSP at EMBL + id: 641 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 640 + location: + countryCode: DE + countryName: Germany + name: Protein Design Group, European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100274 + name: HSSP at EMBL + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://swift.cmbi.kun.nl/swift/hssp/ + sampleId: 102l + urlPattern: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/{$id}.hssp.bz2 + - deprecated: false + deprecationDate: + description: HSSP at CMBI + id: 643 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 642 + location: + countryCode: NL + countryName: Netherlands + name: Nijmegen Centre for Molecular Life Sciences, CMBI, Nijmegen + rorId: + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100458 + name: HSSP at CMBI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/ + sampleId: 102l + urlPattern: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/{$id}.hssp.bz2 + sampleId: 102l + - created: 2019-06-11T14:16:28.639+0000 + deprecated: false + deprecationDate: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. + id: 644 + mirId: MIR:00000216 + modified: 2019-06-11T14:16:28.639+0000 + name: MycoBrowser tuberculosis + namespaceEmbeddedInLui: false + pattern: ^Rv\d{4}(A|B|c)?$ + prefix: myco.tuber + resources: + - deprecated: false + deprecationDate: + description: MycoBrowser tuberculosis at Global Health Institute + id: 646 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 645 + location: + countryCode: CH + countryName: Switzerland + name: Global Health Institute, Lausanne + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100275 + name: MycoBrowser tuberculosis at Global Health Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://tuberculist.epfl.ch/ + sampleId: Rv1908c + urlPattern: http://tuberculist.epfl.ch/quicksearch.php?gene+name={$id} + sampleId: Rv1908c + - created: 2019-06-11T14:16:28.887+0000 + deprecated: false + deprecationDate: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. + id: 647 + mirId: MIR:00000217 + modified: 2019-06-11T14:16:28.887+0000 + name: MycoBrowser leprae + namespaceEmbeddedInLui: false + pattern: ^ML\w+$ + prefix: myco.lepra + resources: + - deprecated: false + deprecationDate: + description: MycoBrowser leprae at Global Health Institute + id: 648 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 645 + location: + countryCode: CH + countryName: Switzerland + name: Global Health Institute, Lausanne + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100276 + name: MycoBrowser leprae at Global Health Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://mycobrowser.epfl.ch/leprosy.html + sampleId: ML0224 + urlPattern: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name={$id} + sampleId: ML0224 + - created: 2019-06-11T14:16:29.087+0000 + deprecated: false + deprecationDate: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. + id: 649 + mirId: MIR:00000218 + modified: 2019-06-11T14:16:29.087+0000 + name: MycoBrowser marinum + namespaceEmbeddedInLui: false + pattern: ^MMAR\_\d+$ + prefix: myco.marinum + resources: + - deprecated: false + deprecationDate: + description: MycoBrowser marinum at Global Health Institute + id: 650 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 645 + location: + countryCode: CH + countryName: Switzerland + name: Global Health Institute, Lausanne + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100277 + name: MycoBrowser marinum at Global Health Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://mycobrowser.epfl.ch/marinolist.html + sampleId: MMAR_2462 + urlPattern: http://mycobrowser.epfl.ch/marinosearch.php?gene+name={$id} + sampleId: MMAR_2462 + - created: 2019-06-11T14:16:29.310+0000 + deprecated: false + deprecationDate: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. + id: 651 + mirId: MIR:00000219 + modified: 2019-06-11T14:16:29.310+0000 + name: MycoBrowser smegmatis + namespaceEmbeddedInLui: false + pattern: ^MSMEG\w+$ + prefix: myco.smeg + resources: + - deprecated: false + deprecationDate: + description: MycoBrowser smegmatis at Global Health Institute + id: 652 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 645 + location: + countryCode: CH + countryName: Switzerland + name: Global Health Institute, Lausanne + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100278 + name: MycoBrowser smegmatis at Global Health Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://mycobrowser.epfl.ch/smegmalist.html + sampleId: MSMEG_3769 + urlPattern: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name={$id} + sampleId: MSMEG_3769 + - created: 2019-06-11T14:16:29.544+0000 + deprecated: false + deprecationDate: + description: Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. + id: 653 + mirId: MIR:00000220 + modified: 2019-06-11T14:16:29.544+0000 + name: Orphanet + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: orphanet + resources: + - deprecated: false + deprecationDate: + description: Orphanet at Inserm + id: 655 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 654 + location: + countryCode: FR + countryName: France + name: Inserm, Hôpital Broussais, Paris + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100279 + name: Orphanet at Inserm + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.orpha.net/consor/ + sampleId: '85163' + urlPattern: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert={$id} + - deprecated: false + deprecationDate: + description: Bio2RDF + id: 656 + institution: + description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. + homeUrl: https://bio2rdf.org + id: 33 + location: + countryCode: US + countryName: United States + name: Bio2RDF.org + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100701 + name: Bio2RDF + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://orphanet.bio2rdf.org/fct + sampleId: '85163' + urlPattern: http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:{$id} + sampleId: '85163' + - created: 2019-06-11T14:16:29.860+0000 + deprecated: false + deprecationDate: + description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups + id: 657 + mirId: MIR:00000221 + modified: 2019-06-11T14:16:29.860+0000 + name: OrthoDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: orthodb + resources: + - deprecated: false + deprecationDate: + description: OrthoDB at Swiss Institute of Bioinformatics + id: 659 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 658 + location: + countryCode: CH + countryName: Switzerland + name: Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, Geneva + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100280 + name: OrthoDB at Swiss Institute of Bioinformatics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cegg.unige.ch/orthodb4 + sampleId: Q9P0K8 + urlPattern: http://cegg.unige.ch/orthodb/results?searchtext={$id} + sampleId: Q9P0K8 + - created: 2019-06-11T14:16:30.097+0000 + deprecated: false + deprecationDate: + description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. + id: 660 + mirId: MIR:00000222 + modified: 2019-06-11T14:16:30.097+0000 + name: Peroxibase + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: peroxibase + resources: + - deprecated: false + deprecationDate: + description: Peroxibase at University of Geneva + id: 662 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 661 + location: + countryCode: CH + countryName: Switzerland + name: Department of Plant Biology, University of Geneva, Geneva + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100281 + name: Peroxibase at University of Geneva + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://peroxibase.toulouse.inra.fr/ + sampleId: '5282' + urlPattern: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id={$id} + sampleId: '5282' + - created: 2019-06-11T14:16:30.326+0000 + deprecated: false + deprecationDate: + description: PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. + id: 663 + mirId: MIR:00000223 + modified: 2019-06-11T14:16:30.326+0000 + name: PhylomeDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phylomedb + resources: + - deprecated: false + deprecationDate: + description: PhylomeDB at Centro de Investigación Príncipe Felipe + id: 665 + institution: + description: The Centre for Genomic Regulation (CRG) is an international biomedical research institute of excellence, created in December 2000. It is a non-profit foundation funded by the Catalan Government through the Departments of Business & Knowledge, the Spanish Ministry of Science, Innovation & Universities, the "la Caixa" Banking Foundation, and includes the participation of Pompeu Fabra University. + homeUrl: https://www.crg.eu + id: 664 + location: + countryCode: ES + countryName: Spain + name: Centre for Genomic Regulation + rorId: https://ror.org/03wyzt892 + location: + countryCode: ES + countryName: Spain + mirId: MIR:00100282 + name: PhylomeDB at Centro de Investigación Príncipe Felipe + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://phylomedb.org/ + sampleId: Phy000CLXM_RAT + urlPattern: http://phylomedb.org/?seqid={$id} + sampleId: Phy000CLXM_RAT + - created: 2019-06-11T14:16:30.547+0000 + deprecated: false + deprecationDate: + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. + id: 666 + mirId: MIR:00000224 + modified: 2019-06-11T14:16:30.547+0000 + name: SubstrateDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pmap.substratedb + resources: + - deprecated: false + deprecationDate: + description: SubstrateDB at The Burnham Institute for Medical Research + id: 668 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 667 + location: + countryCode: US + countryName: United States + name: The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100283 + name: SubstrateDB at The Burnham Institute for Medical Research + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://substrate.burnham.org/ + sampleId: '1915' + urlPattern: http://substrate.burnham.org/protein/annotation/{$id}/html + sampleId: '1915' + - created: 2019-06-11T14:16:30.793+0000 + deprecated: false + deprecationDate: + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). + id: 669 + mirId: MIR:00000225 + modified: 2019-06-11T14:16:30.793+0000 + name: CutDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pmap.cutdb + resources: + - deprecated: false + deprecationDate: + description: CutDB at The Burnham Institute for Medical Research + id: 670 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 667 + location: + countryCode: US + countryName: United States + name: The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100284 + name: CutDB at The Burnham Institute for Medical Research + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cutdb.burnham.org + sampleId: '25782' + urlPattern: http://cutdb.burnham.org/relation/show/{$id} + sampleId: '25782' + - created: 2019-06-11T14:16:31.086+0000 + deprecated: false + deprecationDate: + description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. + id: 671 + mirId: MIR:00000226 + modified: 2019-06-11T14:16:31.086+0000 + name: ProtClustDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: protclustdb + resources: + - deprecated: false + deprecationDate: + description: ProtClustDB at NCBI + id: 672 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100285 + name: ProtClustDB at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters + sampleId: O80725 + urlPattern: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term={$id} + sampleId: O80725 + - created: 2019-06-11T14:16:31.282+0000 + deprecated: false + deprecationDate: + description: The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. + id: 673 + mirId: MIR:00000227 + modified: 2019-06-11T14:16:31.282+0000 + name: PMP + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: pmp + resources: + - deprecated: true + deprecationDate: 2020-03-03T06:27:49.602+0000 + description: PMP at University of Basel + id: 675 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 674 + location: + countryCode: CH + countryName: Switzerland + name: Biozentrum, University of Basel, Basel + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100286 + name: PMP at University of Basel + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.proteinmodelportal.org/ + sampleId: Q0VCA6 + urlPattern: https://registry.identifiers.org/deprecation/resources/MIR:00100286/{$id} + sampleId: Q0VCA6 + - created: 2019-06-11T14:16:31.529+0000 + deprecated: false + deprecationDate: + description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. 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This collection references cluster information. + id: 679 + mirId: MIR:00000229 + modified: 2019-06-11T14:16:31.786+0000 + name: ProtoNet Cluster + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: protonet.cluster + resources: + - deprecated: false + deprecationDate: + description: ProtoNet at Hebrew University + id: 680 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 677 + location: + countryCode: IL + countryName: Israel + name: Hebrew University, Jerusalem + rorId: + location: + countryCode: IL + countryName: Israel + mirId: MIR:00100288 + name: ProtoNet at Hebrew University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.protonet.cs.huji.ac.il/ + sampleId: '4349895' + urlPattern: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster={$id} + sampleId: '4349895' + - created: 2019-06-11T14:16:32.004+0000 + deprecated: false + deprecationDate: + description: REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. + id: 681 + mirId: MIR:00000230 + modified: 2019-06-11T14:16:32.004+0000 + name: REBASE + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rebase + resources: + - deprecated: false + deprecationDate: + description: REBASE at New England Biolabs + id: 683 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 682 + location: + countryCode: US + countryName: United States + name: New England Biolabs, Ipswich, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100289 + name: REBASE at New England Biolabs + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://rebase.neb.com/rebase/ + sampleId: '101' + urlPattern: http://rebase.neb.com/rebase/enz/{$id}.html + sampleId: '101' + - created: 2019-06-11T14:16:32.267+0000 + deprecated: false + deprecationDate: + description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences. + id: 684 + mirId: MIR:00000231 + modified: 2019-06-11T14:16:32.267+0000 + name: SWISS-MODEL Repository + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: swiss-model + resources: + - deprecated: false + deprecationDate: + description: SWISS-MODEL at SIB Swiss Institute of Bioinformatics + id: 686 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 685 + location: + countryCode: CH + countryName: Switzerland + name: Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100290 + name: SWISS-MODEL at SIB Swiss Institute of Bioinformatics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://swissmodel.expasy.org + sampleId: P23298 + urlPattern: https://swissmodel.expasy.org/repository/uniprot/{$id} + sampleId: P23298 + - created: 2019-06-11T14:16:32.515+0000 + deprecated: false + deprecationDate: + description: 'VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.' + id: 687 + mirId: MIR:00000232 + modified: 2019-06-11T14:16:32.515+0000 + name: VectorBase + namespaceEmbeddedInLui: false + pattern: ^\D{4}\d{6}(\-\D{2})?$ + prefix: vectorbase + resources: + - deprecated: false + deprecationDate: + description: Vectorbase at EMBL-EBI + id: 688 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100291 + name: Vectorbase at EMBL-EBI + official: true + providerCode: ebi + resourceHomeUrl: https://www.vectorbase.org/ + sampleId: ISCW007415 + urlPattern: https://www.vectorbase.org/search/site/{$id}?&site="Genome" + sampleId: ISCW007415 + - created: 2019-06-11T14:16:33.213+0000 + deprecated: false + deprecationDate: + description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. + id: 694 + mirId: MIR:00000234 + modified: 2019-06-11T14:16:33.213+0000 + name: Cell Cycle Ontology + namespaceEmbeddedInLui: true + pattern: ^CCO\:\w+$ + prefix: cco + resources: + - deprecated: false + deprecationDate: + description: Cell Cycle Ontology through OLS + id: 695 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100294 + name: Cell Cycle Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO + sampleId: '0000003' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:{$id} + sampleId: '0000003' + - created: 2019-06-11T14:16:33.415+0000 + deprecated: false + deprecationDate: + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. + id: 696 + mirId: MIR:00000235 + modified: 2019-06-11T14:16:33.415+0000 + name: miRBase mature sequence + namespaceEmbeddedInLui: false + pattern: MIMAT\d{7} + prefix: mirbase.mature + resources: + - deprecated: false + deprecationDate: + description: miRBase + id: 697 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 264 + location: + countryCode: GB + countryName: United Kingdom + name: Faculty of Life Sciences, University of Manchester + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100296 + name: miRBase + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mirbase.org/ + sampleId: MIMAT0000001 + urlPattern: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc={$id} + sampleId: MIMAT0000001 + - created: 2019-06-11T14:16:33.634+0000 + deprecated: false + deprecationDate: + description: neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. + id: 698 + mirId: MIR:00000236 + modified: 2019-06-11T14:16:33.634+0000 + name: nextProt + namespaceEmbeddedInLui: false + pattern: ^NX_\w+ + prefix: nextprot + resources: + - deprecated: false + deprecationDate: + description: nextProt at Swiss Institute of Bioinformatics + id: 700 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100300 + name: nextProt at Swiss Institute of Bioinformatics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.nextprot.org/ + sampleId: NX_O00165 + urlPattern: https://www.nextprot.org/db/entry/{$id} + sampleId: NX_O00165 + - created: 2019-06-11T14:16:33.869+0000 + deprecated: false + deprecationDate: + description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. + id: 701 + mirId: MIR:00000237 + modified: 2019-06-11T14:16:33.869+0000 + name: CAS + namespaceEmbeddedInLui: false + pattern: ^\d{1,7}\-\d{2}\-\d$ + prefix: cas + resources: + - deprecated: false + deprecationDate: + description: CAS through Common Chemistry + id: 703 + institution: + description: CAS is a global organization of expert scientists, technologists, and business leaders with a successful and extended history of delivering scientific information opportunities. + homeUrl: https://www.cas.org + id: 702 + location: + countryCode: US + countryName: United States + name: CAS American Chemical Society + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100301 + name: CAS through Common Chemistry + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://commonchemistry.org + sampleId: 50-00-0 + urlPattern: http://commonchemistry.org/ChemicalDetail.aspx?ref={$id} + - deprecated: false + deprecationDate: + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + id: 2454 + institution: + description: >- + Maastricht University (UM) is the most international university in + the Netherlands and, with 18,000 students and 4,400 employees, is + still growing. The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00000732 + name: Scholia + official: false + providerCode: scholia + resourceHomeUrl: https://scholia.toolforge.org/ + sampleId: 50-00-0 + urlPattern: https://scholia.toolforge.org/cas/{$id} + sampleId: 50-00-0 + - created: 2019-06-11T14:16:34.113+0000 + deprecated: false + deprecationDate: + description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced. + id: 704 + mirId: MIR:00000238 + modified: 2019-06-11T14:16:34.113+0000 + name: KEGG Genome + namespaceEmbeddedInLui: false + pattern: ^(T0\d+|\w{3,5})$ + prefix: kegg.genome + resources: + - deprecated: false + deprecationDate: + description: KEGG Genome Database + id: 706 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 705 + location: + countryCode: JP + countryName: Japan + name: Kyoto University Bioinformatics Center, Kyoto + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100303 + name: KEGG Genome Database + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genome.jp/kegg/catalog/org_list.html + sampleId: eco + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: eco + - created: 2019-06-11T14:16:34.345+0000 + deprecated: false + deprecationDate: + description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. + id: 707 + mirId: MIR:00000239 + modified: 2019-06-11T14:16:34.345+0000 + name: KEGG Metagenome + namespaceEmbeddedInLui: false + pattern: ^T3\d+$ + prefix: kegg.metagenome + resources: + - deprecated: false + deprecationDate: + description: KEGG Metagenome Database + id: 708 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 705 + location: + countryCode: JP + countryName: Japan + name: Kyoto University Bioinformatics Center, Kyoto + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100304 + name: KEGG Metagenome Database + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genome.jp/kegg/catalog/org_list3.html + sampleId: T30002 + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: T30002 + - created: 2019-06-11T14:16:34.542+0000 + deprecated: false + deprecationDate: + description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. + id: 709 + mirId: MIR:00000240 + modified: 2019-06-11T14:16:34.542+0000 + name: NARCIS + namespaceEmbeddedInLui: false + pattern: ^oai\:cwi\.nl\:\d+$ + prefix: narcis + resources: + - deprecated: false + deprecationDate: + description: NARCIS at The Hague + id: 711 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 710 + location: + countryCode: NL + countryName: Netherlands + name: NARCIS, Royal Netherlands Academy of Science and Arts + rorId: + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100306 + name: NARCIS at The Hague + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.narcis.nl/?Language=en + sampleId: oai:cwi.nl:4725 + urlPattern: http://www.narcis.nl/publication/RecordID/{$id} + sampleId: oai:cwi.nl:4725 + - created: 2019-06-11T14:16:34.772+0000 + deprecated: false + deprecationDate: + description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). + id: 712 + mirId: MIR:00000241 + modified: 2019-06-11T14:16:34.772+0000 + name: Japan Chemical Substance Dictionary + namespaceEmbeddedInLui: false + pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ + prefix: jcsd + resources: + - deprecated: false + deprecationDate: + description: Japan Chemical Substance Dictionary + id: 714 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 713 + location: + countryCode: JP + countryName: Japan + name: Japan Science and Technology Agency + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100307 + name: Japan Chemical Substance Dictionary + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://jglobal.jst.go.jp/en/ + sampleId: J55.713G + urlPattern: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No={$id} + sampleId: J55.713G + - created: 2019-06-11T14:16:35.052+0000 + deprecated: false + deprecationDate: + description: 'The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.' + id: 715 + mirId: MIR:00000242 + modified: 2019-06-11T14:16:35.052+0000 + name: Pathway Ontology + namespaceEmbeddedInLui: true + pattern: ^PW:\d{7}$ + prefix: pw + resources: + - deprecated: false + deprecationDate: + description: Pathway Ontology at Rat Genome Database + id: 717 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 716 + location: + countryCode: US + countryName: United States + name: Medical College of Wisconsin, Wisconsin + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100309 + name: Pathway Ontology at Rat Genome Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://rgd.mcw.edu/rgdweb/ontology/search.html + sampleId: '0000208' + urlPattern: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:{$id} + - deprecated: false + deprecationDate: + description: Pathway Ontology through OLS + id: 718 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100310 + name: Pathway Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/pw + sampleId: '0000208' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/pw/terms?obo_id=PW:{$id} + - deprecated: false + deprecationDate: + description: Pathway Ontology through BioPortal + id: 720 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 719 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100311 + name: Pathway Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/PW + sampleId: '0000208' + urlPattern: http://purl.bioontology.org/ontology/PW/PW:{$id} + sampleId: '0000208' + - created: 2019-06-11T14:16:35.560+0000 + deprecated: false + deprecationDate: + description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' + id: 721 + mirId: MIR:00000243 + modified: 2019-06-11T14:16:35.560+0000 + name: Sequence Read Archive + namespaceEmbeddedInLui: false + pattern: ^[SED]R[APRSXZ]\d+$ + prefix: insdc.sra + resources: + - deprecated: false + deprecationDate: + description: Sequence Read Archive at NCBI + id: 722 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100312 + name: Sequence Read Archive at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/sra + sampleId: SRX000007 + urlPattern: https://www.ncbi.nlm.nih.gov/sra/{$id} + - deprecated: false + deprecationDate: + description: European Nucleotide Archive (ENA) + id: 723 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100313 + name: European Nucleotide Archive (ENA) + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/ena + sampleId: SRX000007 + urlPattern: https://www.ebi.ac.uk/ena/data/view/{$id} + - deprecated: false + deprecationDate: + description: DDBJ Sequence Read Archive (DRA) + id: 724 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 121 + location: + countryCode: JP + countryName: Japan + name: DNA Data Bank of Japan, Mishima, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100314 + name: DDBJ Sequence Read Archive (DRA) + official: false + providerCode: ddbj + resourceHomeUrl: http://trace.ddbj.nig.ac.jp/dra/ + sampleId: SRX000007 + urlPattern: http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc={$id} + sampleId: SRX000007 + - created: 2019-06-11T14:16:35.987+0000 + deprecated: false + deprecationDate: + description: ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. + id: 725 + mirId: MIR:00000244 + modified: 2019-06-11T14:16:35.987+0000 + name: ScerTF + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: scretf + resources: + - deprecated: false + deprecationDate: + description: ScerTF at Washington University + id: 727 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 726 + location: + countryCode: US + countryName: United States + name: Department of Genetics, Washington University Medical School, St Louis, Missouri + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100315 + name: ScerTF at Washington University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://stormo.wustl.edu/ScerTF/ + sampleId: RSC3 + urlPattern: http://stormo.wustl.edu/ScerTF/details/{$id}/ + sampleId: RSC3 + - created: 2019-06-11T14:16:36.222+0000 + deprecated: false + deprecationDate: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + id: 728 + mirId: MIR:00000245 + modified: 2019-06-11T14:16:36.222+0000 + name: PharmGKB Gene + namespaceEmbeddedInLui: false + pattern: ^PA\w+$ + prefix: pharmgkb.gene + resources: + - deprecated: false + deprecationDate: + description: PharmGKB Gene at Stanford + id: 729 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 298 + location: + countryCode: US + countryName: United States + name: Department of Genetics, School of Medicine, Stanford University, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100316 + name: PharmGKB Gene at Stanford + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pharmgkb.org/ + sampleId: PA131 + urlPattern: http://www.pharmgkb.org/gene/{$id} + sampleId: PA131 + - created: 2019-06-11T14:16:36.416+0000 + deprecated: false + deprecationDate: + description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. + id: 730 + mirId: MIR:00000246 + modified: 2019-06-11T14:16:36.416+0000 + name: miRNEST + namespaceEmbeddedInLui: false + pattern: ^MNEST\d+$ + prefix: mirnest + resources: + - deprecated: false + deprecationDate: + description: miRNEST at Adam Mickiewicz University + id: 732 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 731 + location: + countryCode: PL + countryName: Poland + name: Institute of Molecular Biology, Adam Mickiewicz University, Poznan + rorId: + location: + countryCode: PL + countryName: Poland + mirId: MIR:00100317 + name: miRNEST at Adam Mickiewicz University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://rhesus.amu.edu.pl/mirnest/copy/ + sampleId: MNEST029358 + urlPattern: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id={$id} + sampleId: MNEST029358 + - created: 2019-06-11T14:16:36.669+0000 + deprecated: false + deprecationDate: + description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. + id: 733 + mirId: MIR:00000247 + modified: 2019-06-11T14:16:36.669+0000 + name: NAPP + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: napp + resources: + - deprecated: false + deprecationDate: + description: NAPP at CNRS + id: 735 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 734 + location: + countryCode: FR + countryName: France + name: Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, Paris + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100318 + name: NAPP at CNRS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://napp.u-psud.fr/ + sampleId: '351' + urlPattern: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie={$id} + sampleId: '351' + - created: 2019-06-11T14:16:36.900+0000 + deprecated: false + deprecationDate: + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. + id: 736 + mirId: MIR:00000248 + modified: 2019-06-11T14:16:36.900+0000 + name: NONCODE v3 + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: noncodev3 + resources: + - deprecated: false + deprecationDate: + description: NONCODE at Chinese Academy of Sciences + id: 738 + institution: + description: The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches. + homeUrl: http://english.cas.cn/ + id: 737 + location: + countryCode: CN + countryName: China + name: Chinese Academy of Sciences + rorId: https://ror.org/034t30j35 + location: + countryCode: CN + countryName: China + mirId: MIR:00100319 + name: NONCODE at Chinese Academy of Sciences + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.noncode.org/ + sampleId: '377550' + urlPattern: http://www.noncode.org/NONCODERv3/ncrna.php?ncid={$id} + sampleId: '377550' + - created: 2019-06-11T14:16:37.163+0000 + deprecated: false + deprecationDate: + description: The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region. + id: 739 + mirId: MIR:00000249 + modified: 2019-06-11T14:16:37.163+0000 + name: VIRsiRNA + namespaceEmbeddedInLui: false + pattern: ^virsi\d+$ + prefix: virsirna + resources: + - deprecated: false + deprecationDate: + description: VIRsiRNA at Institute of Microbial Technology + id: 741 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 740 + location: + countryCode: IN + countryName: India + name: Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India + rorId: + location: + countryCode: IN + countryName: India + mirId: MIR:00100320 + name: VIRsiRNA at Institute of Microbial Technology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://crdd.osdd.net/servers/virsirnadb + sampleId: virsi1909 + urlPattern: http://crdd.osdd.net/servers/virsirnadb/record.php?details={$id} + sampleId: virsi1909 + - created: 2019-06-11T14:16:37.386+0000 + deprecated: false + deprecationDate: + description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. + id: 742 + mirId: MIR:00000250 + modified: 2019-06-11T14:16:37.386+0000 + name: ELM + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: elm + resources: + - deprecated: false + deprecationDate: + description: ELM at EMBL (Germany) + id: 744 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 743 + location: + countryCode: DE + countryName: Germany + name: Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100321 + name: ELM at EMBL (Germany) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://elm.eu.org/ + sampleId: CLV_MEL_PAP_1 + urlPattern: http://elm.eu.org/elms/elmPages/{$id}.html + sampleId: CLV_MEL_PAP_1 + - created: 2019-06-11T14:16:37.622+0000 + deprecated: false + deprecationDate: + description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. + id: 745 + mirId: MIR:00000251 + modified: 2019-06-11T14:16:37.622+0000 + name: MimoDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mimodb + resources: + - deprecated: false + deprecationDate: + description: BDB at University of Electronic Science and Technology of China + id: 747 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 746 + location: + countryCode: CN + countryName: China + name: Key Laboratory for Neuroinformation of Ministry of Education, University of Electronic Science and Technology of China, Sichuan + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100322 + name: BDB at University of Electronic Science and Technology of China + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://immunet.cn/bdb/ + sampleId: '1' + urlPattern: http://immunet.cn/bdb/index.php/mimoset/{$id} + sampleId: '1' + - created: 2019-06-11T14:16:37.867+0000 + deprecated: false + deprecationDate: + description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. + id: 748 + mirId: MIR:00000252 + modified: 2019-06-11T14:16:37.867+0000 + name: SitEx + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sitex + resources: + - deprecated: false + deprecationDate: + description: SitEx at Novosibirsk State University + id: 750 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 749 + location: + countryCode: RU + countryName: Russian Federation + name: Novosibirsk State University, Novosibirsk + rorId: + location: + countryCode: RU + countryName: Russian Federation + mirId: MIR:00100323 + name: SitEx at Novosibirsk State University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www-bionet.sscc.ru/sitex/ + sampleId: '1000' + urlPattern: http://www-bionet.sscc.ru/sitex/index.php?siteid={$id} + sampleId: '1000' + - created: 2019-06-11T14:16:38.105+0000 + deprecated: false + deprecationDate: + description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. + id: 751 + mirId: MIR:00000253 + modified: 2019-06-11T14:16:38.105+0000 + name: BYKdb + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: bykdb + resources: + - deprecated: false + deprecationDate: + description: BYKdb at CNRS + id: 753 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 752 + location: + countryCode: FR + countryName: France + name: Unité Bases Moléculaires et Structurales des Systèmes Infectieux; CNRS - Université Claude Bernard, Lyon + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100324 + name: BYKdb at CNRS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://bykdb.ibcp.fr/BYKdb/ + sampleId: A0A009E7X8 + urlPattern: https://bykdb.ibcp.fr/data/html/annotated/{$id}.html + sampleId: A0A009E7X8 + - created: 2019-06-11T14:16:38.340+0000 + deprecated: false + deprecationDate: + description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. + id: 754 + mirId: MIR:00000254 + modified: 2019-06-11T14:16:38.340+0000 + name: Conoserver + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: conoserver + resources: + - deprecated: false + deprecationDate: + description: ConoServer at University of Queensland + id: 755 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 582 + location: + countryCode: AU + countryName: Australia + name: Institute for Molecular Bioscience, The University of Queensland, Brisbane + rorId: + location: + countryCode: AU + countryName: Australia + mirId: MIR:00100325 + name: ConoServer at University of Queensland + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.conoserver.org/ + sampleId: '2639' + urlPattern: http://www.conoserver.org/?page=card&table=protein&id={$id} + sampleId: '2639' + - created: 2019-06-11T14:16:38.521+0000 + deprecated: false + deprecationDate: + description: 'TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.' + id: 756 + mirId: MIR:00000255 + modified: 2019-06-11T14:16:38.521+0000 + name: TopFind + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: topfind + resources: + - deprecated: false + deprecationDate: + description: TopFind at University of British Columbia + id: 758 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 757 + location: + countryCode: CA + countryName: Canada + name: Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100326 + name: TopFind at University of British Columbia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://clipserve.clip.ubc.ca/topfind + sampleId: Q9UKQ2 + urlPattern: http://clipserve.clip.ubc.ca/topfind/proteins/{$id} + sampleId: Q9UKQ2 + - created: 2019-06-11T14:16:38.756+0000 + deprecated: false + deprecationDate: + description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. + id: 759 + mirId: MIR:00000256 + modified: 2019-06-11T14:16:38.756+0000 + name: MIPModDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: mipmod + resources: + - deprecated: false + deprecationDate: + description: MIPModDB at Indian Institute of Technology Kanpur + id: 761 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 760 + location: + countryCode: IN + countryName: India + name: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur + rorId: + location: + countryCode: IN + countryName: India + mirId: MIR:00100327 + name: MIPModDB at Indian Institute of Technology Kanpur + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bioinfo.iitk.ac.in/MIPModDB + sampleId: HOSAPI0399 + urlPattern: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code={$id} + sampleId: HOSAPI0399 + - created: 2019-06-11T14:16:38.984+0000 + deprecated: false + deprecationDate: + description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' + id: 762 + mirId: MIR:00000257 + modified: 2019-06-11T14:16:38.984+0000 + name: Cell Image Library + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cellimage + resources: + - deprecated: false + deprecationDate: + description: Cell Image Library at American Society for Cell Biology + id: 764 + institution: + description: The mission of NCMIR is to develop technologies to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed. + homeUrl: https://ncmir.ucsd.edu + id: 763 + location: + countryCode: US + countryName: United States + name: National Center for Microscopy and Imaging Research + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100328 + name: Cell Image Library at American Society for Cell Biology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cellimagelibrary.org/ + sampleId: '24801' + urlPattern: http://cellimagelibrary.org/images/{$id} + sampleId: '24801' + - created: 2019-06-11T14:16:39.210+0000 + deprecated: false + deprecationDate: + description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. + id: 765 + mirId: MIR:00000258 + modified: 2019-06-11T14:16:39.210+0000 + name: COMBINE specifications + namespaceEmbeddedInLui: false + pattern: ^\w+(\-|\.|\w)*$ + prefix: combine.specifications + resources: + - deprecated: false + deprecationDate: + description: COMBINE at EBI + id: 766 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100329 + name: COMBINE at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://co.mbine.org/standards/ + sampleId: sbgn.er.level-1.version-1.2 + urlPattern: https://co.mbine.org/specifications/{$id} + sampleId: sbgn.er.level-1.version-1.2 + - created: 2019-06-11T14:16:39.396+0000 + deprecated: false + deprecationDate: + description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. + id: 767 + mirId: MIR:00000261 + modified: 2019-06-11T14:16:39.396+0000 + name: CABRI + namespaceEmbeddedInLui: false + pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ + prefix: cabri + resources: + - deprecated: false + deprecationDate: + description: CABRI Cell Lines catalogue in Genova (SRS) + id: 769 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 768 + location: + countryCode: IT + countryName: Italy + name: National Cancer Research Institute of Genova, Genova + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00100334 + name: CABRI Cell Lines catalogue in Genova (SRS) + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cabri.org/ + sampleId: dsmz_mutz-id:ACC 291 + urlPattern: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[{$id}] + - deprecated: false + deprecationDate: + description: CABRI Cell Lines catalogue in Brussels (SRS) + id: 771 + institution: + description: he BCCM consortium has grown to become one of the most important culture collections in the world, both in terms of the size and quality of the collections (bacteria, yeasts, moulds, plasmids, diatoms, DNA libraries) and its expertise. Not only does the consortium keep more than 200,000 quality controlled, characterised and documented units of biological material, but it also offers its expertise through services and partnership projects. + homeUrl: http://bccm.belspo.be/ + id: 770 + location: + countryCode: BE + countryName: Belgium + name: BCCM + rorId: + location: + countryCode: BE + countryName: Belgium + mirId: MIR:00100335 + name: CABRI Cell Lines catalogue in Brussels (SRS) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.be.cabri.org/ + sampleId: dsmz_mutz-id:ACC 291 + urlPattern: http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[{$id}] + sampleId: dsmz_mutz-id:ACC 291 + - created: 2019-06-11T14:16:39.763+0000 + deprecated: false + deprecationDate: + description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. + id: 772 + mirId: MIR:00000263 + modified: 2019-06-11T14:16:39.763+0000 + name: HUGE + namespaceEmbeddedInLui: false + pattern: ^KIAA\d{4}$ + prefix: huge + resources: + - deprecated: false + deprecationDate: + description: HUGE at Kazusa DNA Research Institute + id: 774 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 773 + location: + countryCode: JP + countryName: Japan + name: Kazusa DNA Research Institute, Chiba + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100339 + name: HUGE at Kazusa DNA Research Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.kazusa.or.jp/huge/ + sampleId: KIAA0001 + urlPattern: http://www.kazusa.or.jp/huge/gfpage/{$id}/ + sampleId: KIAA0001 + - created: 2019-06-11T14:16:39.982+0000 + deprecated: false + deprecationDate: + description: BindingDB is the first public database of protein-small molecule affinity data. + id: 775 + mirId: MIR:00000264 + modified: 2019-06-11T14:16:39.982+0000 + name: BindingDB + namespaceEmbeddedInLui: false + pattern: ^\w\d+$ + prefix: bindingdb + resources: + - deprecated: false + deprecationDate: + description: BindingDB + id: 777 + institution: + description: >- + is a public research university in San Diego, California. + + Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students. + homeUrl: https://ucsd.edu/ + id: 190 + location: + countryCode: US + countryName: United States + name: University of California, San Diego + rorId: https://ror.org/0168r3w48 + location: + countryCode: US + countryName: United States + mirId: MIR:00100340 + name: BindingDB + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.bindingdb.org + sampleId: e999 + urlPattern: http://www.bindingdb.org/compact/{$id} + sampleId: e999 + - created: 2019-06-11T14:16:45.247+0000 + deprecated: false + deprecationDate: + description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. + id: 839 + mirId: MIR:00000286 + modified: 2019-06-11T14:16:45.247+0000 + name: Dictybase Gene + namespaceEmbeddedInLui: false + pattern: ^DDB_G\d+$ + prefix: dictybase.gene + resources: + - deprecated: false + deprecationDate: + description: Dictybase Gene at Northwestern University + id: 841 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 840 + location: + countryCode: US + countryName: United States + name: Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100367 + name: Dictybase Gene at Northwestern University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://dictybase.org/ + sampleId: DDB_G0267522 + urlPattern: http://dictybase.org/gene/{$id} + sampleId: DDB_G0267522 + - created: 2019-06-11T14:16:40.213+0000 + deprecated: false + deprecationDate: + description: "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable." + id: 778 + mirId: MIR:00000265 + modified: 2019-06-11T14:16:40.213+0000 + name: STRING + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ + prefix: string + resources: + - deprecated: false + deprecationDate: + description: STRING at Heidelberg + id: 779 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 605 + location: + countryCode: DE + countryName: Germany + name: European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100341 + name: STRING at Heidelberg + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://string.embl.de/ + sampleId: P53350 + urlPattern: http://string.embl.de/interactions/{$id} + - deprecated: false + deprecationDate: + description: STRING Mirror at Heidelberg + id: 780 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 605 + location: + countryCode: DE + countryName: Germany + name: European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100342 + name: STRING Mirror at Heidelberg + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://string-db.org/ + sampleId: P53350 + urlPattern: http://string-db.org/interactions/{$id} + sampleId: P53350 + - created: 2019-06-11T14:16:40.524+0000 + deprecated: false + deprecationDate: + description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. + id: 781 + mirId: MIR:00000266 + modified: 2019-06-11T14:16:40.524+0000 + name: STITCH + namespaceEmbeddedInLui: false + pattern: ^\w{14}$ + prefix: stitch + resources: + - deprecated: false + deprecationDate: + description: STITCH + id: 782 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 605 + location: + countryCode: DE + countryName: Germany + name: European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100343 + name: STITCH + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://stitch.embl.de/ + sampleId: BQJCRHHNABKAKU + urlPattern: http://stitch.embl.de/interactions/{$id} + sampleId: BQJCRHHNABKAKU + - created: 2019-06-11T14:16:40.712+0000 + deprecated: false + deprecationDate: + description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. + id: 783 + mirId: MIR:00000267 + modified: 2019-06-11T14:16:40.712+0000 + name: Anatomical Therapeutic Chemical Vetinary + namespaceEmbeddedInLui: false + pattern: ^Q[A-Z0-9]+$ + prefix: atcvet + resources: + - deprecated: false + deprecationDate: + description: Anatomical Therapeutic Chemical Vet Index at WHO + id: 784 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 295 + location: + countryCode: CH + countryName: Switzerland + name: World Health Organisation + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100344 + name: Anatomical Therapeutic Chemical Vet Index at WHO + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.whocc.no/atcvet/atcvet_index/ + sampleId: QJ51RV02 + urlPattern: http://www.whocc.no/atcvet/atcvet_index/?code={$id} + sampleId: QJ51RV02 + - created: 2019-06-11T14:16:40.928+0000 + deprecated: false + deprecationDate: + description: Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. + id: 785 + mirId: MIR:00000268 + modified: 2019-06-11T14:16:40.928+0000 + name: Phenol-Explorer + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: phenolexplorer + resources: + - deprecated: false + deprecationDate: + description: Phenol-Explorer Database on Phenol content of foods + id: 787 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 786 + location: + countryCode: CA + countryName: Canada + name: INRA and University of Alberta + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100345 + name: Phenol-Explorer Database on Phenol content of foods + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.phenol-explorer.eu/foods/ + sampleId: '75' + urlPattern: http://phenol-explorer.eu/foods/{$id} + sampleId: '75' + - created: 2019-06-11T14:16:41.184+0000 + deprecated: false + deprecationDate: + description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. + id: 788 + mirId: MIR:00000269 + modified: 2019-06-11T14:16:41.184+0000 + name: SNOMED CT + namespaceEmbeddedInLui: false + pattern: ^(\w+)?\d+$ + prefix: snomedct + resources: + - deprecated: false + deprecationDate: + description: SNOMED-CT at The National Pathology Exchange + id: 790 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 789 + location: + countryCode: GB + countryName: United Kingdom + name: The Health Informatics Service, NHS, West Yorkshire + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100405 + name: SNOMED-CT at The National Pathology Exchange + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.snomedbrowser.com/ + sampleId: '284196006' + urlPattern: http://www.snomedbrowser.com/Codes/Details/{$id} + sampleId: '284196006' + - created: 2019-06-11T14:16:41.417+0000 + deprecated: false + deprecationDate: + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. + id: 791 + mirId: MIR:00000270 + modified: 2019-06-11T14:16:41.417+0000 + name: MeSH 2012 + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: mesh.2012 + resources: + - deprecated: false + deprecationDate: + description: MeSH at National Library of Medicine + id: 793 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 792 + location: + countryCode: US + countryName: United States + name: U.S. National Library of Medicine, National Institute of Health, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100349 + name: MeSH at National Library of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.nlm.nih.gov/mesh/ + sampleId: '17186' + urlPattern: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index={$id}&view=expanded + sampleId: '17186' + - created: 2019-06-11T14:16:41.852+0000 + deprecated: false + deprecationDate: + description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). + id: 797 + mirId: MIR:00000272 + modified: 2019-06-11T14:16:41.852+0000 + name: Canadian Drug Product Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cdpd + resources: + - deprecated: false + deprecationDate: + description: Canadian Drug Identification Number at Health Canada + id: 799 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 798 + location: + countryCode: CA + countryName: Canada + name: Health Canada, Ottawa, Ontario + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100351 + name: Canadian Drug Identification Number at Health Canada + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp + sampleId: '63250' + urlPattern: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code={$id} + sampleId: '63250' + - created: 2019-06-11T14:16:42.071+0000 + deprecated: false + deprecationDate: + description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). + id: 800 + mirId: MIR:00000273 + modified: 2019-06-11T14:16:42.071+0000 + name: MassBank + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$ + prefix: massbank + resources: + - deprecated: false + deprecationDate: + description: MassBank in Japan + id: 802 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 801 + location: + countryCode: JP + countryName: Japan + name: The MassBank Consortium + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100353 + name: MassBank in Japan + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.massbank.jp + sampleId: PB000166 + urlPattern: http://www.massbank.jp/RecordDisplay?id={$id} + - deprecated: false + deprecationDate: + description: MassBank in Europe + id: 804 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 803 + location: + countryCode: DE + countryName: Germany + name: NORMAN Network and The MassBank Consortium + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100666 + name: MassBank in Europe + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://massbank.eu/ + sampleId: PB000166 + urlPattern: https://massbank.eu/MassBank/RecordDisplay?id={$id} + sampleId: PB000166 + - created: 2019-06-11T14:16:42.514+0000 + deprecated: false + deprecationDate: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. + id: 805 + mirId: MIR:00000274 + modified: 2019-06-11T14:16:42.514+0000 + name: Golm Metabolome Database + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd + resources: + - deprecated: false + deprecationDate: + description: Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology + id: 807 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 806 + location: + countryCode: DE + countryName: Germany + name: Max Planck Institute of Molecular Plant Physiology, Potsdam + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100354 + name: Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://gmd.mpimp-golm.mpg.de/ + sampleId: 68513255-fc44-4041-bc4b-4fd2fae7541d + urlPattern: http://gmd.mpimp-golm.mpg.de/Metabolites/{$id}.aspx + sampleId: 68513255-fc44-4041-bc4b-4fd2fae7541d + - created: 2019-06-11T14:16:42.733+0000 + deprecated: false + deprecationDate: + description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. + id: 808 + mirId: MIR:00000275 + modified: 2019-06-11T14:16:42.733+0000 + name: HomoloGene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: homologene + resources: + - deprecated: false + deprecationDate: + description: Homologene at NCBI + id: 809 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100355 + name: Homologene at NCBI + official: true + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/homologene/ + sampleId: '1000' + urlPattern: https://www.ncbi.nlm.nih.gov/homologene/{$id} + - deprecated: false + deprecationDate: + description: Bio2RDF + id: 810 + institution: + description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. + homeUrl: https://bio2rdf.org + id: 33 + location: + countryCode: US + countryName: United States + name: Bio2RDF.org + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100699 + name: Bio2RDF + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://homologene.bio2rdf.org/fct + sampleId: '1000' + urlPattern: http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:{$id} + sampleId: '1000' + - created: 2019-06-11T14:16:42.994+0000 + deprecated: false + deprecationDate: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information. + id: 811 + mirId: MIR:00000276 + modified: 2019-06-11T14:16:42.994+0000 + name: UM-BBD Compound + namespaceEmbeddedInLui: false + pattern: ^c\d+$ + prefix: umbbd.compound + resources: + - deprecated: false + deprecationDate: + description: Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich + id: 813 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 812 + location: + countryCode: CH + countryName: Switzerland + name: ETH, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100357 + name: Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://umbbd.ethz.ch/ + sampleId: c0001 + urlPattern: http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID={$id} + sampleId: c0001 + - created: 2019-06-11T14:16:43.224+0000 + deprecated: false + deprecationDate: + description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. + id: 814 + mirId: MIR:00000277 + modified: 2019-06-11T14:16:43.224+0000 + name: ABS + namespaceEmbeddedInLui: false + pattern: ^A\d+$ + prefix: abs + resources: + - deprecated: false + deprecationDate: + description: ABS at IMIM + id: 816 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 815 + location: + countryCode: ES + countryName: Spain + name: Institut Municipal d'Investigació Mèdica, Barcelona + rorId: + location: + countryCode: ES + countryName: Spain + mirId: MIR:00100358 + name: ABS at IMIM + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://genome.crg.es/datasets/abs2005/ + sampleId: A0014 + urlPattern: http://genome.crg.es/datasets/abs2005/entries/{$id}.html + sampleId: A0014 + - created: 2019-06-11T14:16:43.451+0000 + deprecated: false + deprecationDate: + description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. + id: 817 + mirId: MIR:00000278 + modified: 2019-06-11T14:16:43.451+0000 + name: APD + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: apd + resources: + - deprecated: false + deprecationDate: + description: APD at Nebraska + id: 819 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 818 + location: + countryCode: US + countryName: United States + name: Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100359 + name: APD at Nebraska + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://aps.unmc.edu/AP/ + sampleId: '01001' + urlPattern: http://aps.unmc.edu/AP/database/query_output.php?ID={$id} + sampleId: '01001' + - created: 2019-06-11T14:16:43.696+0000 + deprecated: false + deprecationDate: + description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. + id: 820 + mirId: MIR:00000279 + modified: 2019-06-11T14:16:43.696+0000 + name: ChemDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chemdb + resources: + - deprecated: false + deprecationDate: + description: ChemDB at UC Irvine + id: 822 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 821 + location: + countryCode: US + countryName: United States + name: University of California, Irvine + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100360 + name: ChemDB at UC Irvine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cdb.ics.uci.edu/ + sampleId: '3966782' + urlPattern: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id={$id} + sampleId: '3966782' + - created: 2019-06-11T14:16:43.916+0000 + deprecated: false + deprecationDate: + description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. + id: 823 + mirId: MIR:00000280 + modified: 2019-06-11T14:16:43.916+0000 + name: DPV + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dpv + resources: + - deprecated: false + deprecationDate: + description: DPV at Rothamsted + id: 825 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 824 + location: + countryCode: GB + countryName: United Kingdom + name: Plant-Pathogen Interactions Division, Wheat Pathogenesis Programme, Rothamsted Research Harpenden, Hertfordshire + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100361 + name: DPV at Rothamsted + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.dpvweb.net/ + sampleId: '100' + urlPattern: http://www.dpvweb.net/dpv/showdpv.php?dpvno={$id} + sampleId: '100' + - created: 2019-06-11T14:16:44.139+0000 + deprecated: false + deprecationDate: + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. + id: 826 + mirId: MIR:00000281 + modified: 2019-06-11T14:16:44.139+0000 + name: IUPHAR receptor + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.receptor + resources: + - deprecated: false + deprecationDate: + description: IUPHAR Receptor at University of Edinburgh + id: 828 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 827 + location: + countryCode: GB + countryName: United Kingdom + name: Centre for Cardiovascular Science, University of Edinburgh, Edinburgh + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100362 + name: IUPHAR Receptor at University of Edinburgh + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.guidetopharmacology.org/targets.jsp + sampleId: '101' + urlPattern: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId={$id} + sampleId: '101' + - created: 2019-06-11T14:16:44.374+0000 + deprecated: false + deprecationDate: + description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. + id: 829 + mirId: MIR:00000282 + modified: 2019-06-11T14:16:44.374+0000 + name: Aceview Worm + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9-]+$ + prefix: aceview.worm + resources: + - deprecated: false + deprecationDate: + description: AceView Worm at NCBI + id: 830 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100363 + name: AceView Worm at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm + sampleId: aap-1 + urlPattern: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l={$id} + sampleId: aap-1 + - created: 2019-06-11T14:16:45.469+0000 + deprecated: false + deprecationDate: + description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. + id: 842 + mirId: MIR:00000287 + modified: 2019-06-11T14:16:45.469+0000 + name: IMGT LIGM + namespaceEmbeddedInLui: false + pattern: ^M\d+$ + prefix: imgt.ligm + resources: + - deprecated: false + deprecationDate: + description: IMGT LIGM through DKFZ (SRS) + id: 844 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 843 + location: + countryCode: DE + countryName: Germany + name: DKFZ TP3, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100369 + name: IMGT LIGM through DKFZ (SRS) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://genius.embnet.dkfz-heidelberg.de/ + sampleId: M94112 + urlPattern: http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'{$id}'] + - deprecated: false + deprecationDate: + description: IMGT LIGM at CNRS + id: 846 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 845 + location: + countryCode: FR + countryName: France + name: CNRS, Montpellier University, Montpellier + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100428 + name: IMGT LIGM at CNRS + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.imgt.org/ + sampleId: M94112 + urlPattern: http://www.imgt.org/ligmdb/view?id={$id} + sampleId: M94112 + - created: 2019-06-11T14:16:45.846+0000 + deprecated: false + deprecationDate: + description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). + id: 847 + mirId: MIR:00000288 + modified: 2019-06-11T14:16:45.846+0000 + name: Worfdb + namespaceEmbeddedInLui: false + pattern: ^\w+(\.\d+)? + prefix: worfdb + resources: + - deprecated: false + deprecationDate: + description: Worm Orf DB at Harvard + id: 849 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 848 + location: + countryCode: US + countryName: United States + name: Center for Cancer Systems Biology, Harvard Medical School, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100370 + name: Worm Orf DB at Harvard + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://worfdb.dfci.harvard.edu/ + sampleId: T01B6.1 + urlPattern: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query={$id} + sampleId: T01B6.1 + - created: 2019-06-11T14:16:46.065+0000 + deprecated: false + deprecationDate: + description: NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. + id: 850 + mirId: MIR:00000289 + modified: 2019-06-11T14:16:46.065+0000 + name: NEXTDB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: nextdb + resources: + - deprecated: false + deprecationDate: + description: NEXTDB at Shizuoka + id: 852 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 851 + location: + countryCode: JP + countryName: Japan + name: National Institute of Genetics, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100371 + name: NEXTDB at Shizuoka + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://nematode.lab.nig.ac.jp/ + sampleId: 6b1 + urlPattern: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone={$id} + sampleId: 6b1 + - created: 2019-06-11T14:16:46.310+0000 + deprecated: false + deprecationDate: + description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean. + id: 853 + mirId: MIR:00000291 + modified: 2019-06-11T14:16:46.310+0000 + name: SoyBase + namespaceEmbeddedInLui: false + pattern: ^\w+(\-)?\w+(\-)?\w+$ + prefix: soybase + resources: + - deprecated: false + deprecationDate: + description: SoyBase at Iowa State University + id: 855 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 854 + location: + countryCode: US + countryName: United States + name: USDA-ARS-CICGRU, Iowa State University, Iowa + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100373 + name: SoyBase at Iowa State University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://soybase.org/ + sampleId: BARC-013845-01256 + urlPattern: http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term={$id} + sampleId: BARC-013845-01256 + - created: 2019-06-11T14:16:46.532+0000 + deprecated: false + deprecationDate: + description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. + id: 856 + mirId: MIR:00000292 + modified: 2019-06-11T14:16:46.532+0000 + name: HAMAP + namespaceEmbeddedInLui: false + pattern: ^MF_\d+$ + prefix: hamap + resources: + - deprecated: false + deprecationDate: + description: HAPMAP at Swiss Institute of Bioinformatics + id: 857 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100374 + name: HAPMAP at Swiss Institute of Bioinformatics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://hamap.expasy.org/ + sampleId: MF_01400 + urlPattern: https://hamap.expasy.org/unirule/{$id} + sampleId: MF_01400 + - created: 2019-06-11T14:16:46.721+0000 + deprecated: false + deprecationDate: + description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. + id: 858 + mirId: MIR:00000293 + modified: 2019-06-11T14:16:46.721+0000 + name: Rouge + namespaceEmbeddedInLui: false + pattern: ^m\w+$ + prefix: rouge + resources: + - deprecated: false + deprecationDate: + description: Rouge at Kazusa DNA Research Institute + id: 860 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 859 + location: + countryCode: JP + countryName: Japan + name: Kazusa DNA Research Institute, Chiba + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100375 + name: Rouge at Kazusa DNA Research Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.kazusa.or.jp/rouge/ + sampleId: mKIAA4200 + urlPattern: http://www.kazusa.or.jp/rouge/gfpage/{$id}/ + sampleId: mKIAA4200 + - created: 2019-06-11T14:16:46.944+0000 + deprecated: false + deprecationDate: + description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. + id: 861 + mirId: MIR:00000294 + modified: 2019-06-11T14:16:46.944+0000 + name: ArrayExpress Platform + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: arrayexpress.platform + resources: + - deprecated: false + deprecationDate: + description: ArrayExpress Platform at EBI + id: 862 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100376 + name: ArrayExpress Platform at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/arrayexpress/ + sampleId: A-GEOD-50 + urlPattern: https://www.ebi.ac.uk/arrayexpress/arrays/{$id} + sampleId: A-GEOD-50 + - created: 2019-06-11T14:16:47.138+0000 + deprecated: false + deprecationDate: + description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. + id: 863 + mirId: MIR:00000295 + modified: 2019-06-11T14:16:47.138+0000 + name: CGSC Strain + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cgsc + resources: + - deprecated: false + deprecationDate: + description: CGSC at Yale university + id: 865 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 864 + location: + countryCode: US + countryName: United States + name: Dept. of Molecular, Cellular, and Developmental Biology, Yale University, Conneticut + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100377 + name: CGSC at Yale university + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cgsc.biology.yale.edu/index.php + sampleId: '74' + urlPattern: http://cgsc.biology.yale.edu/Site.php?ID={$id} + sampleId: '74' + - created: 2019-06-11T14:16:47.375+0000 + deprecated: false + deprecationDate: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. + id: 866 + mirId: MIR:00000297 + modified: 2019-06-11T14:16:47.375+0000 + name: DragonDB DNA + namespaceEmbeddedInLui: false + pattern: ^\d\w+$ + prefix: dragondb.dna + resources: + - deprecated: false + deprecationDate: + description: DragonDB DNA at University of British Columbia + id: 868 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 867 + location: + countryCode: CA + countryName: Canada + name: University of British Columbia, Vancouver + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100379 + name: DragonDB DNA at University of British Columbia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.antirrhinum.net/ + sampleId: 3hB06 + urlPattern: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name={$id};class=DNA + sampleId: 3hB06 + - created: 2019-06-11T14:16:47.607+0000 + deprecated: false + deprecationDate: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. + id: 869 + mirId: MIR:00000298 + modified: 2019-06-11T14:16:47.607+0000 + name: DragonDB Protein + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.protein + resources: + - deprecated: false + deprecationDate: + description: DragonDB Protein at University of British Columbia + id: 870 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 867 + location: + countryCode: CA + countryName: Canada + name: University of British Columbia, Vancouver + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100380 + name: DragonDB Protein at University of British Columbia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.antirrhinum.net/ + sampleId: AMDEFA + urlPattern: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name={$id};class=Peptide + sampleId: AMDEFA + - created: 2019-06-11T14:16:47.798+0000 + deprecated: false + deprecationDate: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. + id: 871 + mirId: MIR:00000299 + modified: 2019-06-11T14:16:47.798+0000 + name: DragonDB Locus + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.locus + resources: + - deprecated: false + deprecationDate: + description: DragonDB Locus at University of British Columbia + id: 872 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 867 + location: + countryCode: CA + countryName: Canada + name: University of British Columbia, Vancouver + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100381 + name: DragonDB Locus at University of British Columbia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.antirrhinum.net/ + sampleId: DEF + urlPattern: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name={$id}&class=Locus + sampleId: DEF + - created: 2019-06-11T14:16:47.981+0000 + deprecated: false + deprecationDate: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. + id: 873 + mirId: MIR:00000300 + modified: 2019-06-11T14:16:47.981+0000 + name: DragonDB Allele + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.allele + resources: + - deprecated: false + deprecationDate: + description: DragonDB Allele at University of British Columbia + id: 874 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 867 + location: + countryCode: CA + countryName: Canada + name: University of British Columbia, Vancouver + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100382 + name: DragonDB Allele at University of British Columbia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.antirrhinum.net/ + sampleId: cho + urlPattern: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name={$id}&class=Allele + sampleId: cho + - created: 2019-06-11T14:16:48.189+0000 + deprecated: false + deprecationDate: + description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. + id: 875 + mirId: MIR:00000301 + modified: 2019-06-11T14:16:48.189+0000 + name: ISSN + namespaceEmbeddedInLui: false + pattern: ^\d{4}-\d{3}[\dX]$ + prefix: issn + resources: + - deprecated: false + deprecationDate: + description: ISSN at Library of Congress + id: 877 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 876 + location: + countryCode: US + countryName: United States + name: Library of Congress Online Catalogue, Washington DC + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100383 + name: ISSN at Library of Congress + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://catalog.loc.gov/webvoy.htm + sampleId: 0745-4570 + urlPattern: https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg={$id}&searchType=1&recCount=25 + - deprecated: false + deprecationDate: + description: ISSN Portal + id: 879 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 878 + location: + countryCode: FR + countryName: France + name: ISSN International Centre, Paris + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100924 + name: ISSN Portal + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://portal.issn.org + sampleId: 1776-3045 + urlPattern: https://portal.issn.org/resource/ISSN/{$id} + sampleId: 0745-4570 + - created: 2019-06-11T14:16:48.579+0000 + deprecated: false + deprecationDate: + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. + id: 880 + mirId: MIR:00000302 + modified: 2019-06-11T14:16:48.579+0000 + name: MEROPS Family + namespaceEmbeddedInLui: false + pattern: ^[SCTAGMNU]\d+$ + prefix: merops.family + resources: + - deprecated: false + deprecationDate: + description: Merops Family at Sanger Institute + id: 881 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 482 + location: + countryCode: GB + countryName: United Kingdom + name: Wellcome Trust Sanger Institute, Hinxton + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100384 + name: Merops Family at Sanger Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://merops.sanger.ac.uk/index.htm + sampleId: S1 + urlPattern: http://merops.sanger.ac.uk/cgi-bin/famsum?family={$id} + sampleId: S1 + - created: 2019-06-11T14:16:48.772+0000 + deprecated: false + deprecationDate: + description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. + id: 882 + mirId: MIR:00000303 + modified: 2019-06-11T14:16:48.772+0000 + name: MGED Ontology + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: mo + resources: + - deprecated: false + deprecationDate: + description: MGED Ontology at BioPortal + id: 883 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 571 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford University + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100385 + name: MGED Ontology at BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ + sampleId: ArrayGroup + urlPattern: http://purl.bioontology.org/ontology/MO/{$id} + - deprecated: false + deprecationDate: + description: MGED Ontology at SourceForge + id: 885 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 884 + location: + countryCode: GB + countryName: United Kingdom + name: (Ontology Working Group), European Bioinformatics Institute, Hinxton, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100568 + name: MGED Ontology at SourceForge + official: false + providerCode: ebi + resourceHomeUrl: https://mged.sourceforge.net/ontologies/MGEDontology.php + sampleId: ArrayGroup + urlPattern: https://mged.sourceforge.net/ontologies/MGEDontology.php#{$id} + sampleId: ArrayGroup + - created: 2019-06-11T14:16:49.131+0000 + deprecated: false + deprecationDate: + description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. + id: 886 + mirId: MIR:00000304 + modified: 2019-06-11T14:16:49.131+0000 + name: NASC code + namespaceEmbeddedInLui: false + pattern: ^(\w+)?\d+$ + prefix: nasc + resources: + - deprecated: false + deprecationDate: + description: NASC at University of Nottingham + id: 888 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 887 + location: + countryCode: GB + countryName: United Kingdom + name: The Nottingham Arabidopsis Stock Centre, University of Nottingham + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100386 + name: NASC at University of Nottingham + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://arabidopsis.info/ + sampleId: N1899 + urlPattern: http://arabidopsis.info/StockInfo?NASC_id={$id} + sampleId: N1899 + - created: 2019-06-11T14:16:49.376+0000 + deprecated: false + deprecationDate: + description: A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. + id: 889 + mirId: MIR:00000305 + modified: 2019-06-11T14:16:49.376+0000 + name: NIAEST + namespaceEmbeddedInLui: false + pattern: ^\w\d{4}\w\d{2}(\-[35])?$ + prefix: niaest + resources: + - deprecated: false + deprecationDate: + description: NIAEST at National Institute on Aging + id: 891 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 890 + location: + countryCode: US + countryName: United States + name: National Institute on Aging, NIH + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100387 + name: NIAEST at National Institute on Aging + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://lgsun.grc.nia.nih.gov/cDNA/ + sampleId: J0705A10 + urlPattern: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1={$id} + sampleId: J0705A10 + - created: 2019-06-11T14:16:49.605+0000 + deprecated: false + deprecationDate: + description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. + id: 892 + mirId: MIR:00000306 + modified: 2019-06-11T14:16:49.605+0000 + name: Pazar Transcription Factor + namespaceEmbeddedInLui: false + pattern: ^TF\w+$ + prefix: pazar + resources: + - deprecated: false + deprecationDate: + description: Pazar Transcription Factor at University of British Columbia + id: 894 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 893 + location: + countryCode: CA + countryName: Canada + name: Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100388 + name: Pazar Transcription Factor at University of British Columbia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pazar.info/ + sampleId: TF0001053 + urlPattern: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID={$id} + sampleId: TF0001053 + - created: 2019-06-11T14:16:49.830+0000 + deprecated: false + deprecationDate: + description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. + id: 895 + mirId: MIR:00000307 + modified: 2019-06-11T14:16:49.830+0000 + name: Plant Ontology + namespaceEmbeddedInLui: true + pattern: ^PO:\d+$ + prefix: po + resources: + - deprecated: false + deprecationDate: + description: Plant Ontology through Amigo + id: 897 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 896 + location: + countryCode: US + countryName: United States + name: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100389 + name: Plant Ontology through Amigo + official: false + providerCode: amigo + resourceHomeUrl: http://www.plantontology.org/ + sampleId: '0009089' + urlPattern: http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:{$id} + - deprecated: false + deprecationDate: + description: Plant Ontology through BioPortal + id: 898 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100390 + name: Plant Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/PO + sampleId: '0009089' + urlPattern: http://purl.bioontology.org/ontology/PO/PO:{$id} + - deprecated: false + deprecationDate: + description: Plant Ontology through OLS + id: 899 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100676 + name: Plant Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/po + sampleId: '0009089' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/po/terms?obo_id=PO:{$id} + sampleId: '0009089' + - created: 2019-06-11T14:16:50.326+0000 + deprecated: false + deprecationDate: + description: The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. + id: 900 + mirId: MIR:00000308 + modified: 2019-06-11T14:16:50.326+0000 + name: RNA Modification Database + namespaceEmbeddedInLui: false + pattern: ^\d{3}$ + prefix: rnamods + resources: + - deprecated: false + deprecationDate: + description: RNA Modification Database at University of Utah + id: 902 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 901 + location: + countryCode: US + countryName: United States + name: Department of Medicinal Chemistry and Department of Biochemistry, University of Utah, Salt Lake City, Utah + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100391 + name: RNA Modification Database at University of Utah + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm + sampleId: '101' + urlPattern: http://mods.rna.albany.edu/mods/modifications/view/{$id} + sampleId: '101' + - created: 2019-06-11T14:16:50.556+0000 + deprecated: false + deprecationDate: + description: TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. + id: 903 + mirId: MIR:00000312 + modified: 2019-06-11T14:16:50.556+0000 + name: TreeBASE + namespaceEmbeddedInLui: false + pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$ + prefix: treebase + resources: + - deprecated: false + deprecationDate: + description: TreeBASE (hosted at National Evolutionary Synthesis Center) + id: 905 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 904 + location: + countryCode: US + countryName: United States + name: Phyloinformatics Research Foundation, Durham, North Carolina + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100395 + name: TreeBASE (hosted at National Evolutionary Synthesis Center) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://treebase.org/ + sampleId: TB2:S1000 + urlPattern: http://purl.org/phylo/treebase/phylows/study/{$id}?format=html + sampleId: TB2:S1000 + - created: 2019-06-11T14:17:18.559+0000 + deprecated: false + deprecationDate: + description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. + id: 1235 + mirId: MIR:00000430 + modified: 2019-06-11T14:17:18.559+0000 + name: Cell Signaling Technology Antibody + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cst.ab + resources: + - deprecated: false + deprecationDate: + description: CST Antibody at Cell Signaling Technology + id: 1236 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1233 + location: + countryCode: US + countryName: United States + name: Cell Signaling Technology, Inc., Danvers, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100553 + name: CST Antibody at Cell Signaling Technology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cellsignal.com/catalog/index.html + sampleId: '3305' + urlPattern: http://www.cellsignal.com/products/{$id}.html + sampleId: '3305' + - created: 2019-06-11T14:16:50.779+0000 + deprecated: false + deprecationDate: + description: The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. + id: 906 + mirId: MIR:00000313 + modified: 2019-06-11T14:16:50.779+0000 + name: Tetrahymena Genome Database + namespaceEmbeddedInLui: false + pattern: ^TTHERM\_\d+$ + prefix: tgd + resources: + - deprecated: false + deprecationDate: + description: TGD at Stanford University + id: 907 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 298 + location: + countryCode: US + countryName: United States + name: Department of Genetics, School of Medicine, Stanford University, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100396 + name: TGD at Stanford University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ciliate.org/index.php/ + sampleId: TTHERM_00648910 + urlPattern: http://ciliate.org/index.php/feature/details/{$id} + sampleId: TTHERM_00648910 + - created: 2019-06-11T14:16:50.975+0000 + deprecated: false + deprecationDate: + description: TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. + id: 908 + mirId: MIR:00000315 + modified: 2019-06-11T14:16:50.975+0000 + name: TIGRFAMS + namespaceEmbeddedInLui: false + pattern: ^TIGR\d+$ + prefix: tigrfam + resources: + - deprecated: false + deprecationDate: + description: TIGRFAM at JCVI + id: 910 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 909 + location: + countryCode: US + countryName: United States + name: The Institute for Genomic Research, Rockville, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100398 + name: TIGRFAM at JCVI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi + sampleId: TIGR00010 + urlPattern: http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc={$id} + sampleId: TIGR00010 + - created: 2019-06-11T14:16:51.241+0000 + deprecated: false + deprecationDate: + description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. + id: 911 + mirId: MIR:00000316 + modified: 2019-06-11T14:16:51.241+0000 + name: Animal TFDB Family + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: atfdb.family + resources: + - deprecated: false + deprecationDate: + description: Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory + id: 913 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 912 + location: + countryCode: CN + countryName: China + name: Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100399 + name: Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.bioguo.org/AnimalTFDB/family_index.php + sampleId: CUT + urlPattern: http://www.bioguo.org/AnimalTFDB/family.php?fam={$id} + sampleId: CUT + - created: 2019-06-11T14:16:51.481+0000 + deprecated: false + deprecationDate: + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. + id: 914 + mirId: MIR:00000317 + modified: 2019-06-11T14:16:51.481+0000 + name: IUPHAR family + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.family + resources: + - deprecated: false + deprecationDate: + description: The IUPHAR/BPS Guide to PHARMACOLOGY + id: 916 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 915 + location: + countryCode: GB + countryName: United Kingdom + name: International Union of Pharmacology, Edinburgh + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100708 + name: The IUPHAR/BPS Guide to PHARMACOLOGY + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.guidetopharmacology.org/ + sampleId: '78' + urlPattern: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId={$id} + sampleId: '78' + - created: 2019-06-11T14:16:51.708+0000 + deprecated: false + deprecationDate: + description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. + id: 917 + mirId: MIR:00000318 + modified: 2019-06-11T14:16:51.708+0000 + name: DBG2 Introns + namespaceEmbeddedInLui: false + pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ + prefix: dbg2introns + resources: + - deprecated: false + deprecationDate: + description: Bacterial Group II Introns at University of Calgary + id: 919 + institution: + description: The University of Calgary is one of Canada’s top comprehensive research universities, combining the best of university tradition with the city of Calgary’s vibrant energy and diversity. + homeUrl: https://www.ucalgary.ca/ + id: 568 + location: + countryCode: CA + countryName: Canada + name: University of Calgary + rorId: https://ror.org/03yjb2x39 + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100401 + name: Bacterial Group II Introns at University of Calgary + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://webapps2.ucalgary.ca/~groupii/ + sampleId: Cu.me.I1 + urlPattern: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name={$id} + sampleId: Cu.me.I1 + - created: 2019-06-11T14:16:51.940+0000 + deprecated: false + deprecationDate: + description: The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. + id: 920 + mirId: MIR:00000319 + modified: 2019-06-11T14:16:51.940+0000 + name: Spectral Database for Organic Compounds + namespaceEmbeddedInLui: false + pattern: \d+$ + prefix: sdbs + resources: + - deprecated: false + deprecationDate: + description: SDBS at AIST + id: 922 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 921 + location: + countryCode: JP + countryName: Japan + name: National Institute of Advanced Industrial Science and Technology (AIST) + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100402 + name: SDBS at AIST + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi + sampleId: '4544' + urlPattern: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno={$id} + sampleId: '4544' + - created: 2019-06-11T14:16:52.167+0000 + deprecated: false + deprecationDate: + description: The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. + id: 923 + mirId: MIR:00000320 + modified: 2019-06-11T14:16:52.167+0000 + name: Vbase2 + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vbase2 + resources: + - deprecated: false + deprecationDate: + description: Vbase2 at German Research Centre for Biotechnology + id: 925 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 924 + location: + countryCode: DE + countryName: Germany + name: Department of Experimental Immunology, German Research Centre for Biotechnology, Braunschweig + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100403 + name: Vbase2 at German Research Centre for Biotechnology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.vbase2.org/vbase2.php + sampleId: humIGHV025 + urlPattern: http://www.vbase2.org/vgene.php?id={$id} + sampleId: humIGHV025 + - created: 2019-06-11T14:16:52.396+0000 + deprecated: false + deprecationDate: + description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. + id: 926 + mirId: MIR:00000321 + modified: 2019-06-11T14:16:52.396+0000 + name: SPIKE Map + namespaceEmbeddedInLui: false + pattern: ^spike\d{5}$ + prefix: spike.map + resources: + - deprecated: false + deprecationDate: + description: SPIKE database at Tel Aviv University + id: 928 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 927 + location: + countryCode: IL + countryName: Israel + name: School of Computer Sciences and School of Medicine, Tel Aviv University + rorId: + location: + countryCode: IL + countryName: Israel + mirId: MIR:00100404 + name: SPIKE database at Tel Aviv University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cs.tau.ac.il/~spike/ + sampleId: spike00001 + urlPattern: http://www.cs.tau.ac.il/~spike/maps/{$id}.html + sampleId: spike00001 + - created: 2019-06-11T14:16:52.640+0000 + deprecated: false + deprecationDate: + description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. + id: 929 + mirId: MIR:00000322 + modified: 2019-06-11T14:16:52.640+0000 + name: METLIN + namespaceEmbeddedInLui: false + pattern: ^\d{4}$ + prefix: metlin + resources: + - deprecated: false + deprecationDate: + description: METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry, La Jolla + id: 931 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 930 + location: + countryCode: US + countryName: United States + name: Scripps Research Institute, San Diego + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100406 + name: METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry, La Jolla + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://masspec.scripps.edu/ + sampleId: '1455' + urlPattern: http://metlin.scripps.edu/metabo_info.php?molid={$id} + sampleId: '1455' + - created: 2019-06-11T14:16:52.858+0000 + deprecated: false + deprecationDate: + description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. + id: 932 + mirId: MIR:00000323 + modified: 2019-06-11T14:16:52.858+0000 + name: GeneCards + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+(\@)?$ + prefix: genecards + resources: + - deprecated: false + deprecationDate: + description: GeneCards at Weizmann Institute + id: 934 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 933 + location: + countryCode: IL + countryName: Israel + name: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot + rorId: + location: + countryCode: IL + countryName: Israel + mirId: MIR:00100407 + name: GeneCards at Weizmann Institute + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genecards.org/ + sampleId: ABL1 + urlPattern: https://www.genecards.org/cgi-bin/carddisp.pl?gene={$id} + sampleId: ABL1 + - created: 2019-06-11T14:16:53.082+0000 + deprecated: false + deprecationDate: + description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. + id: 935 + mirId: MIR:00000324 + modified: 2019-06-11T14:16:53.082+0000 + name: MMRRC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mmrrc + resources: + - deprecated: false + deprecationDate: + description: MMRRC at University of North Carolina + id: 937 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 936 + location: + countryCode: US + countryName: United States + name: University of North Carolina + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100414 + name: MMRRC at University of North Carolina + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mmrrc.org/ + sampleId: '70' + urlPattern: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id={$id} + sampleId: '70' + - created: 2019-06-11T14:16:53.335+0000 + deprecated: false + deprecationDate: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. + id: 938 + mirId: MIR:00000325 + modified: 2019-06-11T14:16:53.335+0000 + name: UM-BBD Reaction + namespaceEmbeddedInLui: false + pattern: ^r\d+$ + prefix: umbbd.reaction + resources: + - deprecated: false + deprecationDate: + description: Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich + id: 939 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 812 + location: + countryCode: CH + countryName: Switzerland + name: ETH, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100416 + name: Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://umbbd.ethz.ch/ + sampleId: r0001 + urlPattern: http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID={$id} + sampleId: r0001 + - created: 2019-06-11T14:16:53.546+0000 + deprecated: false + deprecationDate: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information. + id: 940 + mirId: MIR:00000326 + modified: 2019-06-11T14:16:53.546+0000 + name: UM-BBD Enzyme + namespaceEmbeddedInLui: false + pattern: ^e\d+$ + prefix: umbbd.enzyme + resources: + - deprecated: false + deprecationDate: + description: Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich + id: 941 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 812 + location: + countryCode: CH + countryName: Switzerland + name: ETH, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100418 + name: Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://umbbd.ethz.ch/ + sampleId: e0333 + urlPattern: http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID={$id} + sampleId: e0333 + - created: 2019-06-11T14:16:53.741+0000 + deprecated: false + deprecationDate: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information. + id: 942 + mirId: MIR:00000327 + modified: 2019-06-11T14:16:53.741+0000 + name: UM-BBD Pathway + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: umbbd.pathway + resources: + - deprecated: false + deprecationDate: + description: Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich + id: 943 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 812 + location: + countryCode: CH + countryName: Switzerland + name: ETH, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100420 + name: Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://umbbd.ethz.ch/ + sampleId: ala + urlPattern: http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr={$id} + sampleId: ala + - created: 2019-06-11T14:16:53.927+0000 + deprecated: false + deprecationDate: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules. + id: 944 + mirId: MIR:00000328 + modified: 2019-06-11T14:16:53.927+0000 + name: UM-BBD Biotransformation Rule + namespaceEmbeddedInLui: false + pattern: ^bt\d+$ + prefix: umbbd.rule + resources: + - deprecated: false + deprecationDate: + description: Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at ETH Zurich + id: 945 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 812 + location: + countryCode: CH + countryName: Switzerland + name: ETH, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100421 + name: Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at ETH Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules + sampleId: bt0001 + urlPattern: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule={$id} + sampleId: bt0001 + - created: 2019-06-11T14:16:54.147+0000 + deprecated: false + deprecationDate: + description: mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. + id: 946 + mirId: MIR:00000329 + modified: 2019-06-11T14:16:54.147+0000 + name: mirEX + namespaceEmbeddedInLui: false + pattern: ^\d+(\w+)?$ + prefix: mirex + resources: + - deprecated: false + deprecationDate: + description: mirEX at Adam Mickiewicz University + id: 947 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 731 + location: + countryCode: PL + countryName: Poland + name: Institute of Molecular Biology, Adam Mickiewicz University, Poznan + rorId: + location: + countryCode: PL + countryName: Poland + mirId: MIR:00100423 + name: mirEX at Adam Mickiewicz University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://comgen.pl/mirex/?page=home + sampleId: 165a + urlPattern: http://comgen.pl/mirex1/?page=results/record&name={$id}&exref=pp2a&limit=yes + sampleId: 165a + - created: 2019-06-11T14:16:54.345+0000 + deprecated: false + deprecationDate: + description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. + id: 948 + mirId: MIR:00000330 + modified: 2019-06-11T14:16:54.345+0000 + name: Dictybase EST + namespaceEmbeddedInLui: false + pattern: ^DDB\d+$ + prefix: dictybase.est + resources: + - deprecated: false + deprecationDate: + description: Dictybase Gene at Northwestern University + id: 949 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 840 + location: + countryCode: US + countryName: United States + name: Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100424 + name: Dictybase Gene at Northwestern University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://dictybase.org/ + sampleId: DDB0016567 + urlPattern: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id={$id} + sampleId: DDB0016567 + - created: 2019-06-11T14:18:08.223+0000 + deprecated: false + deprecationDate: + description: MobiDB is a database of protein disorder and mobility annotations. + id: 1768 + mirId: MIR:00000637 + modified: 2019-06-11T14:18:08.223+0000 + name: MobiDB + namespaceEmbeddedInLui: false + pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ + prefix: mobidb + resources: + - deprecated: false + deprecationDate: + description: MobiDB + id: 1770 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1769 + location: + countryCode: IT + countryName: Italy + name: University of Padua + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00100842 + name: MobiDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://mobidb.bio.unipd.it + sampleId: P10636 + urlPattern: http://mobidb.bio.unipd.it/{$id} + sampleId: P10636 + - created: 2019-06-11T14:16:54.535+0000 + deprecated: false + deprecationDate: + description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. + id: 950 + mirId: MIR:00000331 + modified: 2019-06-11T14:16:54.535+0000 + name: IMGT HLA + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9*:]+$ + prefix: imgt.hla + resources: + - deprecated: false + deprecationDate: + description: IMGT HLA at EBI + id: 951 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100425 + name: IMGT HLA at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/imgt/hla/allele.html + sampleId: A*01:01:01:01 + urlPattern: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?{$id} + sampleId: A*01:01:01:01 + - created: 2019-06-11T14:16:54.741+0000 + deprecated: false + deprecationDate: + description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. + id: 952 + mirId: MIR:00000332 + modified: 2019-06-11T14:16:54.741+0000 + name: Bloomington Drosophila Stock Center + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bdsc + resources: + - deprecated: false + deprecationDate: + description: BDSC at Indiana University + id: 954 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 953 + location: + countryCode: US + countryName: United States + name: Department of Biology, Indiana University, Bloomington + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100426 + name: BDSC at Indiana University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://bdsc.indiana.edu/about/mission.html + sampleId: '33607' + urlPattern: https://bdsc.indiana.edu/stocks/{$id} + sampleId: '33607' + - created: 2019-06-11T14:16:54.970+0000 + deprecated: false + deprecationDate: + description: The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. + id: 955 + mirId: MIR:00000333 + modified: 2019-06-11T14:16:54.970+0000 + name: OPM + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: opm + resources: + - deprecated: false + deprecationDate: + description: OPM at University of Michigan + id: 957 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 956 + location: + countryCode: US + countryName: United States + name: Department of Medicinal Chemistry, College of Pharmacy, University of Michigan + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100427 + name: OPM at University of Michigan + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://opm.phar.umich.edu/ + sampleId: 1h68 + urlPattern: http://opm.phar.umich.edu/protein.php?pdbid={$id} + sampleId: 1h68 + - created: 2019-06-11T14:16:55.214+0000 + deprecated: false + deprecationDate: + description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. + id: 958 + mirId: MIR:00000334 + modified: 2019-06-11T14:16:55.214+0000 + name: Allergome + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: allergome + resources: + - deprecated: false + deprecationDate: + description: Allergome at Rome + id: 960 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 959 + location: + countryCode: IT + countryName: Italy + name: Center for Clinical and Experimental Allergology, Rome + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00100429 + name: Allergome at Rome + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.allergome.org/ + sampleId: '1948' + urlPattern: http://www.allergome.org/script/dettaglio.php?id_molecule={$id} + sampleId: '1948' + - created: 2019-06-11T14:16:55.438+0000 + deprecated: false + deprecationDate: + description: PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. + id: 961 + mirId: MIR:00000335 + modified: 2019-06-11T14:16:55.438+0000 + name: PomBase + namespaceEmbeddedInLui: false + pattern: ^S\w+(\.)?\w+(\.)?$ + prefix: pombase + resources: + - deprecated: false + deprecationDate: + description: PomBase at University of Cambridge + id: 963 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 962 + location: + countryCode: GB + countryName: United Kingdom + name: Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100430 + name: PomBase at University of Cambridge + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pombase.org/ + sampleId: SPCC13B11.01 + urlPattern: http://www.pombase.org/spombe/result/{$id} + sampleId: SPCC13B11.01 + - created: 2019-06-11T14:16:55.662+0000 + deprecated: false + deprecationDate: + description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. + id: 964 + mirId: MIR:00000336 + modified: 2019-06-11T14:16:55.662+0000 + name: HPA + namespaceEmbeddedInLui: false + pattern: ^ENSG\d{11}$ + prefix: hpa + resources: + - deprecated: false + deprecationDate: + description: Human Protein Atlas at AlbaNova University + id: 966 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 965 + location: + countryCode: SE + countryName: Sweden + name: Department of Proteomics, School of Biotechnology, AlbaNova University Center, Stockholm + rorId: + location: + countryCode: SE + countryName: Sweden + mirId: MIR:00100431 + name: Human Protein Atlas at AlbaNova University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.proteinatlas.org/ + sampleId: ENSG00000026508 + urlPattern: http://www.proteinatlas.org/{$id} + sampleId: ENSG00000026508 + - created: 2019-06-11T14:16:55.877+0000 + deprecated: false + deprecationDate: + description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. + id: 967 + mirId: MIR:00000337 + modified: 2019-06-11T14:16:55.877+0000 + name: JAX Mice + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jaxmice + resources: + - deprecated: false + deprecationDate: + description: JAX Mice at Jackson Laboratory + id: 969 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 968 + location: + countryCode: US + countryName: United States + name: The Jackson Laboratory, Sacremento, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100432 + name: JAX Mice at Jackson Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://jaxmice.jax.org/ + sampleId: '005012' + urlPattern: http://jaxmice.jax.org/strain/{$id}.html + sampleId: '005012' + - created: 2019-06-11T14:16:56.122+0000 + deprecated: false + deprecationDate: + description: NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. + id: 970 + mirId: MIR:00000338 + modified: 2019-06-11T14:16:56.122+0000 + name: uBio NameBank + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ubio.namebank + resources: + - deprecated: false + deprecationDate: + description: uBio NameBank at The Marine Biological Laboratory + id: 972 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 971 + location: + countryCode: US + countryName: United States + name: Marine Biological Laboratory, Woods Hole, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100433 + name: uBio NameBank at The Marine Biological Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ubio.org + sampleId: '2555646' + urlPattern: http://www.ubio.org/browser/details.php?namebankID={$id} + sampleId: '2555646' + - created: 2019-06-11T14:16:56.366+0000 + deprecated: false + deprecationDate: + description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. + id: 973 + mirId: MIR:00000339 + modified: 2019-06-11T14:16:56.366+0000 + name: YeTFasCo + namespaceEmbeddedInLui: false + pattern: ^\w+\_\d+(\.\d+)?$ + prefix: yetfasco + resources: + - deprecated: false + deprecationDate: + description: YeTFasCo at University of Toronto + id: 975 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 974 + location: + countryCode: CA + countryName: Canada + name: Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100434 + name: YeTFasCo at University of Toronto + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://yetfasco.ccbr.utoronto.ca/ + sampleId: YOR172W_571.0 + urlPattern: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot={$id} + sampleId: YOR172W_571.0 + - created: 2019-06-11T14:16:56.599+0000 + deprecated: false + deprecationDate: + description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. + id: 976 + mirId: MIR:00000340 + modified: 2019-06-11T14:16:56.599+0000 + name: TarBase + namespaceEmbeddedInLui: false + pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)? + prefix: tarbase + resources: + - deprecated: false + deprecationDate: + description: TarBase v7 at University of Thessaly + id: 978 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 977 + location: + countryCode: GR + countryName: Greece + name: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly + rorId: + location: + countryCode: GR + countryName: Greece + mirId: MIR:00100713 + name: TarBase v7 at University of Thessaly + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index + sampleId: hsa-let-7a-2-3p + urlPattern: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas={$id} + sampleId: hsa-let-7a-2-3p + - created: 2019-06-11T14:16:56.827+0000 + deprecated: false + deprecationDate: + description: CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. + id: 979 + mirId: MIR:00000341 + modified: 2019-06-11T14:16:56.827+0000 + name: CharProt + namespaceEmbeddedInLui: false + pattern: ^CH_\d+$ + prefix: charprot + resources: + - deprecated: false + deprecationDate: + description: CharProt at JCVI + id: 981 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 980 + location: + countryCode: US + countryName: United States + name: J Craig Venter institute, Rockville, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100436 + name: CharProt at JCVI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.jcvi.org/charprotdb + sampleId: CH_001923 + urlPattern: http://www.jcvi.org/charprotdb/index.cgi/view/{$id} + sampleId: CH_001923 + - created: 2019-06-11T14:16:57.058+0000 + deprecated: false + deprecationDate: + description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. + id: 982 + mirId: MIR:00000342 + modified: 2019-06-11T14:16:57.058+0000 + name: OMA Protein + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]{5}\d+$ + prefix: oma.protein + resources: + - deprecated: false + deprecationDate: + description: OMA Protein through OMA browser at ETH Zurich + id: 984 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 983 + location: + countryCode: CH + countryName: Switzerland + name: ETH Zurich, Computer Science, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100437 + name: OMA Protein through OMA browser at ETH Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://omabrowser.org/cgi-bin/gateway.pl + sampleId: HUMAN16963 + urlPattern: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1={$id} + sampleId: HUMAN16963 + - created: 2019-06-11T14:16:57.285+0000 + deprecated: false + deprecationDate: + description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. + id: 985 + mirId: MIR:00000343 + modified: 2019-06-11T14:16:57.285+0000 + name: OMA Group + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+$ + prefix: oma.grp + resources: + - deprecated: false + deprecationDate: + description: OMA Group through OMA browser at ETH Zurich + id: 986 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 983 + location: + countryCode: CH + countryName: Switzerland + name: ETH Zurich, Computer Science, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100438 + name: OMA Group through OMA browser at ETH Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://omabrowser.org/cgi-bin/gateway.pl + sampleId: LCSCCPN + urlPattern: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1={$id} + sampleId: LCSCCPN + - created: 2019-06-11T14:16:57.477+0000 + deprecated: false + deprecationDate: + description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. + id: 987 + mirId: MIR:00000344 + modified: 2019-06-11T14:16:57.477+0000 + name: NCBI Protein + namespaceEmbeddedInLui: false + pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$ + prefix: ncbiprotein + resources: + - deprecated: false + deprecationDate: + description: NCBI Protein at NCBI + id: 988 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100439 + name: NCBI Protein at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/protein + sampleId: CAA71118.1 + urlPattern: https://www.ncbi.nlm.nih.gov/protein/{$id} + sampleId: CAA71118.1 + - created: 2019-06-11T14:16:57.671+0000 + deprecated: false + deprecationDate: + description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. + id: 989 + mirId: MIR:00000345 + modified: 2019-06-11T14:16:57.671+0000 + name: GenPept + namespaceEmbeddedInLui: false + pattern: ^\w{3}\d{5}(\.\d+)?$ + prefix: genpept + resources: + - deprecated: false + deprecationDate: + description: GenPept at NCBI + id: 990 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100440 + name: GenPept at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/protein + sampleId: CAA71118.1 + urlPattern: https://www.ncbi.nlm.nih.gov/protein/{$id}?report=genpept + sampleId: CAA71118.1 + - created: 2019-06-11T14:16:57.856+0000 + deprecated: false + deprecationDate: + description: A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + id: 991 + mirId: MIR:00000346 + modified: 2019-06-11T14:16:57.856+0000 + name: UniGene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unigene + resources: + - deprecated: false + deprecationDate: + description: UniGene at NCBI + id: 993 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100441 + name: UniGene at NCBI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ncbi.nlm.nih.gov/unigene + sampleId: '4900' + urlPattern: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID={$id} + sampleId: '4900' + - created: 2019-06-11T14:16:58.089+0000 + deprecated: false + deprecationDate: + description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. + id: 994 + mirId: MIR:00000347 + modified: 2019-06-11T14:16:58.089+0000 + name: BitterDB Receptor + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bitterdb.rec + resources: + - deprecated: false + deprecationDate: + description: BitterDB Receptor at The Hebrew University of Jerusalem + id: 996 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 995 + location: + countryCode: IL + countryName: Israel + name: The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot + rorId: + location: + countryCode: IL + countryName: Israel + mirId: MIR:00100442 + name: BitterDB Receptor at The Hebrew University of Jerusalem + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bitterdb.agri.huji.ac.il/dbbitter.php + sampleId: '1' + urlPattern: http://bitterdb.agri.huji.ac.il/Receptor.php?id={$id} + sampleId: '1' + - created: 2019-06-11T14:16:58.347+0000 + deprecated: false + deprecationDate: + description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. + id: 997 + mirId: MIR:00000348 + modified: 2019-06-11T14:16:58.347+0000 + name: BitterDB Compound + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bitterdb.cpd + resources: + - deprecated: false + deprecationDate: + description: BitterDB Compound at The Hebrew University of Jerusalem + id: 998 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 995 + location: + countryCode: IL + countryName: Israel + name: The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot + rorId: + location: + countryCode: IL + countryName: Israel + mirId: MIR:00100443 + name: BitterDB Compound at The Hebrew University of Jerusalem + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bitterdb.agri.huji.ac.il/dbbitter.php + sampleId: '46' + urlPattern: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id={$id} + sampleId: '46' + - created: 2019-06-11T14:16:58.543+0000 + deprecated: false + deprecationDate: + description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. + id: 999 + mirId: MIR:00000349 + modified: 2019-06-11T14:16:58.543+0000 + name: BioProject + namespaceEmbeddedInLui: false + pattern: ^PRJ[DEN][A-Z]\d+$ + prefix: bioproject + resources: + - deprecated: false + deprecationDate: + description: BioProject at DNA Data Bank of Japan + id: 1001 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1000 + location: + countryCode: JP + countryName: Japan + name: DNA Data Bank of Japan, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100444 + name: BioProject at DNA Data Bank of Japan + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://trace.ddbj.nig.ac.jp/bioproject/ + sampleId: PRJDB3 + urlPattern: http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc={$id} + - deprecated: false + deprecationDate: + description: BioProject at NCBI + id: 1002 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100445 + name: BioProject at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/bioproject + sampleId: PRJDB3 + urlPattern: https://www.ncbi.nlm.nih.gov/bioproject?term={$id} + - deprecated: false + deprecationDate: + description: BioProject at European Nucleotide Archive (ENA) + id: 1003 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100446 + name: BioProject at European Nucleotide Archive (ENA) + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/ena/ + sampleId: PRJDB3 + urlPattern: https://www.ebi.ac.uk/ena/data/view/{$id} + sampleId: PRJDB3 + - created: 2019-06-11T14:16:59.017+0000 + deprecated: false + deprecationDate: + description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. + id: 1004 + mirId: MIR:00000350 + modified: 2019-06-11T14:16:59.017+0000 + name: BioSample + namespaceEmbeddedInLui: false + pattern: ^SAM[NED](\w)?\d+$ + prefix: biosample + resources: + - deprecated: false + deprecationDate: + description: BioSamples Database at EBI + id: 1005 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100447 + name: BioSamples Database at EBI + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/biosamples/ + sampleId: SAMEA2397676 + urlPattern: https://www.ebi.ac.uk/biosamples/sample/{$id} + - deprecated: false + deprecationDate: + description: BioSample at NCBI + id: 1006 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100706 + name: BioSample at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: http://www.ncbi.nlm.nih.gov/biosample + sampleId: SAMN00000002 + urlPattern: http://www.ncbi.nlm.nih.gov/biosample?term={$id} + - deprecated: false + deprecationDate: + description: BioSample at DNA Data Bank of Japan + id: 1008 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1007 + location: + countryCode: JP + countryName: Japan + name: Institution DNA Data Bank of Japan, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100707 + name: BioSample at DNA Data Bank of Japan + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://trace.ddbj.nig.ac.jp/biosample/ + sampleId: SAMD00005257 + urlPattern: http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc={$id} + sampleId: SAMEA2397676 + - created: 2019-06-11T14:16:59.494+0000 + deprecated: false + deprecationDate: + description: PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: 1009 + mirId: MIR:00000351 + modified: 2019-06-11T14:16:59.494+0000 + name: PiroplasmaDB + namespaceEmbeddedInLui: false + pattern: ^TA\d+$ + prefix: piroplasma + resources: + - deprecated: false + deprecationDate: + description: PiroplasmaBD at EuPathDB + id: 1011 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1010 + location: + countryCode: US + countryName: United States + name: Center for Tropical & Emerging Global Diseases, University of Georgia, Georgia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100448 + name: PiroplasmaBD at EuPathDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://piroplasmadb.org/ + sampleId: TA14985 + urlPattern: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id} + sampleId: TA14985 + - created: 2019-06-11T14:16:59.723+0000 + deprecated: false + deprecationDate: + description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. + id: 1012 + mirId: MIR:00000352 + modified: 2019-06-11T14:16:59.723+0000 + name: Unite + namespaceEmbeddedInLui: false + pattern: ^UDB\d{6}$ + prefix: unite + resources: + - deprecated: false + deprecationDate: + description: Unite at University of Tartu + id: 1014 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1013 + location: + countryCode: EE + countryName: Estonia + name: Institute of Botany, University of Tartu, Tartu + rorId: + location: + countryCode: EE + countryName: Estonia + mirId: MIR:00100449 + name: Unite at University of Tartu + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://unite.ut.ee/ + sampleId: UDB000691 + urlPattern: http://unite.ut.ee/bl_forw.php?nimi={$id} + sampleId: UDB000691 + - created: 2019-06-11T14:16:59.945+0000 + deprecated: false + deprecationDate: + description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. + id: 1015 + mirId: MIR:00000353 + modified: 2019-06-11T14:16:59.945+0000 + name: NCIm + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: ncim + resources: + - deprecated: false + deprecationDate: + description: NCIm at National Cancer Institue + id: 1016 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 442 + location: + countryCode: US + countryName: United States + name: National Cancer Institute, Center for Bioinformatics, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100450 + name: NCIm at National Cancer Institue + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ncim.nci.nih.gov/ + sampleId: C0026339 + urlPattern: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code={$id} + sampleId: C0026339 + - created: 2019-06-11T14:17:00.162+0000 + deprecated: false + deprecationDate: + description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. + id: 1017 + mirId: MIR:00000354 + modified: 2019-06-11T14:17:00.162+0000 + name: ProGlycProt + namespaceEmbeddedInLui: false + pattern: ^[A-Z]C\d{1,3}$ + prefix: proglyc + resources: + - deprecated: false + deprecationDate: + description: ProGlycProt at IMT + id: 1019 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1018 + location: + countryCode: IN + countryName: India + name: Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh + rorId: + location: + countryCode: IN + countryName: India + mirId: MIR:00100451 + name: ProGlycProt at IMT + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.proglycprot.org/ + sampleId: AC119 + urlPattern: http://www.proglycprot.org/detail.aspx?ProId={$id} + sampleId: AC119 + - created: 2019-06-11T14:17:00.403+0000 + deprecated: false + deprecationDate: + description: Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. + id: 1020 + mirId: MIR:00000355 + modified: 2019-06-11T14:17:00.403+0000 + name: PolBase + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9]+$ + prefix: polbase + resources: + - deprecated: false + deprecationDate: + description: PolBase at New England BioLabs + id: 1021 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 682 + location: + countryCode: US + countryName: United States + name: New England Biolabs, Ipswich, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100452 + name: PolBase at New England BioLabs + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://polbase.neb.com/ + sampleId: 19-T4 + urlPattern: https://polbase.neb.com/polymerases/{$id}#sequences + sampleId: 19-T4 + - created: 2019-06-11T14:17:00.593+0000 + deprecated: false + deprecationDate: + description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. + id: 1022 + mirId: MIR:00000356 + modified: 2019-06-11T14:17:00.593+0000 + name: NucleaRDB + namespaceEmbeddedInLui: false + pattern: ^\w+\_\w+$ + prefix: nuclearbd + resources: + - deprecated: false + deprecationDate: + description: NucleaRDB at Radboud University Nijmegen Medical Centre + id: 1024 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1023 + location: + countryCode: NL + countryName: Netherlands + name: CMBI, Radboud University Nijmegen Medical Centre, Dreijenplein, Wageningen + rorId: + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100453 + name: NucleaRDB at Radboud University Nijmegen Medical Centre + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.receptors.org/nucleardb/ + sampleId: prgr_human + urlPattern: http://www.receptors.org/nucleardb/proteins/{$id} + sampleId: prgr_human + - created: 2019-06-11T14:17:00.815+0000 + deprecated: false + deprecationDate: + description: SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. + id: 1025 + mirId: MIR:00000357 + modified: 2019-06-11T14:17:00.815+0000 + name: SUPFAM + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: supfam + resources: + - deprecated: false + deprecationDate: + description: SUPFAM at MRC and University of Bristol + id: 1027 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1026 + location: + countryCode: GB + countryName: United Kingdom + name: MRC Laboratory of Molecular Biology, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100454 + name: SUPFAM at MRC and University of Bristol + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://supfam.org/SUPERFAMILY/ + sampleId: SSF57615 + urlPattern: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid={$id} + sampleId: SSF57615 + - created: 2019-06-11T14:17:01.041+0000 + deprecated: false + deprecationDate: + description: The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. + id: 1028 + mirId: MIR:00000358 + modified: 2019-06-11T14:17:01.041+0000 + name: Rice Genome Annotation Project + namespaceEmbeddedInLui: false + pattern: ^LOC\_Os\d{1,2}g\d{5}$ + prefix: ricegap + resources: + - deprecated: false + deprecationDate: + description: Rice Genome Annotation Project at TIGR + id: 1029 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 909 + location: + countryCode: US + countryName: United States + name: The Institute for Genomic Research, Rockville, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100455 + name: Rice Genome Annotation Project at TIGR + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml + sampleId: LOC_Os02g13300 + urlPattern: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf={$id} + sampleId: LOC_Os02g13300 + - created: 2019-06-11T14:17:01.276+0000 + deprecated: false + deprecationDate: + description: Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. + id: 1030 + mirId: MIR:00000359 + modified: 2019-06-11T14:17:01.276+0000 + name: PINA + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: pina + resources: + - deprecated: false + deprecationDate: + description: Protein Interaction Network Analysis (PINA) at Garvan Institute + id: 1032 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1031 + location: + countryCode: AU + countryName: Australia + name: Garvan Institute of Medical Research, Sydney + rorId: + location: + countryCode: AU + countryName: Australia + mirId: MIR:00100456 + name: Protein Interaction Network Analysis (PINA) at Garvan Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cbg.garvan.unsw.edu.au/pina/ + sampleId: Q13485 + urlPattern: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac={$id}&showExtend=null + sampleId: Q13485 + - created: 2019-06-11T14:17:01.500+0000 + deprecated: false + deprecationDate: + description: The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified. + id: 1033 + mirId: MIR:00000360 + modified: 2019-06-11T14:17:01.500+0000 + name: Tissue List + namespaceEmbeddedInLui: false + pattern: ^TS-\d{4}$ + prefix: tissuelist + resources: + - deprecated: false + deprecationDate: + description: Tissue List at Swiss Institute of Bioinformatics + id: 1035 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100457 + name: Tissue List at Swiss Institute of Bioinformatics + official: false + providerCode: sib + resourceHomeUrl: https://www.uniprot.org/docs/tisslist.txt + sampleId: TS-0285 + urlPattern: https://www.uniprot.org/tissues/{$id} + sampleId: TS-0285 + - created: 2019-06-11T14:17:01.735+0000 + deprecated: false + deprecationDate: + description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. + id: 1036 + mirId: MIR:00000361 + modified: 2019-06-11T14:17:01.735+0000 + name: BacMap Biography + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bacmap.biog + resources: + - deprecated: false + deprecationDate: + description: BacMap Biography at University of Alberta + id: 1038 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1037 + location: + countryCode: CA + countryName: Canada + name: Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100459 + name: BacMap Biography at University of Alberta + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bacmap.wishartlab.com/ + sampleId: '1050' + urlPattern: http://bacmap.wishartlab.com/organisms/{$id} + sampleId: '1050' + - created: 2019-06-11T14:17:01.955+0000 + deprecated: false + deprecationDate: + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. + id: 1039 + mirId: MIR:00000362 + modified: 2019-06-11T14:17:01.955+0000 + name: HGNC Symbol + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+(\@)?$ + prefix: hgnc.symbol + resources: + - deprecated: false + deprecationDate: + description: HGNC Symbol at HUGO Genome Nomenclature Committee + id: 1040 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100460 + name: HGNC Symbol at HUGO Genome Nomenclature Committee + official: false + providerCode: ebi + resourceHomeUrl: https://www.genenames.org/ + sampleId: DAPK1 + urlPattern: https://www.genenames.org/cgi-bin/gene_symbol_report?match={$id} + sampleId: DAPK1 + - created: 2019-06-11T14:17:02.153+0000 + deprecated: false + deprecationDate: + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. + id: 1041 + mirId: MIR:00000363 + modified: 2019-06-11T14:17:02.153+0000 + name: PANTHER Pathway + namespaceEmbeddedInLui: false + pattern: ^P\d{5}$ + prefix: panther.pathway + resources: + - deprecated: false + deprecationDate: + description: PANTHER Pathway at USC (Los Angeles) + id: 1042 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 94 + location: + countryCode: US + countryName: United States + name: Keck School of Medicine, University of Southern California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100461 + name: PANTHER Pathway at USC (Los Angeles) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pantherdb.org/ + sampleId: P00024 + urlPattern: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession={$id} + sampleId: P00024 + - created: 2019-06-11T14:17:02.358+0000 + deprecated: false + deprecationDate: + description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. + id: 1043 + mirId: MIR:00000364 + modified: 2019-06-11T14:17:02.358+0000 + name: FAIRsharing + namespaceEmbeddedInLui: false + pattern: ^bsg-[dscp]?\d{6}$ + prefix: fairsharing + resources: + - deprecated: false + deprecationDate: + description: FAIRSharing at University of Oxford + id: 1045 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1044 + location: + countryCode: GB + countryName: United Kingdom + name: Oxford e-Research Centre, University of Oxford, Oxford + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100463 + name: FAIRSharing at University of Oxford + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://fairsharing.org/ + sampleId: bsg-000052 + urlPattern: https://fairsharing.org/{$id} + sampleId: bsg-000052 + - created: 2019-06-11T14:17:02.591+0000 + deprecated: false + deprecationDate: + description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. + id: 1046 + mirId: MIR:00000365 + modified: 2019-06-11T14:17:02.591+0000 + name: FungiDB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: fungidb + resources: + - deprecated: false + deprecationDate: + description: FungiDB at University of California + id: 1048 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1047 + location: + countryCode: US + countryName: United States + name: Department of Plant Pathology & Microbiology, University of California, Riverside, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100464 + name: FungiDB at University of California + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://fungidb.org/fungidb + sampleId: CNBG_0001 + urlPattern: https://fungidb.org/fungidb/app/record/gene/{$id} + sampleId: CNBG_0001 + - created: 2019-06-11T14:18:08.473+0000 + deprecated: false + deprecationDate: + description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images. + id: 1771 + mirId: MIR:00000638 + modified: 2019-06-11T14:18:08.473+0000 + name: NeuroVault Image + namespaceEmbeddedInLui: false + pattern: ^[1-9][0-9]*$ + prefix: neurovault.image + resources: + - deprecated: false + deprecationDate: + description: NeuroVault + id: 1772 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 98 + location: + countryCode: US + countryName: United States + name: Stanford University + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100843 + name: NeuroVault + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://neurovault.org + sampleId: '58788' + urlPattern: https://neurovault.org/images/{$id} + sampleId: '58788' + - created: 2019-06-11T14:17:02.814+0000 + deprecated: false + deprecationDate: + description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. + id: 1049 + mirId: MIR:00000366 + modified: 2019-06-11T14:17:02.814+0000 + name: DARC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: darc + resources: + - deprecated: false + deprecationDate: + description: DARC at University of Munich + id: 1051 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1050 + location: + countryCode: DE + countryName: Germany + name: Gene Center and Department for Biochemistry and Center for integrated Protein Science Munich, University of Munich, Munich + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100465 + name: DARC at University of Munich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://darcsite.genzentrum.lmu.de/darc/index.php + sampleId: '1250' + urlPattern: http://darcsite.genzentrum.lmu.de/darc/view.php?id={$id} + sampleId: '1250' + - created: 2019-06-11T14:17:03.033+0000 + deprecated: false + deprecationDate: + description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. + id: 1052 + mirId: MIR:00000367 + modified: 2019-06-11T14:17:03.033+0000 + name: DRSC + namespaceEmbeddedInLui: false + pattern: ^DRSC\d+$ + prefix: drsc + resources: + - deprecated: false + deprecationDate: + description: DRSC at Harvard Medical School + id: 1054 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1053 + location: + countryCode: US + countryName: United States + name: Department of Genetics, Harvard Medical School, Boston, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100466 + name: DRSC at Harvard Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://flyrnai.org/ + sampleId: DRSC05221 + urlPattern: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname={$id} + sampleId: DRSC05221 + - created: 2019-06-11T14:17:03.255+0000 + deprecated: false + deprecationDate: + description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. + id: 1055 + mirId: MIR:00000368 + modified: 2019-06-11T14:17:03.255+0000 + name: OriDB Schizosaccharomyces + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oridb.schizo + resources: + - deprecated: false + deprecationDate: + description: OriDB Schizosaccharomyces at University of Nottingham + id: 1057 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1056 + location: + countryCode: GB + countryName: United Kingdom + name: Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100467 + name: OriDB Schizosaccharomyces at University of Nottingham + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pombe.oridb.org/index.php + sampleId: '1' + urlPattern: http://pombe.oridb.org/details.php?id={$id} + sampleId: '1' + - created: 2019-06-11T14:17:03.475+0000 + deprecated: false + deprecationDate: + description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. + id: 1058 + mirId: MIR:00000369 + modified: 2019-06-11T14:17:03.475+0000 + name: OriDB Saccharomyces + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oridb.sacch + resources: + - deprecated: false + deprecationDate: + description: OriDB Saccharomyces at University of Nottingham + id: 1059 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1056 + location: + countryCode: GB + countryName: United Kingdom + name: Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100468 + name: OriDB Saccharomyces at University of Nottingham + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cerevisiae.oridb.org/index.php + sampleId: '1' + urlPattern: http://cerevisiae.oridb.org/details.php?id={$id} + sampleId: '1' + - created: 2019-06-11T14:17:03.650+0000 + deprecated: false + deprecationDate: + description: The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. + id: 1060 + mirId: MIR:00000370 + modified: 2019-06-11T14:17:03.650+0000 + name: PSCDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pscdb + resources: + - deprecated: false + deprecationDate: + description: PSCDB at Nagoya University + id: 1062 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1061 + location: + countryCode: JP + countryName: Japan + name: Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100469 + name: PSCDB at Nagoya University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html + sampleId: '051' + urlPattern: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/{$id}.html + sampleId: '051' + - created: 2019-06-11T14:17:03.870+0000 + deprecated: false + deprecationDate: + description: The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes. + id: 1063 + mirId: MIR:00000371 + modified: 2019-06-11T14:17:03.870+0000 + name: SCOP + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: scop + resources: + - deprecated: false + deprecationDate: + description: SCOP at MRC + id: 1065 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1064 + location: + countryCode: GB + countryName: United Kingdom + name: MRC Laboratory of Molecular Biology, Centre for Protein Engineering, Hills Road, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100470 + name: SCOP at MRC + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://scop.mrc-lmb.cam.ac.uk/scop/ + sampleId: '47419' + urlPattern: http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid={$id} + - deprecated: false + deprecationDate: + description: SCOP at Berkeley + id: 1067 + institution: + description: From a group of academic pioneers in 1868 to the Free Speech Movement in 1964, Berkeley is a place where the brightest minds from across the globe come together to explore, ask questions and improve the world. + homeUrl: https://www.berkeley.edu/ + id: 1066 + location: + countryCode: US + countryName: United States + name: University of California, Berkeley + rorId: https://ror.org/01an7q238 + location: + countryCode: US + countryName: United States + mirId: MIR:00100471 + name: SCOP at Berkeley + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://scop.berkeley.edu/ + sampleId: '47419' + urlPattern: http://scop.berkeley.edu/sunid={$id} + sampleId: '47419' + - created: 2019-06-11T14:17:04.223+0000 + deprecated: false + deprecationDate: + description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. + id: 1068 + mirId: MIR:00000372 + modified: 2019-06-11T14:17:04.223+0000 + name: ENA + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+(\.\d+)?$ + prefix: ena.embl + resources: + - deprecated: false + deprecationDate: + description: ENA through GenBank + id: 1070 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100889 + name: ENA through GenBank + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/Genbank/ + sampleId: BN000065 + urlPattern: https://www.ncbi.nlm.nih.gov/nuccore/{$id} + - deprecated: false + deprecationDate: + description: ENA at European Bioinformatics Institute + id: 1069 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100473 + name: ENA at European Bioinformatics Institute + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/ena/ + sampleId: BN000065 + urlPattern: https://www.ebi.ac.uk/ena/data/view/{$id} + sampleId: BN000065 + - created: 2019-06-11T14:17:04.514+0000 + deprecated: false + deprecationDate: + description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. + id: 1071 + mirId: MIR:00000373 + modified: 2019-06-11T14:17:04.514+0000 + name: DOMMINO + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: dommino + resources: + - deprecated: false + deprecationDate: + description: DOMMINO at University of Missouri + id: 1073 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1072 + location: + countryCode: US + countryName: United States + name: Informatics Institute and Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100474 + name: DOMMINO at University of Missouri + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://dommino.org/ + sampleId: 2GC4 + urlPattern: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/{$id} + sampleId: 2GC4 + - created: 2019-06-11T14:17:04.735+0000 + deprecated: false + deprecationDate: + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes. + id: 1074 + mirId: MIR:00000374 + modified: 2019-06-11T14:17:04.735+0000 + name: PANTHER Node + namespaceEmbeddedInLui: false + pattern: ^PTN\d{9}$ + prefix: panther.node + resources: + - deprecated: false + deprecationDate: + description: PANTHER Node at USC (Los Angeles) + id: 1075 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 94 + location: + countryCode: US + countryName: United States + name: Keck School of Medicine, University of Southern California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100475 + name: PANTHER Node at USC (Los Angeles) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pantree.org/ + sampleId: PTN000000026 + urlPattern: http://www.pantree.org/node/annotationNode.jsp?id={$id} + sampleId: PTN000000026 + - created: 2019-06-11T14:17:04.925+0000 + deprecated: false + deprecationDate: + description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. + id: 1076 + mirId: MIR:00000375 + modified: 2019-06-11T14:17:04.925+0000 + name: Consensus CDS + namespaceEmbeddedInLui: false + pattern: ^CCDS\d+\.\d+$ + prefix: ccds + resources: + - deprecated: false + deprecationDate: + description: Consensus CDS at NCBI + id: 1077 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100477 + name: Consensus CDS at NCBI + official: true + providerCode: ncbi + resourceHomeUrl: http://www.ncbi.nlm.nih.gov/CCDS/ + sampleId: CCDS13573.1 + urlPattern: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA={$id} + sampleId: CCDS13573.1 + - created: 2019-06-11T14:17:05.741+0000 + deprecated: false + deprecationDate: + description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. + id: 1086 + mirId: MIR:00000377 + modified: 2019-06-11T14:17:05.741+0000 + name: HPRD + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hprd + resources: + - deprecated: false + deprecationDate: + description: Human Protein Reference Database + id: 1088 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1087 + location: + countryCode: IN + countryName: India + name: Institute of Bioinformatics, International Tech Park, Bangalore + rorId: + location: + countryCode: IN + countryName: India + mirId: MIR:00100479 + name: Human Protein Reference Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.hprd.org/ + sampleId: '00001' + urlPattern: http://www.hprd.org/protein/{$id} + sampleId: '00001' + - created: 2019-06-11T14:17:05.964+0000 + deprecated: false + deprecationDate: + description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. + id: 1089 + mirId: MIR:00000378 + modified: 2019-06-11T14:17:05.964+0000 + name: GXA Gene + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gxa.gene + resources: + - deprecated: false + deprecationDate: + description: GXA Gene at EBI + id: 1090 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100482 + name: GXA Gene at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/gxa/ + sampleId: AT4G01080 + urlPattern: https://www.ebi.ac.uk/gxa/genes/{$id} + sampleId: AT4G01080 + - created: 2019-06-11T14:17:06.163+0000 + deprecated: false + deprecationDate: + description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. + id: 1091 + mirId: MIR:00000379 + modified: 2019-06-11T14:17:06.163+0000 + name: GXA Expt + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: gxa.expt + resources: + - deprecated: false + deprecationDate: + description: GXA Expt at EBI + id: 1092 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100483 + name: GXA Expt at EBI + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/gxa/ + sampleId: E-MTAB-2037 + urlPattern: https://www.ebi.ac.uk/gxa/experiments/{$id} + - deprecated: false + deprecationDate: + description: GXA Expt through OmicsDI + id: 1093 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100857 + name: GXA Expt through OmicsDI + official: false + providerCode: omicsdi + resourceHomeUrl: https://www.omicsdi.org/ + sampleId: E-MTAB-2037 + urlPattern: https://www.omicsdi.org/dataset/atlas-experiments/{$id} + sampleId: E-MTAB-2037 + - created: 2019-06-11T14:17:06.457+0000 + deprecated: false + deprecationDate: + description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. + id: 1094 + mirId: MIR:00000380 + modified: 2019-06-11T14:17:06.457+0000 + name: MetaboLights + namespaceEmbeddedInLui: false + pattern: ^MTBLS\d+$ + prefix: metabolights + resources: + - deprecated: false + deprecationDate: + description: MetaboLights at EBI + id: 1095 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100486 + name: MetaboLights at EBI + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/metabolights/ + sampleId: MTBLS1 + urlPattern: https://www.ebi.ac.uk/metabolights/{$id} + - deprecated: false + deprecationDate: + description: MataboLights through OmicsDI + id: 1096 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100853 + name: MataboLights through OmicsDI + official: false + providerCode: omicsdi + resourceHomeUrl: https://www.omicsdi.org/ + sampleId: MTBLS1 + urlPattern: https://www.omicsdi.org/dataset/metabolights_dataset/{$id} + sampleId: MTBLS1 + - created: 2019-06-11T14:17:06.748+0000 + deprecated: false + deprecationDate: + description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. + id: 1097 + mirId: MIR:00000381 + modified: 2019-06-11T14:17:06.748+0000 + name: National Bibliography Number + namespaceEmbeddedInLui: false + pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ + prefix: nbn + resources: + - deprecated: false + deprecationDate: + description: NBN through URN Resolver at German National Library + id: 1099 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1098 + location: + countryCode: DE + countryName: Germany + name: Deutsche Nationalbibliothek, Frankfurt + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100488 + name: NBN through URN Resolver at German National Library + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://nbn-resolving.org/resolve_urn.htm + sampleId: urn:nbn:fi:tkk-004781 + urlPattern: http://nbn-resolving.org/resolver?identifier={$id}&verb=redirect + sampleId: urn:nbn:fi:tkk-004781 + - created: 2019-06-11T14:17:06.994+0000 + deprecated: false + deprecationDate: + description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. + id: 1100 + mirId: MIR:00000382 + modified: 2019-06-11T14:17:06.994+0000 + name: ORCID + namespaceEmbeddedInLui: false + pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ + prefix: orcid + resources: + - deprecated: false + deprecationDate: + description: ORCID at Bethesda + id: 1102 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1101 + location: + countryCode: US + countryName: United States + name: ORCID Inc, Bethesda, Mayrland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100489 + name: ORCID at Bethesda + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://orcid.org + sampleId: 0000-0002-5355-2576 + urlPattern: https://orcid.org/{$id} + sampleId: 0000-0002-5355-2576 + - created: 2019-06-11T14:17:07.236+0000 + deprecated: false + deprecationDate: + description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. + id: 1103 + mirId: MIR:00000383 + modified: 2019-06-11T14:17:07.236+0000 + name: InChI + namespaceEmbeddedInLui: false + pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ + prefix: inchi + resources: + - deprecated: false + deprecationDate: + description: InChI through Chemspider + id: 1106 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 439 + location: + countryCode: GB + countryName: United Kingdom + name: Royal Society of Chemistry, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100492 + name: InChI through Chemspider + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.chemspider.com/ + sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + urlPattern: http://www.chemspider.com/{$id} + - deprecated: false + deprecationDate: + description: InChI through NIST + id: 1108 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1107 + location: + countryCode: US + countryName: United States + name: National Institute of Standards and Technology, Gaithersburg, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100493 + name: InChI through NIST + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://webbook.nist.gov/chemistry + sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + urlPattern: http://webbook.nist.gov/cgi/cbook.cgi?{$id} + - deprecated: false + deprecationDate: + description: InChI through ChEBI + id: 1109 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100494 + name: InChI through ChEBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/chebi/ + sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + urlPattern: https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString={$id} + - deprecated: false + deprecationDate: + description: InChI through RDF Open Molecules + id: 1105 + institution: + description: >- + Maastricht University (UM) is the most international university in + the Netherlands and, with 18,000 students and 4,400 employees, is + still growing. The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100491 + name: InChI through RDF Open Molecules + official: false + providerCode: um + resourceHomeUrl: http://rdf.openmolecules.net/ + sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + urlPattern: http://rdf.openmolecules.net/?{$id} + sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + - created: 2019-06-11T14:17:07.845+0000 + deprecated: false + deprecationDate: + description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. + id: 1110 + mirId: MIR:00000384 + modified: 2019-06-11T14:17:07.845+0000 + name: Wikipedia (En) + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+$ + prefix: wikipedia.en + resources: + - deprecated: false + deprecationDate: + description: Wikipedia (English) + id: 1112 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1111 + location: + countryCode: US + countryName: United States + name: Wikimedia Foundation, San Francisco, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100495 + name: Wikipedia (English) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://en.wikipedia.org/wiki/Main_Page + sampleId: SM_UB-81 + urlPattern: http://en.wikipedia.org/wiki/{$id} + - deprecated: false + deprecationDate: + description: Wikipedia structured content through DBpedia + id: 1114 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1113 + location: + countryCode: US + countryName: United States + name: OpenLink Software, Burlington, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100496 + name: Wikipedia structured content through DBpedia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://wiki.dbpedia.org/ + sampleId: SM_UB-81 + urlPattern: http://dbpedia.org/page/{$id} + sampleId: SM_UB-81 + - created: 2019-06-11T14:17:08.222+0000 + deprecated: false + deprecationDate: + description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. + id: 1115 + mirId: MIR:00000385 + modified: 2019-06-11T14:17:08.222+0000 + name: PhosphoPoint Kinase + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phosphopoint.kinase + resources: + - deprecated: false + deprecationDate: + description: PhosphoPoint Kinase at National Taiwan University + id: 1117 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1116 + location: + countryCode: CN + countryName: China + name: Department of Computer Science and Information Engineering, National Taiwan University + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100499 + name: PhosphoPoint Kinase at National Taiwan University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://kinase.bioinformatics.tw/ + sampleId: AURKA + urlPattern: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name={$id}&drawing=0&sorting=0&kinome=1 + sampleId: AURKA + - created: 2019-06-11T14:17:08.458+0000 + deprecated: false + deprecationDate: + description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. + id: 1118 + mirId: MIR:00000386 + modified: 2019-06-11T14:17:08.458+0000 + name: PhosphoPoint Phosphoprotein + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phosphopoint.protein + resources: + - deprecated: false + deprecationDate: + description: PhosphoPoint Phosphoprotein at National Taiwan University + id: 1119 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1116 + location: + countryCode: CN + countryName: China + name: Department of Computer Science and Information Engineering, National Taiwan University + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100500 + name: PhosphoPoint Phosphoprotein at National Taiwan University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://kinase.bioinformatics.tw/ + sampleId: AURKA + urlPattern: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name={$id}&drawing=0&sorting=0&kinome=0 + sampleId: AURKA + - created: 2019-06-11T14:17:08.649+0000 + deprecated: false + deprecationDate: + description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. + id: 1120 + mirId: MIR:00000387 + modified: 2019-06-11T14:17:08.649+0000 + name: InChIKey + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? + prefix: inchikey + resources: + - deprecated: false + deprecationDate: + description: InChIKey through ChemSpider + id: 1121 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 439 + location: + countryCode: GB + countryName: United Kingdom + name: Royal Society of Chemistry, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100501 + name: InChIKey through ChemSpider + official: true + providerCode: chemspider + resourceHomeUrl: http://www.chemspider.com/ + sampleId: RYYVLZVUVIJVGH-UHFFFAOYSA-N + urlPattern: http://www.chemspider.com/inchikey={$id} + - deprecated: false + deprecationDate: + description: InChiKey resolver at NCI + id: 1122 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 425 + location: + countryCode: US + countryName: United States + name: National Cancer Institute, Rockville, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100505 + name: InChiKey resolver at NCI + official: true + providerCode: cactus + resourceHomeUrl: http://cactus.nci.nih.gov/chemical/structure + sampleId: RYYVLZVUVIJVGH-UHFFFAOYSA-N + urlPattern: http://cactus.nci.nih.gov/chemical/structure/{$id}/names + - deprecated: false + deprecationDate: + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + id: 2470 + institution: + description: >- + Maastricht University (UM) is the most international university in + the Netherlands and, with 18,000 students and 4,400 employees, is + still growing. The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00000779 + name: Scholia + official: false + providerCode: scholia + resourceHomeUrl: https://scholia.toolforge.org/ + sampleId: WUUVSJBKHXDKBS-ROFOPDMZSA-N + urlPattern: https://scholia.toolforge.org/inchikey/{$id} + sampleId: RYYVLZVUVIJVGH-UHFFFAOYSA-N + - created: 2019-06-11T14:17:08.943+0000 + deprecated: false + deprecationDate: + description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. + id: 1123 + mirId: MIR:00000388 + modified: 2019-06-11T14:17:08.943+0000 + name: UniProt Isoform + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ + prefix: uniprot.isoform + resources: + - deprecated: false + deprecationDate: + description: UniProt Isoform through Universal Protein Resource + id: 1124 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 24 + location: + countryCode: GB + countryName: United Kingdom + name: UniProt Consortium + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100502 + name: UniProt Isoform through Universal Protein Resource + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.uniprot.org/ + sampleId: Q5BJF6-3 + urlPattern: http://www.uniprot.org/uniprot/{$id} + - deprecated: false + deprecationDate: + description: UniProt Isoform through Universal Protein Resource using Persistent URL system + id: 1125 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 24 + location: + countryCode: GB + countryName: United Kingdom + name: UniProt Consortium + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100503 + name: UniProt Isoform through Universal Protein Resource using Persistent URL system + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://purl.uniprot.org/ + sampleId: Q5BJF6-3 + urlPattern: http://purl.uniprot.org/uniprot/{$id} + - deprecated: false + deprecationDate: + description: UniProt Isoform through UniParc + id: 1126 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 24 + location: + countryCode: GB + countryName: United Kingdom + name: UniProt Consortium + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100504 + name: UniProt Isoform through UniParc + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.uniprot.org/uniparc/ + sampleId: Q5BJF6-3 + urlPattern: http://www.uniprot.org/uniparc/?query={$id} + sampleId: Q5BJF6-3 + - created: 2019-06-11T14:17:09.349+0000 + deprecated: false + deprecationDate: + description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. + id: 1127 + mirId: MIR:00000389 + modified: 2019-06-11T14:17:09.349+0000 + name: KEGG Environ + namespaceEmbeddedInLui: false + pattern: ^(ev\:)?E\d+$ + prefix: kegg.environ + resources: + - deprecated: false + deprecationDate: + description: KEGG ENVIRON Database + id: 1128 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 15 + location: + countryCode: JP + countryName: Japan + name: Kyoto University Bioinformatics Center + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100506 + name: KEGG ENVIRON Database + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genome.jp/kegg/drug/environ.html + sampleId: ev:E00032 + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: ev:E00032 + - created: 2019-06-11T14:17:09.531+0000 + deprecated: false + deprecationDate: + description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. + id: 1129 + mirId: MIR:00000390 + modified: 2019-06-11T14:17:09.531+0000 + name: CLDB + namespaceEmbeddedInLui: false + pattern: ^(cl|tum)\d+$ + prefix: cldb + resources: + - deprecated: false + deprecationDate: + description: CLDB at Genova + id: 1131 + institution: + description: NOTE - No international description has been found on its website, so it's not been possible to include a brief summary here. + homeUrl: http://www.ospedalesanmartino.it + id: 1130 + location: + countryCode: IT + countryName: Italy + name: Ospedale San Martino + rorId: https://ror.org/04d7es448 + location: + countryCode: IT + countryName: Italy + mirId: MIR:00100508 + name: CLDB at Genova + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html + sampleId: cl3603 + urlPattern: http://bioinformatics.hsanmartino.it/hypercldb/{$id}.html + sampleId: cl3603 + - created: 2019-06-11T14:17:09.753+0000 + deprecated: false + deprecationDate: + description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. + id: 1132 + mirId: MIR:00000391 + modified: 2019-06-11T14:17:09.753+0000 + name: Experimental Factor Ontology + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: efo + resources: + - deprecated: false + deprecationDate: + description: EFO through OLS + id: 1133 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100509 + name: EFO through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/efo + sampleId: '0004859' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=EFO:{$id} + - deprecated: false + deprecationDate: + description: EFO through BioPortal + id: 1134 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100510 + name: EFO through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/EFO + sampleId: '0004859' + urlPattern: http://purl.bioontology.org/ontology/EFO/efo:EFO_{$id} + - deprecated: false + deprecationDate: + description: EFO through Functional Genomics Group (EBI) + id: 1135 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100511 + name: EFO through Functional Genomics Group (EBI) + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/efo/ + sampleId: '0004859' + urlPattern: https://www.ebi.ac.uk/efo/EFO_{$id} + sampleId: '0004859' + - created: 2019-06-11T14:17:10.208+0000 + deprecated: false + deprecationDate: + description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. + id: 1136 + mirId: MIR:00000392 + modified: 2019-06-11T14:17:10.208+0000 + name: HGMD + namespaceEmbeddedInLui: false + pattern: ^[A-Z_0-9]+$ + prefix: hgmd + resources: + - deprecated: false + deprecationDate: + description: HGMD at Cardiff University + id: 1138 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1137 + location: + countryCode: GB + countryName: United Kingdom + name: Cardiff University, Cardiff + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100512 + name: HGMD at Cardiff University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.hgmd.cf.ac.uk/ac/index.php + sampleId: CALM1 + urlPattern: http://www.hgmd.cf.ac.uk/ac/gene.php?gene={$id} + sampleId: CALM1 + - created: 2019-06-11T14:17:10.425+0000 + deprecated: false + deprecationDate: + description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. + id: 1139 + mirId: MIR:00000393 + modified: 2019-06-11T14:17:10.425+0000 + name: AphidBase Transcript + namespaceEmbeddedInLui: false + pattern: ^ACYPI\d{6}(-RA)?$ + prefix: aphidbase.transcript + resources: + - deprecated: false + deprecationDate: + description: AphidBase at INRA + id: 1141 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1140 + location: + countryCode: FR + countryName: France + name: INRA UMR, Le Rheu + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100513 + name: AphidBase at INRA + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.aphidbase.com/aphidbase + sampleId: ACYPI000159 + urlPattern: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID={$id} + sampleId: ACYPI000159 + - created: 2019-06-11T14:17:10.647+0000 + deprecated: false + deprecationDate: + description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. + id: 1142 + mirId: MIR:00000394 + modified: 2019-06-11T14:17:10.647+0000 + name: Affymetrix Probeset + namespaceEmbeddedInLui: false + pattern: \d{4,}((_[asx])?_at)? + prefix: affy.probeset + resources: + - deprecated: false + deprecationDate: + description: Affymetrix ProbeSet in Santa Clara + id: 1144 + institution: + description: Thermo Fisher Scientific provides innovative Affymetrix™ products, tools, and resources that help advance the work of researchers via microarray analysis + homeUrl: https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis.html + id: 1143 + location: + countryCode: US + countryName: United States + name: Affymetrix + rorId: https://ror.org/012kjw534 + location: + countryCode: US + countryName: United States + mirId: MIR:00100514 + name: Affymetrix ProbeSet in Santa Clara + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.affymetrix.com/ + sampleId: 243002_at + urlPattern: https://www.affymetrix.com/LinkServlet?probeset={$id} + - deprecated: false + deprecationDate: + description: Bio2RDF + id: 1145 + institution: + description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. + homeUrl: https://bio2rdf.org + id: 33 + location: + countryCode: US + countryName: United States + name: Bio2RDF.org + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100672 + name: Bio2RDF + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cu.affymetrix.bio2rdf.org/fct/ + sampleId: 243002_at + urlPattern: http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:{$id} + sampleId: 243002_at + - created: 2019-06-11T14:17:10.973+0000 + deprecated: false + deprecationDate: + description: TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. + id: 1146 + mirId: MIR:00000395 + modified: 2019-06-11T14:17:10.973+0000 + name: TreeFam + namespaceEmbeddedInLui: false + pattern: ^\w{1,2}\d+$ + prefix: treefam + resources: + - deprecated: false + deprecationDate: + description: TreeFam database + id: 1148 + institution: + description: >- + BGI Genomics is a publicly listed commercial genomics company, + providing a wide range of next generation sequencing services and + a broad portfolio of genetic tests for medical institutions, + research institutions and other public and private partners. + + Established in 1999, we have almost 20 years of genomics experience. Our mission is to leverage our genomics expertise in order to advance life science research and improve human health for the benefit of mankind. + homeUrl: https://www.bgi.com + id: 1147 + location: + countryCode: CN + countryName: China + name: Beijing Genomics Institute + rorId: https://ror.org/045pn2j94 + location: + countryCode: CN + countryName: China + mirId: MIR:00100515 + name: TreeFam database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.treefam.org/ + sampleId: TF101014 + urlPattern: http://www.treefam.org/family/{$id} + sampleId: TF101014 + - created: 2019-06-11T14:17:11.199+0000 + deprecated: false + deprecationDate: + description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. + id: 1149 + mirId: MIR:00000396 + modified: 2019-06-11T14:17:11.199+0000 + name: CAPS-DB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: caps + resources: + - deprecated: false + deprecationDate: + description: CAPS-DB at Leeds Institute of Molecular Medicine + id: 1151 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1150 + location: + countryCode: GB + countryName: United Kingdom + name: Leeds Institute of Molecular Medicine, Section of Experimental Therapeutics, University of Leeds, Leeds + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100516 + name: CAPS-DB at Leeds Institute of Molecular Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home + sampleId: '434' + urlPattern: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl={$id} + sampleId: '434' + - created: 2019-06-11T14:17:11.437+0000 + deprecated: false + deprecationDate: + description: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. + id: 1152 + mirId: MIR:00000397 + modified: 2019-06-11T14:17:11.437+0000 + name: Cube db + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: cubedb + resources: + - deprecated: false + deprecationDate: + description: Cube db at Bioinformatics Institute (Singapore) + id: 1154 + institution: + description: The BII focuses on theoretical approaches aimed at understanding biomolecular mechanisms that underlie biological phenomena, the development of computational methods to support this discovery process, and experimental verification of predicted molecular and cellular functions of genes and proteins with biochemical methods. + homeUrl: http://www.bii.a-star.edu.sg + id: 1153 + location: + countryCode: SG + countryName: Singapore + name: BII Bioinformatics Institute + rorId: https://ror.org/044w3nw43 + location: + countryCode: CN + countryName: China + mirId: MIR:00100517 + name: Cube db at Bioinformatics Institute (Singapore) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html + sampleId: AKR + urlPattern: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/{$id}/ + sampleId: AKR + - created: 2019-06-11T14:17:11.651+0000 + deprecated: false + deprecationDate: + description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. + id: 1155 + mirId: MIR:00000398 + modified: 2019-06-11T14:17:11.651+0000 + name: IDEAL + namespaceEmbeddedInLui: false + pattern: ^IID\d+$ + prefix: ideal + resources: + - deprecated: false + deprecationDate: + description: IDEAL at Nagoya University + id: 1157 + institution: + description: Nagoya University has a 144-year history, dating from when the Temporary　Medical School/Public Hospital -- the forerunner of today's Nagoya University -- was established in 1871. The University became the last Imperial University of Japan in 1939, and the educational reforms in 1949 led to the beginning of Nagoya University under the new education system. From that time to this day, the University has been pursuing steady development. + homeUrl: http://en.nagoya-u.ac.jp/ + id: 1156 + location: + countryCode: JP + countryName: Japan + name: Nagoya University + rorId: https://ror.org/04chrp450 + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100518 + name: IDEAL at Nagoya University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ + sampleId: IID00001 + urlPattern: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id={$id} + sampleId: IID00001 + - created: 2019-06-11T14:17:11.871+0000 + deprecated: false + deprecationDate: + description: STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). + id: 1158 + mirId: MIR:00000399 + modified: 2019-06-11T14:17:11.871+0000 + name: STAP + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: stap + resources: + - deprecated: false + deprecationDate: + description: STAP at Korean Bioinformation Center + id: 1160 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1159 + location: + countryCode: KR + countryName: Korea, Republic of + name: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon + rorId: + location: + countryCode: KR + countryName: Korea, Republic of + mirId: MIR:00100519 + name: STAP at Korean Bioinformation Center + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://psb.kobic.re.kr/STAP/refinement/ + sampleId: 1a24 + urlPattern: http://psb.kobic.re.kr/STAP/refinement1/result.php?search={$id} + sampleId: 1a24 + - created: 2019-06-11T14:17:12.099+0000 + deprecated: false + deprecationDate: + description: Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. + id: 1161 + mirId: MIR:00000400 + modified: 2019-06-11T14:17:12.099+0000 + name: Pocketome + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+ + prefix: pocketome + resources: + - deprecated: false + deprecationDate: + description: Pocketome at UCSD Skaggs School + id: 1163 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1162 + location: + countryCode: US + countryName: United States + name: UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100520 + name: Pocketome at UCSD Skaggs School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pocketome.org/sfSearch.cgi?act=browseall + sampleId: 1433C_TOBAC_1_252 + urlPattern: http://www.pocketome.org/files/{$id}.html + sampleId: 1433C_TOBAC_1_252 + - created: 2019-06-11T14:17:12.749+0000 + deprecated: false + deprecationDate: + description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. + id: 1169 + mirId: MIR:00000403 + modified: 2019-06-11T14:17:12.749+0000 + name: BugBase Protocol + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bugbase.protocol + resources: + - deprecated: false + deprecationDate: + description: BugBase Protocol at University of London + id: 1171 + institution: + description: >- + St George’s Hospital Medical School was established in 1733 and + initially based at Hyde Park Corner, before moving to our Tooting + site in 1980. It was the second institution in England to provide + formal training courses for doctors. + + St George’s has a dynamic research culture, with teams working to improve the health of people of all ages, from children to the elderly, in populations locally and globally. + homeUrl: https://www.sgul.ac.uk/ + id: 1170 + location: + countryCode: GB + countryName: United Kingdom + name: St George's, University of London + rorId: https://ror.org/040f08y74 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100523 + name: BugBase Protocol at University of London + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bugs.sgul.ac.uk/E-BUGS + sampleId: '67' + urlPattern: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id={$id}&action=view + sampleId: '67' + - created: 2019-06-11T14:17:12.968+0000 + deprecated: false + deprecationDate: + description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. + id: 1172 + mirId: MIR:00000404 + modified: 2019-06-11T14:17:12.968+0000 + name: BugBase Expt + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bugbase.expt + resources: + - deprecated: false + deprecationDate: + description: BugBase Expt at University of London + id: 1173 + institution: + description: >- + St George’s Hospital Medical School was established in 1733 and + initially based at Hyde Park Corner, before moving to our Tooting + site in 1980. It was the second institution in England to provide + formal training courses for doctors. + + St George’s has a dynamic research culture, with teams working to improve the health of people of all ages, from children to the elderly, in populations locally and globally. + homeUrl: https://www.sgul.ac.uk/ + id: 1170 + location: + countryCode: GB + countryName: United Kingdom + name: St George's, University of London + rorId: https://ror.org/040f08y74 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100524 + name: BugBase Expt at University of London + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bugs.sgul.ac.uk/E-BUGS + sampleId: '288' + urlPattern: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id={$id}&action=view + sampleId: '288' + - created: 2019-06-11T14:17:13.167+0000 + deprecated: false + deprecationDate: + description: "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things." + id: 1174 + mirId: MIR:00000405 + modified: 2019-06-11T14:17:13.167+0000 + name: Tree of Life + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: tol + resources: + - deprecated: false + deprecationDate: + description: Tree of Life Web + id: 1176 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1175 + location: + countryCode: US + countryName: United States + name: University of Arizona + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100525 + name: Tree of Life Web + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://tolweb.org/tree/ + sampleId: '98034' + urlPattern: http://tolweb.org/{$id} + sampleId: '98034' + - created: 2019-06-11T14:17:13.429+0000 + deprecated: false + deprecationDate: + description: The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. + id: 1177 + mirId: MIR:00000406 + modified: 2019-06-11T14:17:13.429+0000 + name: VariO + namespaceEmbeddedInLui: true + pattern: ^VariO:\d+$ + prefix: vario + resources: + - deprecated: false + deprecationDate: + description: VariO through BioPortal + id: 1180 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100566 + name: VariO through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/VARIO + sampleId: '0294' + urlPattern: http://purl.bioontology.org/ontology/VARIO/VariO:{$id} + - deprecated: false + deprecationDate: + description: VariO through OLS + id: 1181 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100677 + name: VariO through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/vario + sampleId: '0294' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/vario/terms?obo_id=VariO:{$id} + - deprecated: false + deprecationDate: + description: VariO at Lund University + id: 1179 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1178 + location: + countryCode: SE + countryName: Sweden + name: Department of Experimental Medical Science, Lund University + rorId: + location: + countryCode: SE + countryName: Sweden + mirId: MIR:00100526 + name: VariO at Lund University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.variationontology.org/ + sampleId: '0294' + urlPattern: http://www.ontobee.org/search?ontology=VariO&keywords=VariO_{$id}&submit=Search+terms + sampleId: '0294' + - created: 2019-06-11T14:17:13.893+0000 + deprecated: false + deprecationDate: + description: The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. + id: 1182 + mirId: MIR:00000407 + modified: 2019-06-11T14:17:13.893+0000 + name: ViPR Strain + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z 0-9]+$ + prefix: vipr + resources: + - deprecated: false + deprecationDate: + description: ViPR Strain at J. Craig Venter Institute + id: 1184 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1183 + location: + countryCode: US + countryName: United States + name: J. Craig Venter Institute, San Diego, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100527 + name: ViPR Strain at J. Craig Venter Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.viprbrc.org/brc/home.do?decorator=vipr + sampleId: BeAn 70563 + urlPattern: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName={$id}&decorator=arena + sampleId: BeAn 70563 + - created: 2019-06-11T14:17:14.109+0000 + deprecated: false + deprecationDate: + description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. + id: 1185 + mirId: MIR:00000408 + modified: 2019-06-11T14:17:14.109+0000 + name: EPD + namespaceEmbeddedInLui: false + pattern: ^[A-Z-_0-9]+$ + prefix: epd + resources: + - deprecated: false + deprecationDate: + description: EPD at Swiss Institute of Bioinformatics + id: 1186 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100528 + name: EPD at Swiss Institute of Bioinformatics + official: false + providerCode: sib + resourceHomeUrl: http://epd.vital-it.ch/ + sampleId: TA_H3 + urlPattern: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0={$id} + sampleId: TA_H3 + - created: 2019-06-11T14:17:14.331+0000 + deprecated: false + deprecationDate: + description: 'The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.' + id: 1187 + mirId: MIR:00000409 + modified: 2019-06-11T14:17:14.331+0000 + name: RFAM + namespaceEmbeddedInLui: false + pattern: ^RF\d{5}$ + prefix: rfam + resources: + - deprecated: false + deprecationDate: + description: Rfam at EMBL-EBI + id: 1188 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100686 + name: Rfam at EMBL-EBI + official: true + providerCode: ebi + resourceHomeUrl: https://rfam.xfam.org/ + sampleId: RF00230 + urlPattern: https://rfam.xfam.org/family/{$id} + sampleId: RF00230 + - created: 2019-06-11T14:17:14.533+0000 + deprecated: false + deprecationDate: + description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. + id: 1189 + mirId: MIR:00000410 + modified: 2019-06-11T14:17:14.533+0000 + name: Fungal Barcode + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: fbol + resources: + - deprecated: false + deprecationDate: + description: Fungal Barcode at Fungal Biodiversity Centre + id: 1191 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1190 + location: + countryCode: NL + countryName: Netherlands + name: Fungal Biodiversity Centre, Utrecht + rorId: + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00100532 + name: Fungal Barcode at Fungal Biodiversity Centre + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.fungalbarcoding.org/ + sampleId: '2224' + urlPattern: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec={$id}&Fields=All&ExactMatch=T + sampleId: '2224' + - created: 2019-06-11T14:17:14.756+0000 + deprecated: false + deprecationDate: + description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. + id: 1192 + mirId: MIR:00000411 + modified: 2019-06-11T14:17:14.756+0000 + name: AFTOL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aftol.taxonomy + resources: + - deprecated: false + deprecationDate: + description: AFTOL at University of Minnesota + id: 1194 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1193 + location: + countryCode: US + countryName: United States + name: Department of Plant Biology, University of Minnesota, Minnesota + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100533 + name: AFTOL at University of Minnesota + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://aftol.org/data.php + sampleId: '959' + urlPattern: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id={$id} + sampleId: '959' + - created: 2019-06-11T14:17:14.975+0000 + deprecated: false + deprecationDate: + description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. + id: 1195 + mirId: MIR:00000412 + modified: 2019-06-11T14:17:14.975+0000 + name: AspGD Locus + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: aspgd.locus + resources: + - deprecated: false + deprecationDate: + description: AspGD at Stanford Medical School + id: 1197 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1196 + location: + countryCode: US + countryName: United States + name: Department of Genetics, Stanford University Medical School, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100534 + name: AspGD at Stanford Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.aspgd.org/ + sampleId: ASPL0000349247 + urlPattern: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid={$id} + sampleId: ASPL0000349247 + - created: 2019-06-11T14:17:15.227+0000 + deprecated: false + deprecationDate: + description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. + id: 1198 + mirId: MIR:00000413 + modified: 2019-06-11T14:17:15.227+0000 + name: AspGD Protein + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: aspgd.protein + resources: + - deprecated: false + deprecationDate: + description: AspGD Protein at Stanford Medical School + id: 1199 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1196 + location: + countryCode: US + countryName: United States + name: Department of Genetics, Stanford University Medical School, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100535 + name: AspGD Protein at Stanford Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.aspgd.org/ + sampleId: ASPL0000349247 + urlPattern: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid={$id} + sampleId: ASPL0000349247 + - created: 2019-06-11T14:17:18.754+0000 + deprecated: false + deprecationDate: + description: The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. + id: 1237 + mirId: MIR:00000431 + modified: 2019-06-11T14:17:18.754+0000 + name: National Drug Code + namespaceEmbeddedInLui: false + pattern: ^\d+\-\d+\-\d+ + prefix: ndc + resources: + - deprecated: false + deprecationDate: + description: National Drug Code at Food and Drug Administration + id: 1239 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1238 + location: + countryCode: US + countryName: United States + name: U.S. Food and Drug Administration, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100554 + name: National Drug Code at Food and Drug Administration + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.accessdata.fda.gov/scripts/cder/ndc/ + sampleId: 0002-1975-61 + urlPattern: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/{$id} + - deprecated: false + deprecationDate: + description: Bio2RDF + id: 1240 + institution: + description: Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers. + homeUrl: https://bio2rdf.org + id: 33 + location: + countryCode: US + countryName: United States + name: Bio2RDF.org + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100700 + name: Bio2RDF + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ndc.bio2rdf.org/fct + sampleId: 0002-1975-61 + urlPattern: http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:{$id} + sampleId: 0002-1975-61 + - created: 2019-06-11T14:17:15.426+0000 + deprecated: false + deprecationDate: + description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. + id: 1200 + mirId: MIR:00000415 + modified: 2019-06-11T14:17:15.426+0000 + name: AutDB + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[A-Z-0-9]{2,}$ + prefix: autdb + resources: + - deprecated: false + deprecationDate: + description: AutDB at MindSpec + id: 1202 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1201 + location: + countryCode: US + countryName: United States + name: MindSpec Inc., Fairfax, Virginia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100538 + name: AutDB at MindSpec + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://autism.mindspec.org/autdb/ + sampleId: ADA + urlPattern: http://autism.mindspec.org/GeneDetail/{$id} + sampleId: ADA + - created: 2019-06-11T14:17:15.634+0000 + deprecated: false + deprecationDate: + description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. + id: 1203 + mirId: MIR:00000416 + modified: 2019-06-11T14:17:15.634+0000 + name: BacMap Map + namespaceEmbeddedInLui: false + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: bacmap.map + resources: + - deprecated: false + deprecationDate: + description: BacMap Genome Map at University of Alberta + id: 1204 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1037 + location: + countryCode: CA + countryName: Canada + name: Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100539 + name: BacMap Genome Map at University of Alberta + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bacmap.wishartlab.com/ + sampleId: AP011135 + urlPattern: http://bacmap.wishartlab.com/maps/{$id}/index.html + sampleId: AP011135 + - created: 2019-06-11T14:17:15.821+0000 + deprecated: false + deprecationDate: + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. + id: 1205 + mirId: MIR:00000417 + modified: 2019-06-11T14:17:15.821+0000 + name: Bgee family + namespaceEmbeddedInLui: false + pattern: ^(ENSFM|ENSGTV:)\d+$ + prefix: bgee.family + resources: + - deprecated: false + deprecationDate: + description: Bgee at Lausanne + id: 1207 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100540 + name: Bgee at Lausanne + official: false + providerCode: sib + resourceHomeUrl: http://bgee.unil.ch/bgee/bgee + sampleId: ENSFM00500000270089 + urlPattern: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id={$id} + sampleId: ENSFM00500000270089 + - created: 2019-06-11T14:17:16.067+0000 + deprecated: false + deprecationDate: + description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. + id: 1208 + mirId: MIR:00000418 + modified: 2019-06-11T14:17:16.067+0000 + name: Bgee gene + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+\d+$ + prefix: bgee.gene + resources: + - deprecated: false + deprecationDate: + description: Bgee gene + id: 1210 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100541 + name: Bgee gene + official: false + providerCode: sib + resourceHomeUrl: https://bgee.org/ + sampleId: FBgn0000015 + urlPattern: https://bgee.org/?page=gene&gene_id={$id} + sampleId: FBgn0000015 + - created: 2019-06-11T14:17:16.333+0000 + deprecated: false + deprecationDate: + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. + id: 1211 + mirId: MIR:00000419 + modified: 2019-06-11T14:17:16.333+0000 + name: Bgee stage + namespaceEmbeddedInLui: false + pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ + prefix: bgee.stage + resources: + - deprecated: false + deprecationDate: + description: Bgee at Lausanne + id: 1212 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100542 + name: Bgee at Lausanne + official: false + providerCode: sib + resourceHomeUrl: http://bgee.unil.ch/bgee/bgee + sampleId: HsapDO:0000004 + urlPattern: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id={$id}&stage_children=on + sampleId: HsapDO:0000004 + - created: 2019-06-11T14:17:16.514+0000 + deprecated: false + deprecationDate: + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. + id: 1213 + mirId: MIR:00000420 + modified: 2019-06-11T14:17:16.514+0000 + name: Bgee organ + namespaceEmbeddedInLui: false + pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ + prefix: bgee.organ + resources: + - deprecated: false + deprecationDate: + description: Bgee at Lausanne + id: 1214 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100543 + name: Bgee at Lausanne + official: false + providerCode: sib + resourceHomeUrl: http://bgee.unil.ch/bgee/bgee + sampleId: EHDAA:2185 + urlPattern: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id={$id}&organ_children=on + sampleId: EHDAA:2185 + - created: 2019-06-11T14:17:16.688+0000 + deprecated: false + deprecationDate: + description: BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. + id: 1215 + mirId: MIR:00000421 + modified: 2019-06-11T14:17:16.688+0000 + name: BioCarta Pathway + namespaceEmbeddedInLui: false + pattern: ^([hm]\_)?\w+Pathway$ + prefix: biocarta.pathway + resources: + - deprecated: false + deprecationDate: + description: BioCarta Pathway at NCI + id: 1216 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 442 + location: + countryCode: US + countryName: United States + name: National Cancer Institute, Center for Bioinformatics, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100544 + name: BioCarta Pathway at NCI + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.biocarta.com/ + sampleId: h_aktPathway + urlPattern: https://cgap.nci.nih.gov/Pathways/BioCarta/{$id} + sampleId: h_aktPathway + - created: 2019-06-11T14:17:16.858+0000 + deprecated: false + deprecationDate: + description: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation." + id: 1217 + mirId: MIR:00000422 + modified: 2019-06-11T14:17:16.858+0000 + name: PANTHER Pathway Component + namespaceEmbeddedInLui: false + pattern: ^G|P|U|C|S\d{5}$ + prefix: panther.pthcmp + resources: + - deprecated: false + deprecationDate: + description: PANTHER Pathway Component at USC (Los Angeles) + id: 1218 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 94 + location: + countryCode: US + countryName: United States + name: Keck School of Medicine, University of Southern California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100545 + name: PANTHER Pathway Component at USC (Los Angeles) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.pantherdb.org/ + sampleId: P00266 + urlPattern: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession={$id} + sampleId: P00266 + - created: 2019-06-11T14:17:17.038+0000 + deprecated: false + deprecationDate: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. + id: 1219 + mirId: MIR:00000423 + modified: 2019-06-11T14:17:17.038+0000 + name: Golm Metabolome Database Profile + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.profile + resources: + - deprecated: false + deprecationDate: + description: Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology + id: 1220 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 806 + location: + countryCode: DE + countryName: Germany + name: Max Planck Institute of Molecular Plant Physiology, Potsdam + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100546 + name: Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://gmd.mpimp-golm.mpg.de/ + sampleId: 10b38aaf-b977-4950-85b8-f4775f66658d + urlPattern: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId={$id} + sampleId: 10b38aaf-b977-4950-85b8-f4775f66658d + - created: 2019-06-11T14:17:17.255+0000 + deprecated: false + deprecationDate: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. + id: 1221 + mirId: MIR:00000424 + modified: 2019-06-11T14:17:17.255+0000 + name: Golm Metabolome Database GC-MS spectra + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.gcms + resources: + - deprecated: false + deprecationDate: + description: Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology + id: 1222 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 806 + location: + countryCode: DE + countryName: Germany + name: Max Planck Institute of Molecular Plant Physiology, Potsdam + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100547 + name: Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://gmd.mpimp-golm.mpg.de/ + sampleId: 53d583d8-40c6-40e1-9296-23f821cd77a5 + urlPattern: http://gmd.mpimp-golm.mpg.de/Spectrums/{$id} + sampleId: 53d583d8-40c6-40e1-9296-23f821cd77a5 + - created: 2019-06-11T14:17:17.475+0000 + deprecated: false + deprecationDate: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. + id: 1223 + mirId: MIR:00000425 + modified: 2019-06-11T14:17:17.475+0000 + name: Golm Metabolome Database Reference Substance + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.ref + resources: + - deprecated: false + deprecationDate: + description: Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology + id: 1224 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 806 + location: + countryCode: DE + countryName: Germany + name: Max Planck Institute of Molecular Plant Physiology, Potsdam + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100548 + name: Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://gmd.mpimp-golm.mpg.de/ + sampleId: 8cf84adb-b4db-4807-ac98-0004247c35df + urlPattern: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/{$id} + sampleId: 8cf84adb-b4db-4807-ac98-0004247c35df + - created: 2019-06-11T14:17:17.661+0000 + deprecated: false + deprecationDate: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. + id: 1225 + mirId: MIR:00000426 + modified: 2019-06-11T14:17:17.661+0000 + name: Golm Metabolome Database Analyte + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.analyte + resources: + - deprecated: false + deprecationDate: + description: Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology + id: 1226 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 806 + location: + countryCode: DE + countryName: Germany + name: Max Planck Institute of Molecular Plant Physiology, Potsdam + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100549 + name: Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://gmd.mpimp-golm.mpg.de/ + sampleId: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 + urlPattern: http://gmd.mpimp-golm.mpg.de/Analytes/{$id} + sampleId: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 + - created: 2019-06-11T14:17:17.850+0000 + deprecated: false + deprecationDate: + description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. + id: 1227 + mirId: MIR:00000427 + modified: 2019-06-11T14:17:17.850+0000 + name: IntAct Molecule + namespaceEmbeddedInLui: false + pattern: ^EBI\-[0-9]+$ + prefix: intact.molecule + resources: + - deprecated: false + deprecationDate: + description: IntAct Molecule at EBI + id: 1228 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100550 + name: IntAct Molecule at EBI + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/intact/ + sampleId: EBI-366083 + urlPattern: https://www.ebi.ac.uk/intact/molecule/{$id} + sampleId: EBI-366083 + - created: 2019-06-11T14:17:18.034+0000 + deprecated: false + deprecationDate: + description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. + id: 1229 + mirId: MIR:00000428 + modified: 2019-06-11T14:17:18.034+0000 + name: DEPOD + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: depod + resources: + - deprecated: false + deprecationDate: + description: DEPOD at EMBL + id: 1231 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1230 + location: + countryCode: DE + countryName: Germany + name: European Molecular Biology Laboratory EMBL, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100551 + name: DEPOD at EMBL + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.depod.bioss.uni-freiburg.de + sampleId: PTPN1 + urlPattern: http://www.depod.bioss.uni-freiburg.de/showp.php?gene={$id} + sampleId: PTPN1 + - created: 2019-06-11T14:17:18.324+0000 + deprecated: false + deprecationDate: + description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. + id: 1232 + mirId: MIR:00000429 + modified: 2019-06-11T14:17:18.324+0000 + name: Cell Signaling Technology Pathways + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9_-]+$ + prefix: cst + resources: + - deprecated: false + deprecationDate: + description: CST Pathways at Cell Signaling Technology + id: 1234 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1233 + location: + countryCode: US + countryName: United States + name: Cell Signaling Technology, Inc., Danvers, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100552 + name: CST Pathways at Cell Signaling Technology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cellsignal.com/pathways/index.html + sampleId: Akt_PKB + urlPattern: http://www.cellsignal.com/reference/pathway/{$id}.html + sampleId: Akt_PKB + - created: 2019-06-11T14:17:19.049+0000 + deprecated: false + deprecationDate: + description: Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information. + id: 1241 + mirId: MIR:00000432 + modified: 2019-06-11T14:17:19.049+0000 + name: Phytozome Locus + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: phytozome.locus + resources: + - deprecated: false + deprecationDate: + description: Phytozome Locus at Joint Genome Institute + id: 1243 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1242 + location: + countryCode: US + countryName: United States + name: Joint Genome Institute, California, and the Center for Integrative Genomics, Lausanne + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100556 + name: Phytozome Locus at Joint Genome Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.phytozome.net/ + sampleId: Glyma0021s00410 + urlPattern: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:{$id} + sampleId: Glyma0021s00410 + - created: 2019-06-11T14:17:19.310+0000 + deprecated: false + deprecationDate: + description: "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments." + id: 1244 + mirId: MIR:00000433 + modified: 2019-06-11T14:17:19.310+0000 + name: SubtiList + namespaceEmbeddedInLui: false + pattern: ^BG\d+$ + prefix: subtilist + resources: + - deprecated: false + deprecationDate: + description: SubtiList at Pasteur Institute + id: 1246 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1245 + location: + countryCode: FR + countryName: France + name: Pasteur Institute, Paris + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100557 + name: SubtiList at Pasteur Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://genolist.pasteur.fr/SubtiList/ + sampleId: BG11523 + urlPattern: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+{$id} + sampleId: BG11523 + - created: 2019-06-11T14:17:19.532+0000 + deprecated: false + deprecationDate: + description: DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. + id: 1247 + mirId: MIR:00000434 + modified: 2019-06-11T14:17:19.532+0000 + name: DailyMed + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+ + prefix: dailymed + resources: + - deprecated: false + deprecationDate: + description: DailyMed at NLM + id: 1249 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1248 + location: + countryCode: US + countryName: United States + name: U.S. National Library of Medicine, Bethesda, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100558 + name: DailyMed at NLM + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://dailymed.nlm.nih.gov/dailymed/ + sampleId: 973a9333-fec7-46dd-8eb5-25738f06ee54 + urlPattern: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid={$id} + sampleId: 973a9333-fec7-46dd-8eb5-25738f06ee54 + - created: 2019-06-11T14:17:19.846+0000 + deprecated: false + deprecationDate: + description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. + id: 1250 + mirId: MIR:00000435 + modified: 2019-06-11T14:17:19.846+0000 + name: SIDER Drug + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sider.drug + resources: + - deprecated: false + deprecationDate: + description: SIDER Drug v2 at EMBL (Heidelberg) + id: 1252 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1251 + location: + countryCode: DE + countryName: Germany + name: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100559 + name: SIDER Drug v2 at EMBL (Heidelberg) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://sideeffects.embl.de/ + sampleId: '2244' + urlPattern: http://sideeffects.embl.de/drugs/{$id}/ + sampleId: '2244' + - created: 2019-06-11T14:17:20.079+0000 + deprecated: false + deprecationDate: + description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. + id: 1253 + mirId: MIR:00000436 + modified: 2019-06-11T14:17:20.079+0000 + name: SIDER Side Effect + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: sider.effect + resources: + - deprecated: false + deprecationDate: + description: SIDER Side Effect v2 at EMBL (Heidelberg) + id: 1254 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1251 + location: + countryCode: DE + countryName: Germany + name: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100560 + name: SIDER Side Effect v2 at EMBL (Heidelberg) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://sideeffects.embl.de/ + sampleId: C0017565 + urlPattern: http://sideeffects.embl.de/se/{$id}/ + sampleId: C0017565 + - created: 2019-06-11T14:17:20.303+0000 + deprecated: false + deprecationDate: + description: WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process. + id: 1255 + mirId: MIR:00000437 + modified: 2019-06-11T14:17:20.303+0000 + name: WikiGenes + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: wikigenes + resources: + - deprecated: false + deprecationDate: + description: WikiGenes at Massachusetts Institute of Technology + id: 1257 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1256 + location: + countryCode: US + countryName: United States + name: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100567 + name: WikiGenes at Massachusetts Institute of Technology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.wikigenes.org/ + sampleId: '3771877' + urlPattern: http://www.wikigenes.org/e/gene/e/{$id}.html + sampleId: '3771877' + - created: 2019-06-11T14:17:20.539+0000 + deprecated: false + deprecationDate: + description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. + id: 1258 + mirId: MIR:00000438 + modified: 2019-06-11T14:17:20.539+0000 + name: Broad Fungal Genome Initiative + namespaceEmbeddedInLui: false + pattern: ^S\d+$ + prefix: broad + resources: + - deprecated: false + deprecationDate: + description: Broad Fungal Genome Initiative at Broad Institute + id: 1260 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1259 + location: + countryCode: US + countryName: United States + name: Broad Institute of MIT and Harvard, Cambridge, Massachuchetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100569 + name: Broad Fungal Genome Initiative at Broad Institute + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ + sampleId: S7000002168151102 + urlPattern: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp={$id} + sampleId: S7000002168151102 + - created: 2019-06-11T14:17:20.763+0000 + deprecated: false + deprecationDate: + description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. + id: 1261 + mirId: MIR:00000439 + modified: 2019-06-11T14:17:20.763+0000 + name: Coriell Cell Repositories + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}\d+$ + prefix: coriell + resources: + - deprecated: false + deprecationDate: + description: Coriell Cell Repositories at Coriell Institute + id: 1263 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1262 + location: + countryCode: US + countryName: United States + name: Coriell Institute for Medical Research, New Jersey + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100570 + name: Coriell Cell Repositories at Coriell Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ccr.coriell.org/ + sampleId: GM17027 + urlPattern: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref={$id} + sampleId: GM17027 + - created: 2019-06-11T14:17:20.995+0000 + deprecated: false + deprecationDate: + description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. + id: 1264 + mirId: MIR:00000440 + modified: 2019-06-11T14:17:20.995+0000 + name: CORUM + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: corum + resources: + - deprecated: false + deprecationDate: + description: CORUM at Institute for Bioinformatics and Systems Biology (Germany) + id: 1266 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1265 + location: + countryCode: DE + countryName: Germany + name: Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum M&uuml;nchen-German Research Center for Environmental Health, Neuherberg + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100571 + name: CORUM at Institute for Bioinformatics and Systems Biology (Germany) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://mips.helmholtz-muenchen.de/genre/proj/corum/ + sampleId: '100' + urlPattern: https://mips.helmholtz-muenchen.de/corum/?id={$id} + sampleId: '100' + - created: 2019-06-11T14:17:21.287+0000 + deprecated: false + deprecationDate: + description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. + id: 1267 + mirId: MIR:00000442 + modified: 2019-06-11T14:17:21.287+0000 + name: EcoliWiki + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+$ + prefix: ecoliwiki + resources: + - deprecated: false + deprecationDate: + description: EcoliWiki at Texas Agrilife Research + id: 1269 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1268 + location: + countryCode: US + countryName: United States + name: Texas Agrilife Research, Texas A&M University College Station + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100573 + name: EcoliWiki at Texas Agrilife Research + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ecoliwiki.net/colipedia/ + sampleId: aaeA + urlPattern: http://ecoliwiki.net/colipedia/index.php/{$id}:Gene + sampleId: aaeA + - created: 2019-06-11T14:17:21.507+0000 + deprecated: false + deprecationDate: + description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. + id: 1270 + mirId: MIR:00000443 + modified: 2019-06-11T14:17:21.507+0000 + name: Genome Properties + namespaceEmbeddedInLui: false + pattern: ^GenProp\d+$ + prefix: genprop + resources: + - deprecated: false + deprecationDate: + description: Genome Properties + id: 1271 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100910 + name: Genome Properties + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/interpro/genomeproperties/ + sampleId: GenProp0699 + urlPattern: https://www.ebi.ac.uk/interpro/genomeproperties/#{$id} + sampleId: GenProp0699 + - created: 2019-06-11T14:17:21.690+0000 + deprecated: false + deprecationDate: + description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. + id: 1272 + mirId: MIR:00000444 + modified: 2019-06-11T14:17:21.690+0000 + name: JSTOR + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jstor + resources: + - deprecated: false + deprecationDate: + description: JSTOR Online + id: 1274 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1273 + location: + countryCode: US + countryName: United States + name: Ithaka Harbors, Inc., New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100575 + name: JSTOR Online + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.jstor.org/ + sampleId: '3075966' + urlPattern: http://www.jstor.org/stable/{$id} + sampleId: '3075966' + - created: 2019-06-11T14:17:21.919+0000 + deprecated: false + deprecationDate: + description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) + id: 1275 + mirId: MIR:00000445 + modified: 2019-06-11T14:17:21.919+0000 + name: Mouse Adult Gross Anatomy + namespaceEmbeddedInLui: true + pattern: ^MA:\d+$ + prefix: ma + resources: + - deprecated: false + deprecationDate: + description: Mouse Adult Gross Anatomy through BioPortal + id: 1276 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100576 + name: Mouse Adult Gross Anatomy through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/MA + sampleId: '0002502' + urlPattern: http://purl.bioontology.org/ontology/MA/MA:{$id} + - deprecated: false + deprecationDate: + description: Mouse Adult Gross Anatomy through OLS + id: 1277 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100577 + name: Mouse Adult Gross Anatomy through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/ma + sampleId: '0002502' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/ma/terms?obo_id=MA:{$id} + - deprecated: false + deprecationDate: + description: Mouse Adult Gross Anatomy at The Jackson Laboratory + id: 1279 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1278 + location: + countryCode: US + countryName: United States + name: The Jackson Laboratory, Bar Harbor, Maine + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100578 + name: Mouse Adult Gross Anatomy at The Jackson Laboratory + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.informatics.jax.org/ + sampleId: '0002502' + urlPattern: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:{$id} + sampleId: '0002502' + - created: 2019-06-11T14:17:22.748+0000 + deprecated: false + deprecationDate: + description: Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). + id: 1283 + mirId: MIR:00000447 + modified: 2019-06-11T14:17:22.748+0000 + name: Unimod + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unimod + resources: + - deprecated: false + deprecationDate: + description: Unimod at Matrix Sciences Ltd. + id: 1285 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1284 + location: + countryCode: GB + countryName: United Kingdom + name: Matrix Science Ltd., London + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100581 + name: Unimod at Matrix Sciences Ltd. + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.unimod.org/ + sampleId: '1200' + urlPattern: http://www.unimod.org/modifications_view.php?editid1={$id} + sampleId: '1200' + - created: 2019-06-11T14:17:22.962+0000 + deprecated: false + deprecationDate: + description: The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. + id: 1286 + mirId: MIR:00000448 + modified: 2019-06-11T14:17:22.962+0000 + name: VBRC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: vbrc + resources: + - deprecated: false + deprecationDate: + description: VBRC at University of Alabama + id: 1288 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1287 + location: + countryCode: US + countryName: United States + name: University of Alabama, Birmingham and the University of Victoria, British Columbia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100582 + name: VBRC at University of Alabama + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://vbrc.org/ + sampleId: '35742' + urlPattern: http://vbrc.org/gene_detail.asp?gene_id={$id} + sampleId: '35742' + - created: 2019-06-11T14:17:23.207+0000 + deprecated: false + deprecationDate: + description: ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures. + id: 1289 + mirId: MIR:00000449 + modified: 2019-06-11T14:17:23.207+0000 + name: ViralZone + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: viralzone + resources: + - deprecated: false + deprecationDate: + description: ViralZone at SIB + id: 1291 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100583 + name: ViralZone at SIB + official: false + providerCode: sib + resourceHomeUrl: http://www.expasy.org/viralzone/ + sampleId: '992' + urlPattern: http://viralzone.expasy.org/all_by_protein/{$id}.html + sampleId: '992' + - created: 2019-06-11T14:17:23.659+0000 + deprecated: false + deprecationDate: + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. + id: 1294 + mirId: MIR:00000451 + modified: 2019-06-11T14:17:23.659+0000 + name: Rat Genome Database qTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rgd.qtl + resources: + - deprecated: false + deprecationDate: + description: Rat Genome Database qTL at Medical College of Wisconsin + id: 1296 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1295 + location: + countryCode: US + countryName: United States + name: Medical College of Wisconsin, Milwaukee, Wisconsin + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100586 + name: Rat Genome Database qTL at Medical College of Wisconsin + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://rgd.mcw.edu/ + sampleId: '1354581' + urlPattern: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id={$id} + sampleId: '1354581' + - created: 2019-06-11T14:17:23.876+0000 + deprecated: false + deprecationDate: + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. + id: 1297 + mirId: MIR:00000452 + modified: 2019-06-11T14:17:23.876+0000 + name: Rat Genome Database strain + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rgd.strain + resources: + - deprecated: false + deprecationDate: + description: Rat Genome Database strain at Medical College of Wisconsin + id: 1298 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1295 + location: + countryCode: US + countryName: United States + name: Medical College of Wisconsin, Milwaukee, Wisconsin + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100587 + name: Rat Genome Database strain at Medical College of Wisconsin + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://rgd.mcw.edu/ + sampleId: '5688061' + urlPattern: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id={$id} + sampleId: '5688061' + - created: 2019-06-11T14:17:24.062+0000 + deprecated: false + deprecationDate: + description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. + id: 1299 + mirId: MIR:00000453 + modified: 2019-06-11T14:17:24.062+0000 + name: DOOR + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: door + resources: + - deprecated: false + deprecationDate: + description: DOOR v1 at University of Georgia + id: 1301 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1300 + location: + countryCode: US + countryName: United States + name: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100588 + name: DOOR v1 at University of Georgia + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://csbl.bmb.uga.edu/DOOR/operon.php + sampleId: '1398574' + urlPattern: http://csbl.bmb.uga.edu/DOOR/operon.php?id={$id} + sampleId: '1398574' + - created: 2019-06-11T14:17:24.294+0000 + deprecated: false + deprecationDate: + description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. + id: 1302 + mirId: MIR:00000454 + modified: 2019-06-11T14:17:24.294+0000 + name: Degradome Database + namespaceEmbeddedInLui: false + pattern: ^[AMCST][0-9x][0-9]$ + prefix: degradome + resources: + - deprecated: false + deprecationDate: + description: Degradome Database at + id: 1304 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1303 + location: + countryCode: ES + countryName: Spain + name: Departamento de Bioqu&amp;iacute;mica y Biolog&amp;iacute;a Molecular, Facultad de Medicina, Universidad de Oviedo + rorId: + location: + countryCode: ES + countryName: Spain + mirId: MIR:00100589 + name: Degradome Database at + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://degradome.uniovi.es/ + sampleId: Ax1 + urlPattern: http://degradome.uniovi.es/cgi-bin/protease/{$id} + sampleId: Ax1 + - created: 2019-06-11T14:17:24.514+0000 + deprecated: false + deprecationDate: + description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. + id: 1305 + mirId: MIR:00000455 + modified: 2019-06-11T14:17:24.514+0000 + name: DBD + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dbd + resources: + - deprecated: false + deprecationDate: + description: DBD at MRC Laboratory of Molecular Biology + id: 1306 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1026 + location: + countryCode: GB + countryName: United Kingdom + name: MRC Laboratory of Molecular Biology, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100590 + name: DBD at MRC Laboratory of Molecular Biology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.transcriptionfactor.org/ + sampleId: '0045310' + urlPattern: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:{$id}+cat:DBD + sampleId: '0045310' + - created: 2019-06-11T14:17:24.701+0000 + deprecated: false + deprecationDate: + description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. + id: 1307 + mirId: MIR:00000456 + modified: 2019-06-11T14:17:24.701+0000 + name: DATF + namespaceEmbeddedInLui: false + pattern: ^AT[1-5]G\d{5}(\.\d+)?$ + prefix: datf + resources: + - deprecated: false + deprecationDate: + description: DATF through PlantTFDB + id: 1309 + institution: + description: >- + Peking University is a comprehensive and national key university. + The campus, known as "Yan Yuan"（the garden of Yan）, is situated at + Haidian District in the western suburb of Beijing, with a total + area of 2,743,532 square metres (or 274 hectares). It stands near + to the Yuanmingyuan Garden and the Summer Palace. + + Peking University is proud of its outstanding faculty, including 48 members of the Chinese Academy of Sciences (CAS), 9 members of the Chinese Academy of Engineering (CAE), and 21 members of the Third World Academy of Sciences (TWAS). + homeUrl: http://english.pku.edu.cn/ + id: 1612 + location: + countryCode: CN + countryName: China + name: Peking University + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100591 + name: DATF through PlantTFDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://datf.cbi.pku.edu.cn/ + sampleId: AT1G01030.1 + urlPattern: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did={$id} + sampleId: AT1G01030.1 + - created: 2019-06-11T14:17:24.936+0000 + deprecated: false + deprecationDate: + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. + id: 1310 + mirId: MIR:00000457 + modified: 2019-06-11T14:17:24.936+0000 + name: IUPHAR ligand + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.ligand + resources: + - deprecated: false + deprecationDate: + description: IUPHAR ligand at University of Edinburgh + id: 1311 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 827 + location: + countryCode: GB + countryName: United Kingdom + name: Centre for Cardiovascular Science, University of Edinburgh, Edinburgh + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100592 + name: IUPHAR ligand at University of Edinburgh + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all + sampleId: '1755' + urlPattern: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId={$id} + sampleId: '1755' + - created: 2019-06-11T14:17:25.144+0000 + deprecated: false + deprecationDate: + description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. + id: 1312 + mirId: MIR:00000458 + modified: 2019-06-11T14:17:25.144+0000 + name: Molbase + namespaceEmbeddedInLui: false + pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ + prefix: molbase + resources: + - deprecated: false + deprecationDate: + description: Molbase at Chinese Academy of Sciences + id: 1314 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1313 + location: + countryCode: CN + countryName: China + name: Chinese Academy of Sciences, Xuhui District Shanghai + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100593 + name: Molbase at Chinese Academy of Sciences + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.molbase.com/ + sampleId: 128796-39-4 + urlPattern: http://www.molbase.com/en/index.php?app=search&search_keyword={$id} + sampleId: 128796-39-4 + - created: 2019-06-11T14:17:25.397+0000 + deprecated: false + deprecationDate: + description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. + id: 1315 + mirId: MIR:00000459 + modified: 2019-06-11T14:17:25.397+0000 + name: YRC PDR + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: yrcpdr + resources: + - deprecated: false + deprecationDate: + description: YRC PDR at University of Washington + id: 1317 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1316 + location: + countryCode: US + countryName: United States + name: Department of Biochemistry, University of Washington, Seattle + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100594 + name: YRC PDR at University of Washington + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.yeastrc.org/pdr/ + sampleId: '2673500' + urlPattern: http://yeastrc.org/pdr/viewProtein.do?id={$id} + sampleId: '2673500' + - created: 2019-06-11T14:17:25.610+0000 + deprecated: false + deprecationDate: + description: The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. + id: 1318 + mirId: MIR:00000460 + modified: 2019-06-11T14:17:25.610+0000 + name: Yeast Intron Database v3 + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: yid + resources: + - deprecated: false + deprecationDate: + description: Yeast Intron Database version 3 at Baskin School of Engineering + id: 1320 + institution: + description: > + UC Santa Cruz opened in 1965 with 650 students. During the + 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate + students were enrolled. + homeUrl: https://www.ucsc.edu + id: 1319 + location: + countryCode: US + countryName: United States + name: University of California, Santa Cruz + rorId: https://ror.org/03s65by71 + location: + countryCode: US + countryName: United States + mirId: MIR:00100595 + name: Yeast Intron Database version 3 at Baskin School of Engineering + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://compbio.soe.ucsc.edu/yeast_introns.html + sampleId: SNR17A + urlPattern: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName={$id} + sampleId: SNR17A + - created: 2019-06-11T14:17:25.854+0000 + deprecated: false + deprecationDate: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. + id: 1321 + mirId: MIR:00000461 + modified: 2019-06-11T14:17:25.854+0000 + name: FuncBase Fly + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.fly + resources: + - deprecated: false + deprecationDate: + description: FuncBase Fly at Harvard Medical School + id: 1323 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1322 + location: + countryCode: US + countryName: United States + name: Harvard Medical School, Boston, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100596 + name: FuncBase Fly at Harvard Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://func.mshri.on.ca/fly + sampleId: '10194' + urlPattern: http://func.mshri.on.ca/fly/genes/list_functional_scores/{$id} + sampleId: '10194' + - created: 2019-06-11T14:17:26.074+0000 + deprecated: false + deprecationDate: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. + id: 1324 + mirId: MIR:00000462 + modified: 2019-06-11T14:17:26.074+0000 + name: FuncBase Human + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.human + resources: + - deprecated: false + deprecationDate: + description: FuncBase Human at Harvard Medical School + id: 1325 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1322 + location: + countryCode: US + countryName: United States + name: Harvard Medical School, Boston, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100597 + name: FuncBase Human at Harvard Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://func.mshri.on.ca/human/ + sampleId: '119514' + urlPattern: http://func.mshri.on.ca/human/genes/list_functional_scores/{$id} + sampleId: '119514' + - created: 2019-06-11T14:17:26.285+0000 + deprecated: false + deprecationDate: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. + id: 1326 + mirId: MIR:00000463 + modified: 2019-06-11T14:17:26.285+0000 + name: FuncBase Mouse + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.mouse + resources: + - deprecated: false + deprecationDate: + description: FuncBase Mouse at Harvard Medical School + id: 1327 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1322 + location: + countryCode: US + countryName: United States + name: Harvard Medical School, Boston, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100598 + name: FuncBase Mouse at Harvard Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://func.mshri.on.ca/mouse/ + sampleId: '1351341' + urlPattern: http://func.mshri.on.ca/mouse/genes/list_functional_scores/{$id} + sampleId: '1351341' + - created: 2019-06-11T14:18:18.874+0000 + deprecated: false + deprecationDate: + description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. + id: 1881 + mirId: MIR:00000679 + modified: 2019-06-11T14:18:18.874+0000 + name: The cBioPortal for Cancer Genomics + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\_]+$ + prefix: cbioportal + resources: + - deprecated: false + deprecationDate: + description: The cBioPortal for Cancer Genomics + id: 1883 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1882 + location: + countryCode: US + countryName: United States + name: Memorial Sloan Kettering Cancer Center + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100909 + name: The cBioPortal for Cancer Genomics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cbioportal.org + sampleId: laml_tcga_pub + urlPattern: http://www.cbioportal.org/study?id={$id}#summary + sampleId: laml_tcga_pub + - created: 2019-06-11T14:17:26.470+0000 + deprecated: false + deprecationDate: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. + id: 1328 + mirId: MIR:00000464 + modified: 2019-06-11T14:17:26.470+0000 + name: FuncBase Yeast + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.yeast + resources: + - deprecated: false + deprecationDate: + description: FuncBase Yeast at Harvard Medical School + id: 1329 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1322 + location: + countryCode: US + countryName: United States + name: Harvard Medical School, Boston, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100599 + name: FuncBase Yeast at Harvard Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://func.mshri.on.ca/yeast + sampleId: '2701' + urlPattern: http://func.mshri.on.ca/yeast/genes/list_functional_scores/{$id} + sampleId: '2701' + - created: 2019-06-11T14:17:26.654+0000 + deprecated: false + deprecationDate: + description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. + id: 1330 + mirId: MIR:00000465 + modified: 2019-06-11T14:17:26.654+0000 + name: YDPM + namespaceEmbeddedInLui: false + pattern: ^Y[A-Z]{2}\d+[CW]$ + prefix: ydpm + resources: + - deprecated: false + deprecationDate: + description: YDPM at Stanford University School of Medicine + id: 1332 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1331 + location: + countryCode: US + countryName: United States + name: Stanford University School of Medicine, Stanford, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100600 + name: YDPM at Stanford University School of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www-deletion.stanford.edu/YDPM/ + sampleId: YAL001C + urlPattern: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id} + sampleId: YAL001C + - created: 2019-06-11T14:17:26.886+0000 + deprecated: false + deprecationDate: + description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. + id: 1333 + mirId: MIR:00000466 + modified: 2019-06-11T14:17:26.886+0000 + name: WormBase RNAi + namespaceEmbeddedInLui: false + pattern: ^WBRNAi\d{8}$ + prefix: wb.rnai + resources: + - deprecated: false + deprecationDate: + description: WormBase RNAi + id: 1334 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100601 + name: WormBase RNAi + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.wormbase.org/ + sampleId: WBRNAi00086878 + urlPattern: https://www.wormbase.org/species/c_elegans/rnai/{$id} + sampleId: WBRNAi00086878 + - created: 2019-06-11T14:17:27.086+0000 + deprecated: false + deprecationDate: + description: The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. + id: 1335 + mirId: MIR:00000468 + modified: 2019-06-11T14:17:27.086+0000 + name: PASS2 + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pass2 + resources: + - deprecated: false + deprecationDate: + description: PASS2 at National centre for Biological Sciences (India) + id: 1337 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1336 + location: + countryCode: IN + countryName: India + name: National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka + rorId: + location: + countryCode: IN + countryName: India + mirId: MIR:00100603 + name: PASS2 at National centre for Biological Sciences (India) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://caps.ncbs.res.in/pass2/ + sampleId: '46977' + urlPattern: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id={$id} + sampleId: '46977' + - created: 2019-06-11T14:17:27.338+0000 + deprecated: false + deprecationDate: + description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. + id: 1338 + mirId: MIR:00000469 + modified: 2019-06-11T14:17:27.338+0000 + name: ICEberg element + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iceberg.element + resources: + - deprecated: false + deprecationDate: + description: ICEberg element at Shanghai Jiaotong University + id: 1340 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1339 + location: + countryCode: CN + countryName: China + name: State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100604 + name: ICEberg element at Shanghai Jiaotong University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://db-mml.sjtu.edu.cn/ICEberg/ + sampleId: '100' + urlPattern: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id={$id} + sampleId: '100' + - created: 2019-06-11T14:17:27.601+0000 + deprecated: false + deprecationDate: + description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. + id: 1341 + mirId: MIR:00000470 + modified: 2019-06-11T14:17:27.601+0000 + name: ICEberg family + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iceberg.family + resources: + - deprecated: false + deprecationDate: + description: ICEberg family at Shanghai Jiaotong University + id: 1343 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1342 + location: + countryCode: CN + countryName: China + name: State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp; Biotechnology, Shanghai Jiaotong University, Shanghai + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100605 + name: ICEberg family at Shanghai Jiaotong University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://db-mml.sjtu.edu.cn/ICEberg/ + sampleId: '1' + urlPattern: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id={$id} + sampleId: '1' + - created: 2019-06-11T14:17:27.811+0000 + deprecated: false + deprecationDate: + description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. + id: 1344 + mirId: MIR:00000471 + modified: 2019-06-11T14:17:27.811+0000 + name: VFDB Genus + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vfdb.genus + resources: + - deprecated: false + deprecationDate: + description: VFDB Genus at Institute of Pathogen Biology + id: 1346 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1345 + location: + countryCode: CN + countryName: China + name: State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100606 + name: VFDB Genus at Institute of Pathogen Biology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mgc.ac.cn/VFs/ + sampleId: Chlamydia + urlPattern: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus={$id} + sampleId: Chlamydia + - created: 2019-06-11T14:17:28.027+0000 + deprecated: false + deprecationDate: + description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. + id: 1347 + mirId: MIR:00000472 + modified: 2019-06-11T14:17:28.027+0000 + name: VFDB Gene + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vfdb.gene + resources: + - deprecated: false + deprecationDate: + description: VFDB Gene at Institute of Pathogen Biology + id: 1348 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1345 + location: + countryCode: CN + countryName: China + name: State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100607 + name: VFDB Gene at Institute of Pathogen Biology + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mgc.ac.cn/VFs/ + sampleId: VFG2154 + urlPattern: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID={$id} + sampleId: VFG2154 + - created: 2019-06-11T14:17:28.224+0000 + deprecated: false + deprecationDate: + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. + id: 1349 + mirId: MIR:00000473 + modified: 2019-06-11T14:17:28.224+0000 + name: MeSH 2013 + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: mesh.2013 + resources: + - deprecated: false + deprecationDate: + description: MeSH 2013 at National Library of Medicine + id: 1350 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 792 + location: + countryCode: US + countryName: United States + name: U.S. National Library of Medicine, National Institute of Health, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100608 + name: MeSH 2013 at National Library of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.nlm.nih.gov/mesh/ + sampleId: '17165' + urlPattern: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index={$id}&view=expanded + sampleId: '17165' + - created: 2019-06-11T14:17:28.414+0000 + deprecated: false + deprecationDate: + description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. + id: 1351 + mirId: MIR:00000474 + modified: 2019-06-11T14:17:28.414+0000 + name: KEGG Module + namespaceEmbeddedInLui: false + pattern: ^([a-z]{3,5}_)?M\d{5}$ + prefix: kegg.module + resources: + - deprecated: false + deprecationDate: + description: KEGG Module at Kyoto University Bioinformatics Center + id: 1352 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 367 + location: + countryCode: JP + countryName: Japan + name: Department of Computational Biology, University of Tokyo, Tokyo + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100609 + name: KEGG Module at Kyoto University Bioinformatics Center + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.kegg.jp/kegg/module.html + sampleId: M00002 + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: M00002 + - created: 2019-06-11T14:17:28.601+0000 + deprecated: false + deprecationDate: + description: The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. + id: 1353 + mirId: MIR:00000475 + modified: 2019-06-11T14:17:28.601+0000 + name: KEGG Disease + namespaceEmbeddedInLui: false + pattern: ^H\d+$ + prefix: kegg.disease + resources: + - deprecated: false + deprecationDate: + description: KEGG Disease at Kyoto University Bioinformatics Center + id: 1354 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 705 + location: + countryCode: JP + countryName: Japan + name: Kyoto University Bioinformatics Center, Kyoto + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100610 + name: KEGG Disease at Kyoto University Bioinformatics Center + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genome.jp/kegg/disease/ + sampleId: H00076 + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: H00076 + - created: 2019-06-11T14:17:28.795+0000 + deprecated: false + deprecationDate: + description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. + id: 1355 + mirId: MIR:00000476 + modified: 2019-06-11T14:17:28.795+0000 + name: MedlinePlus + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: medlineplus + resources: + - deprecated: false + deprecationDate: + description: MedlinePlus at NCBI + id: 1356 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100611 + name: MedlinePlus at NCBI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.nlm.nih.gov/medlineplus/ + sampleId: '002804' + urlPattern: http://www.nlm.nih.gov/medlineplus/ency/article/{$id}.htm + sampleId: '002804' + - created: 2019-06-11T14:17:29.214+0000 + deprecated: false + deprecationDate: + description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. + id: 1360 + mirId: MIR:00000478 + modified: 2019-06-11T14:17:29.214+0000 + name: GlycoEpitope + namespaceEmbeddedInLui: false + pattern: ^EP\d{4}$ + prefix: glycoepitope + resources: + - deprecated: false + deprecationDate: + description: GlycoEpitope at Ritsumeikan University + id: 1362 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1361 + location: + countryCode: JP + countryName: Japan + name: Kawasaki laboratory, Research Center for Glycobiotechnology, Ritsumeikan University + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100613 + name: GlycoEpitope at Ritsumeikan University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.glycoepitope.jp/epitopes/ + sampleId: EP0311 + urlPattern: https://www.glycoepitope.jp/epitopes/{$id} + sampleId: EP0311 + - created: 2019-06-11T14:17:29.437+0000 + deprecated: false + deprecationDate: + description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. + id: 1363 + mirId: MIR:00000479 + modified: 2019-06-11T14:17:29.437+0000 + name: JCGGDB + namespaceEmbeddedInLui: false + pattern: ^JCGG-STR\d{6}$ + prefix: jcggdb + resources: + - deprecated: false + deprecationDate: + description: JCGGDB at Advanced Science Institute (Japan) + id: 1365 + institution: + description: Established by RIKEN in April 2008, based on the DRI (Discovery Research Institute) and the FRS (Frontier Research System). ASI is unique since it is structured as comprehensive system supporting the full range of scientific fields including high energy/nuclear/astro-physics, condensed matter physics, chemistry, electronic engineering, biology and medicine. + homeUrl: http://www.riken.jp/en/about/reports/evaluation/asi/ + id: 1364 + location: + countryCode: JP + countryName: Japan + name: RIKEN Advanced Science Institute + rorId: https://ror.org/030vbmf58 + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100614 + name: JCGGDB at Advanced Science Institute (Japan) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://jcggdb.jp/index_en.html + sampleId: JCGG-STR008690 + urlPattern: http://jcggdb.jp/idb/jcggdb/{$id} + sampleId: JCGG-STR008690 + - created: 2019-06-11T14:17:29.649+0000 + deprecated: false + deprecationDate: + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. + id: 1366 + mirId: MIR:00000480 + modified: 2019-06-11T14:17:29.649+0000 + name: NONCODE v4 Gene + namespaceEmbeddedInLui: false + pattern: ^NONHSAG\d{5}$ + prefix: noncodev4.gene + resources: + - deprecated: false + deprecationDate: + description: NONCODE v4 Gene at Chinese Academy of Sciences + id: 1367 + institution: + description: The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches. + homeUrl: http://english.cas.cn/ + id: 737 + location: + countryCode: CN + countryName: China + name: Chinese Academy of Sciences + rorId: https://ror.org/034t30j35 + location: + countryCode: CN + countryName: China + mirId: MIR:00100616 + name: NONCODE v4 Gene at Chinese Academy of Sciences + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.bioinfo.org/NONCODEv4/ + sampleId: NONHSAG00001 + urlPattern: http://www.bioinfo.org/NONCODEv4/show_gene.php?id={$id} + sampleId: NONHSAG00001 + - created: 2019-06-11T14:18:19.150+0000 + deprecated: false + deprecationDate: + description: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster. + id: 1884 + mirId: MIR:00000680 + modified: 2019-06-11T14:18:19.150+0000 + name: Virtual Fly Brain + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z]{8}$ + prefix: vfb + resources: + - deprecated: false + deprecationDate: + description: Virtual Fly Brain + id: 1886 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1885 + location: + countryCode: GB + countryName: United Kingdom + name: The University of Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100911 + name: Virtual Fly Brain + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://VirtualFlyBrain.org + sampleId: '00000001' + urlPattern: http://virtualflybrain.org/reports/{$id} + sampleId: '00000001' + - created: 2019-06-11T14:17:29.833+0000 + deprecated: false + deprecationDate: + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts. + id: 1368 + mirId: MIR:00000481 + modified: 2019-06-11T14:17:29.833+0000 + name: NONCODE v4 Transcript + namespaceEmbeddedInLui: false + pattern: ^NONHSAT\d{6}$ + prefix: noncodev4.rna + resources: + - deprecated: false + deprecationDate: + description: NONCODE v4 Transcript at Chinese Academy of Sciences + id: 1369 + institution: + description: The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches. + homeUrl: http://english.cas.cn/ + id: 737 + location: + countryCode: CN + countryName: China + name: Chinese Academy of Sciences + rorId: https://ror.org/034t30j35 + location: + countryCode: CN + countryName: China + mirId: MIR:00100617 + name: NONCODE v4 Transcript at Chinese Academy of Sciences + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.bioinfo.org/NONCODEv4/ + sampleId: NONHSAT000001 + urlPattern: http://www.bioinfo.org/NONCODEv4/show_rna.php?id={$id} + sampleId: NONHSAT000001 + - created: 2019-06-11T14:17:30.027+0000 + deprecated: false + deprecationDate: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. + id: 1370 + mirId: MIR:00000482 + modified: 2019-06-11T14:17:30.027+0000 + name: Oryzabase Gene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.gene + resources: + - deprecated: false + deprecationDate: + description: Oryzabase v4 Gene at National Institute of Genetics (Japan) + id: 1372 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1371 + location: + countryCode: JP + countryName: Japan + name: Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100618 + name: Oryzabase v4 Gene at National Institute of Genetics (Japan) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + sampleId: '117' + urlPattern: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/{$id} + sampleId: '117' + - created: 2019-06-11T14:17:30.248+0000 + deprecated: false + deprecationDate: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. + id: 1373 + mirId: MIR:00000483 + modified: 2019-06-11T14:17:30.248+0000 + name: Oryzabase Mutant + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.mutant + resources: + - deprecated: false + deprecationDate: + description: Oryzabase v4 Mutant at National Institute of Genetics (Japan) + id: 1374 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1371 + location: + countryCode: JP + countryName: Japan + name: Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100619 + name: Oryzabase v4 Mutant at National Institute of Genetics (Japan) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + sampleId: '21393' + urlPattern: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/{$id} + sampleId: '21393' + - created: 2019-06-11T14:17:30.425+0000 + deprecated: false + deprecationDate: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. + id: 1375 + mirId: MIR:00000484 + modified: 2019-06-11T14:17:30.425+0000 + name: Oryzabase Strain + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.strain + resources: + - deprecated: false + deprecationDate: + description: Oryzabase v4 Strain at National Institute of Genetics (Japan) + id: 1376 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1371 + location: + countryCode: JP + countryName: Japan + name: Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100620 + name: Oryzabase v4 Strain at National Institute of Genetics (Japan) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + sampleId: '1' + urlPattern: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/{$id} + sampleId: '1' + - created: 2019-06-11T14:17:30.616+0000 + deprecated: false + deprecationDate: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information. + id: 1377 + mirId: MIR:00000485 + modified: 2019-06-11T14:17:30.616+0000 + name: Oryzabase Stage + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.stage + resources: + - deprecated: false + deprecationDate: + description: Oryzabase v4 Stage at National Institute of Genetics (Japan) + id: 1378 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1371 + location: + countryCode: JP + countryName: Japan + name: Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100621 + name: Oryzabase v4 Stage at National Institute of Genetics (Japan) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + sampleId: '34' + urlPattern: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/{$id} + sampleId: '34' + - created: 2019-06-11T14:17:30.833+0000 + deprecated: false + deprecationDate: + description: Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. + id: 1379 + mirId: MIR:00000486 + modified: 2019-06-11T14:17:30.833+0000 + name: Oryza Tag Line + namespaceEmbeddedInLui: false + pattern: ^A[A-Z]+\d+$ + prefix: otl + resources: + - deprecated: false + deprecationDate: + description: Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI + id: 1381 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1380 + location: + countryCode: FR + countryName: France + name: CIRAD-INRA-SUPAGRO-UMII, Biological Systems Department, Montpellier + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100622 + name: Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://oryzatagline.cirad.fr/ + sampleId: AADB12 + urlPattern: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line={$id} + sampleId: AADB12 + - created: 2019-06-11T14:17:31.086+0000 + deprecated: false + deprecationDate: + description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. + id: 1382 + mirId: MIR:00000487 + modified: 2019-06-11T14:17:31.086+0000 + name: Gene Wiki + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: genewiki + resources: + - deprecated: false + deprecationDate: + description: Gene Wiki through BioGPS + id: 1383 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1111 + location: + countryCode: US + countryName: United States + name: Wikimedia Foundation, San Francisco, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100623 + name: Gene Wiki through BioGPS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://en.wikipedia.org/wiki/Gene_Wiki + sampleId: '1017' + urlPattern: http://plugins.biogps.org/cgi-bin/wp.cgi?id={$id} + sampleId: '1017' + - created: 2019-06-11T14:17:31.315+0000 + deprecated: false + deprecationDate: + description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. + id: 1384 + mirId: MIR:00000488 + modified: 2019-06-11T14:17:31.315+0000 + name: PaxDb Organism + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paxdb.organism + resources: + - deprecated: false + deprecationDate: + description: PaxDb v3 at University of Zurich + id: 1386 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1385 + location: + countryCode: CH + countryName: Switzerland + name: Institute of Molecular Life Sciences, University of Zurich, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100624 + name: PaxDb v3 at University of Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pax-db.org/ + sampleId: '9606' + urlPattern: http://pax-db.org/#!species/{$id} + sampleId: '9606' + - created: 2019-06-11T14:17:31.566+0000 + deprecated: false + deprecationDate: + description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. + id: 1387 + mirId: MIR:00000489 + modified: 2019-06-11T14:17:31.566+0000 + name: PaxDb Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paxdb.protein + resources: + - deprecated: false + deprecationDate: + description: PaxDb v3 at University of Zurich + id: 1388 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1385 + location: + countryCode: CH + countryName: Switzerland + name: Institute of Molecular Life Sciences, University of Zurich, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100625 + name: PaxDb v3 at University of Zurich + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pax-db.org/ + sampleId: '977869' + urlPattern: http://pax-db.org/#!protein/{$id} + sampleId: '977869' + - created: 2019-06-11T14:17:31.784+0000 + deprecated: false + deprecationDate: + description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. + id: 1389 + mirId: MIR:00000490 + modified: 2019-06-11T14:17:31.784+0000 + name: Protein Data Bank Ligand + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: pdb.ligand + resources: + - deprecated: false + deprecationDate: + description: PDB Ligand at RCSB + id: 1390 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 79 + location: + countryCode: US + countryName: United States + name: Rutgers, The State University of New Jersey + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100626 + name: PDB Ligand at RCSB + official: false + providerCode: rcsb + resourceHomeUrl: http://www.pdb.org/ + sampleId: TRQ + urlPattern: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId={$id} + - deprecated: false + deprecationDate: + description: PDB Ligand at Protein Databank in Europe (PDBe) + id: 1391 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100650 + name: PDB Ligand at Protein Databank in Europe (PDBe) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.pdbe.org/ + sampleId: TRQ + urlPattern: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/{$id} + sampleId: TRQ + - created: 2019-06-11T14:17:32.129+0000 + deprecated: false + deprecationDate: + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. + id: 1392 + mirId: MIR:00000491 + modified: 2019-06-11T14:17:32.129+0000 + name: MEROPS Inhibitor + namespaceEmbeddedInLui: false + pattern: ^I\d{2}\.\d{3}$ + prefix: merops.inhibitor + resources: + - deprecated: false + deprecationDate: + description: MEROPS Inhibitor at Sanger Institute + id: 1394 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1393 + location: + countryCode: GB + countryName: United Kingdom + name: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100632 + name: MEROPS Inhibitor at Sanger Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://merops.sanger.ac.uk/index.htm + sampleId: I31.952 + urlPattern: http://merops.sanger.ac.uk/cgi-bin/pepsum?id={$id} + sampleId: I31.952 + - created: 2019-06-11T14:17:32.366+0000 + deprecated: false + deprecationDate: + description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. + id: 1395 + mirId: MIR:00000492 + modified: 2019-06-11T14:17:32.366+0000 + name: Animal Diversity Web + namespaceEmbeddedInLui: false + pattern: ^[A-Z_a-z]+$ + prefix: adw + resources: + - deprecated: false + deprecationDate: + description: Animal Diversity Web at University of Michigan + id: 1397 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1396 + location: + countryCode: US + countryName: United States + name: University of Michigan Museum of Zoology, Ann Arbor, Michigan + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100633 + name: Animal Diversity Web at University of Michigan + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://animaldiversity.org/ + sampleId: Lycalopex_vetulus + urlPattern: https://animaldiversity.org/accounts/{$id}/ + sampleId: Lycalopex_vetulus + - created: 2019-06-11T14:17:32.633+0000 + deprecated: false + deprecationDate: + description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. + id: 1398 + mirId: MIR:00000493 + modified: 2019-06-11T14:17:32.633+0000 + name: GLIDA GPCR + namespaceEmbeddedInLui: false + pattern: ^[A-Z-_0-9]+$ + prefix: glida.gpcr + resources: + - deprecated: false + deprecationDate: + description: GLIDA GPCR at Kyoto University + id: 1400 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1399 + location: + countryCode: JP + countryName: Japan + name: Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100634 + name: GLIDA GPCR at Kyoto University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ + sampleId: ACM1_HUMAN + urlPattern: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id={$id} + sampleId: ACM1_HUMAN + - created: 2019-06-11T14:17:32.872+0000 + deprecated: false + deprecationDate: + description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. + id: 1401 + mirId: MIR:00000494 + modified: 2019-06-11T14:17:32.872+0000 + name: GLIDA Ligand + namespaceEmbeddedInLui: false + pattern: ^L\d+$ + prefix: glida.ligand + resources: + - deprecated: false + deprecationDate: + description: GLIDA Ligand at Kyoto University + id: 1402 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1399 + location: + countryCode: JP + countryName: Japan + name: Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100635 + name: GLIDA Ligand at Kyoto University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ + sampleId: L000001 + urlPattern: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id={$id} + sampleId: L000001 + - created: 2019-06-11T14:17:33.087+0000 + deprecated: false + deprecationDate: + description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. + id: 1403 + mirId: MIR:00000495 + modified: 2019-06-11T14:17:33.087+0000 + name: GRSDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: grsdb + resources: + - deprecated: false + deprecationDate: + description: GRSDB v2 at Ramapo College of New Jersey + id: 1405 + institution: + description: Established in 1969, Ramapo College offers bachelor’s degrees in the arts, business, humanities, social sciences and the sciences, as well as in professional studies, which include business, elementary education, nursing and social work. In fall 2020, the College will be enrolling students in both a bachelor’s and master’s degree in data science, only one of two higher education institutions in New Jersey to offer both programs. + homeUrl: https://www.ramapo.edu/ + id: 1404 + location: + countryCode: US + countryName: United States + name: Ramapo College + rorId: https://ror.org/03s2x9d90 + location: + countryCode: US + countryName: United States + mirId: MIR:00100636 + name: GRSDB v2 at Ramapo College of New Jersey + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bioinformatics.ramapo.edu/GRSDB2/ + sampleId: '10142' + urlPattern: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID={$id} + sampleId: '10142' + - created: 2019-06-11T14:17:37.549+0000 + deprecated: false + deprecationDate: + description: The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. + id: 1447 + mirId: MIR:00000513 + modified: 2019-06-11T14:17:37.549+0000 + name: ProteomeXchange + namespaceEmbeddedInLui: false + pattern: ^(R)?PXD\d{6}$ + prefix: px + resources: + - deprecated: false + deprecationDate: + description: ProteomeXchange at Seattle + id: 1449 + institution: + description: ISB was created in 2000 as the first-ever institute dedicated to systems biology. + homeUrl: https://isbscience.org/ + id: 193 + location: + countryCode: US + countryName: United States + name: Institute for Systems Biology + rorId: https://ror.org/02tpgw303 + location: + countryCode: US + countryName: United States + mirId: MIR:00100660 + name: ProteomeXchange at Seattle + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.proteomexchange.org/ + sampleId: PXD000500 + urlPattern: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID={$id} + sampleId: PXD000500 + - created: 2019-06-11T14:17:37.784+0000 + deprecated: false + deprecationDate: + description: Vocabulary used in the RDF representation of SBML models. + id: 1450 + mirId: MIR:00000514 + modified: 2019-06-11T14:17:37.784+0000 + name: SBML RDF Vocabulary + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+$ + prefix: biomodels.vocabulary + resources: + - deprecated: false + deprecationDate: + description: Vocabulary via BioModels.net + id: 1452 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100661 + name: Vocabulary via BioModels.net + official: false + providerCode: ebi + resourceHomeUrl: http://biomodels.net/rdf/vocabulary.rdf + sampleId: rateRule + urlPattern: http://biomodels.net/rdf/vocabulary.rdf#{$id} + sampleId: rateRule + - created: 2019-06-11T14:17:33.340+0000 + deprecated: false + deprecationDate: + description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. + id: 1406 + mirId: MIR:00000496 + modified: 2019-06-11T14:17:33.340+0000 + name: F-SNP + namespaceEmbeddedInLui: false + pattern: ^rs\d+$ + prefix: fsnp + resources: + - deprecated: false + deprecationDate: + description: F-SNP at Queen's University (Canada) + id: 1408 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1407 + location: + countryCode: CA + countryName: Canada + name: Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, Ontario + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100637 + name: F-SNP at Queen's University (Canada) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://compbio.cs.queensu.ca/F-SNP/ + sampleId: rs17852708 + urlPattern: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val={$id} + sampleId: rs17852708 + - created: 2019-06-11T14:17:33.593+0000 + deprecated: false + deprecationDate: + description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. + id: 1409 + mirId: MIR:00000497 + modified: 2019-06-11T14:17:33.593+0000 + name: Homeodomain Research + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hdr + resources: + - deprecated: false + deprecationDate: + description: Homeodomain Research at National Human Genome Research Institute (NIH) + id: 1411 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1410 + location: + countryCode: US + countryName: United States + name: Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100638 + name: Homeodomain Research at National Human Genome Research Institute (NIH) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://research.nhgri.nih.gov/apps/homeodomain/web/ + sampleId: '63' + urlPattern: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id={$id} + sampleId: '63' + - created: 2019-06-11T14:17:33.862+0000 + deprecated: false + deprecationDate: + description: Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. + id: 1412 + mirId: MIR:00000498 + modified: 2019-06-11T14:17:33.862+0000 + name: NORINE + namespaceEmbeddedInLui: false + pattern: ^NOR\d+$ + prefix: norine + resources: + - deprecated: false + deprecationDate: + description: NORINE at Computer Science Laboratory of Lille + id: 1414 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1413 + location: + countryCode: FR + countryName: France + name: Computer Science Laboratory of Lille, INRIA and ProBioGEM, University of Sciences and Technologies of Lille, Lille + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100639 + name: NORINE at Computer Science Laboratory of Lille + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bioinfo.lifl.fr/norine/ + sampleId: NOR00681 + urlPattern: http://bioinfo.lifl.fr/norine/result.jsp?ID={$id} + sampleId: NOR00681 + - created: 2019-06-11T14:17:34.104+0000 + deprecated: false + deprecationDate: + description: The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). + id: 1415 + mirId: MIR:00000499 + modified: 2019-06-11T14:17:34.104+0000 + name: Olfactory Receptor Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ordb + resources: + - deprecated: false + deprecationDate: + description: Olfactory Receptor Database at Yale University School of Medicine + id: 1417 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1416 + location: + countryCode: US + countryName: United States + name: Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100640 + name: Olfactory Receptor Database at Yale University School of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://senselab.med.yale.edu/OrDB/ + sampleId: '8497' + urlPattern: http://senselab.med.yale.edu/ORDB/Data/{$id} + sampleId: '8497' + - created: 2019-06-11T14:17:34.340+0000 + deprecated: false + deprecationDate: + description: OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors + id: 1418 + mirId: MIR:00000500 + modified: 2019-06-11T14:17:34.340+0000 + name: Odor Molecules DataBase + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: odor + resources: + - deprecated: false + deprecationDate: + description: Odor Molecules DataBase at Yale University School of Medicine + id: 1419 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1416 + location: + countryCode: US + countryName: United States + name: Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100641 + name: Odor Molecules DataBase at Yale University School of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://senselab.med.yale.edu/OdorDB + sampleId: '74' + urlPattern: http://senselab.med.yale.edu/OdorDB/Data/{$id}/?db=5 + sampleId: '74' + - created: 2019-06-11T14:17:34.528+0000 + deprecated: false + deprecationDate: + description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. + id: 1420 + mirId: MIR:00000501 + modified: 2019-06-11T14:17:34.528+0000 + name: P3DB Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: p3db.protein + resources: + - deprecated: false + deprecationDate: + description: P3DB Protein at University of Missouri + id: 1422 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1421 + location: + countryCode: US + countryName: United States + name: Department of Computer Science, University of Missouri, Columbia, Missouri + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100642 + name: P3DB Protein at University of Missouri + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.p3db.org/ + sampleId: '70' + urlPattern: http://www.p3db.org/protein.php?id={$id}&ref=0 + sampleId: '70' + - created: 2019-06-11T14:17:34.763+0000 + deprecated: false + deprecationDate: + description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. + id: 1423 + mirId: MIR:00000502 + modified: 2019-06-11T14:17:34.763+0000 + name: P3DB Site + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: p3db.site + resources: + - deprecated: false + deprecationDate: + description: P3DB Site at University of Missouri + id: 1424 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1421 + location: + countryCode: US + countryName: United States + name: Department of Computer Science, University of Missouri, Columbia, Missouri + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100643 + name: P3DB Site at University of Missouri + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.p3db.org/ + sampleId: '65' + urlPattern: http://www.p3db.org/phosphosite.php?id={$id}&ref=0 + sampleId: '65' + - created: 2019-06-11T14:17:35.217+0000 + deprecated: false + deprecationDate: + description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. + id: 1425 + mirId: MIR:00000503 + modified: 2019-06-11T14:17:35.217+0000 + name: TOPDB + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: topdb + resources: + - deprecated: false + deprecationDate: + description: TOPDB at Hungarian Academy of Sciences + id: 1427 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1426 + location: + countryCode: HU + countryName: Hungary + name: Institute of Enzymology, Hungarian Academy of Sciences, Budapest + rorId: + location: + countryCode: HU + countryName: Hungary + mirId: MIR:00100644 + name: TOPDB at Hungarian Academy of Sciences + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://topdb.enzim.hu/ + sampleId: AP00378 + urlPattern: http://topdb.enzim.hu/?m=show&id={$id} + sampleId: AP00378 + - created: 2019-06-11T14:17:35.485+0000 + deprecated: false + deprecationDate: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. + id: 1428 + mirId: MIR:00000504 + modified: 2019-06-11T14:17:35.485+0000 + name: Animal Genome Cattle QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cattleqtldb + resources: + - deprecated: false + deprecationDate: + description: Animal QTL Cattle at Iowa State University + id: 1430 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1429 + location: + countryCode: US + countryName: United States + name: Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100645 + name: Animal QTL Cattle at Iowa State University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.animalgenome.org/QTLdb + sampleId: '4685' + urlPattern: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id} + sampleId: '4685' + - created: 2019-06-11T14:17:35.752+0000 + deprecated: false + deprecationDate: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. + id: 1431 + mirId: MIR:00000505 + modified: 2019-06-11T14:17:35.752+0000 + name: Animal Genome Chicken QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chickenqtldb + resources: + - deprecated: false + deprecationDate: + description: Animal QTL Chicken at Iowa State University + id: 1432 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1429 + location: + countryCode: US + countryName: United States + name: Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100646 + name: Animal QTL Chicken at Iowa State University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.animalgenome.org/QTLdb + sampleId: '14362' + urlPattern: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id} + sampleId: '14362' + - created: 2019-06-11T14:17:35.969+0000 + deprecated: false + deprecationDate: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs. + id: 1433 + mirId: MIR:00000506 + modified: 2019-06-11T14:17:35.969+0000 + name: Animal Genome Pig QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pigqtldb + resources: + - deprecated: false + deprecationDate: + description: Animal QTL Pig at Iowa State University + id: 1434 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1429 + location: + countryCode: US + countryName: United States + name: Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100647 + name: Animal QTL Pig at Iowa State University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.animalgenome.org/QTLdb + sampleId: '14' + urlPattern: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id} + sampleId: '14' + - created: 2019-06-11T14:17:36.183+0000 + deprecated: false + deprecationDate: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. + id: 1435 + mirId: MIR:00000507 + modified: 2019-06-11T14:17:36.183+0000 + name: Animal Genome Sheep QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sheepqtldb + resources: + - deprecated: false + deprecationDate: + description: Animal QTL Sheep at Iowa State University + id: 1436 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1429 + location: + countryCode: US + countryName: United States + name: Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100648 + name: Animal QTL Sheep at Iowa State University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.animalgenome.org/QTLdb + sampleId: '19803' + urlPattern: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id} + sampleId: '19803' + - created: 2019-06-11T14:17:36.384+0000 + deprecated: false + deprecationDate: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. + id: 1437 + mirId: MIR:00000508 + modified: 2019-06-11T14:17:36.384+0000 + name: Gramene Growth Stage Ontology + namespaceEmbeddedInLui: true + pattern: ^GRO\:\d+$ + prefix: gramene.growthstage + resources: + - deprecated: false + deprecationDate: + description: Gramene Growth Stage Ontology at Cold Spring Harbor + id: 1438 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 556 + location: + countryCode: US + countryName: United States + name: Cold Spring Harbor Laboratory, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100649 + name: Gramene Growth Stage Ontology at Cold Spring Harbor + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gramene.org/ + sampleId: '0007133' + urlPattern: http://www.gramene.org/db/ontology/search?id=GRO:{$id} + sampleId: '0007133' + - created: 2019-06-11T14:17:36.594+0000 + deprecated: false + deprecationDate: + description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. + id: 1439 + mirId: MIR:00000510 + modified: 2019-06-11T14:17:36.594+0000 + name: MGnify Sample + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+$ + prefix: mgnify.samp + resources: + - deprecated: false + deprecationDate: + description: MGnify Sample + id: 1440 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100656 + name: MGnify Sample + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/metagenomics + sampleId: SRS086444 + urlPattern: https://www.ebi.ac.uk/metagenomics/samples/{$id} + sampleId: SRS086444 + - created: 2019-06-11T14:17:36.823+0000 + deprecated: false + deprecationDate: + description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. + id: 1441 + mirId: MIR:00000511 + modified: 2019-06-11T14:17:36.823+0000 + name: European Genome-phenome Archive Study + namespaceEmbeddedInLui: false + pattern: ^EGAS\d{11}$ + prefix: ega.study + resources: + - deprecated: false + deprecationDate: + description: EGA Study at European Bioinformatics Institute + id: 1442 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100657 + name: EGA Study at European Bioinformatics Institute + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/ega/studies + sampleId: EGAS00000000001 + urlPattern: https://www.ebi.ac.uk/ega/studies/{$id} + - deprecated: false + deprecationDate: + description: EGA Study through OmicsDI + id: 1443 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100851 + name: EGA Study through OmicsDI + official: false + providerCode: omicsdi + resourceHomeUrl: https://www.omicsdi.org/ + sampleId: EGAS00000000001 + urlPattern: https://www.omicsdi.org/dataset/ega/{$id} + sampleId: EGAS00000000001 + - created: 2019-06-11T14:17:37.233+0000 + deprecated: false + deprecationDate: + description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. + id: 1444 + mirId: MIR:00000512 + modified: 2019-06-11T14:17:37.233+0000 + name: European Genome-phenome Archive Dataset + namespaceEmbeddedInLui: false + pattern: ^EGAD\d{11}$ + prefix: ega.dataset + resources: + - deprecated: false + deprecationDate: + description: EGA Dataset at European Bioinformatics Institute + id: 1445 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100658 + name: EGA Dataset at European Bioinformatics Institute + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/ega/dataset + sampleId: EGAD00000000001 + urlPattern: https://www.ebi.ac.uk/ega/datasets/{$id} + - deprecated: false + deprecationDate: + description: EGA Dataset through OmicsDI + id: 1446 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100852 + name: EGA Dataset through OmicsDI + official: false + providerCode: omicsdi + resourceHomeUrl: https://www.omicsdi.org/ + sampleId: EGAD00000000001 + urlPattern: https://www.omicsdi.org/dataset/ega/{$id} + sampleId: EGAD00000000001 + - created: 2019-06-11T14:17:38.030+0000 + deprecated: false + deprecationDate: + description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. + id: 1453 + mirId: MIR:00000515 + modified: 2019-06-11T14:17:38.030+0000 + name: PRIDE Project + namespaceEmbeddedInLui: false + pattern: ^P(X|R)D\d{6}$ + prefix: pride.project + resources: + - deprecated: false + deprecationDate: + description: PRIDE Project at EBI + id: 1454 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100662 + name: PRIDE Project at EBI + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/pride/ + sampleId: PXD000440 + urlPattern: https://www.ebi.ac.uk/pride/archive/projects/{$id} + - deprecated: false + deprecationDate: + description: PRIDE Project through OmicsDI + id: 1455 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100858 + name: PRIDE Project through OmicsDI + official: false + providerCode: omicsdi + resourceHomeUrl: https://www.omicsdi.org/ + sampleId: PXD000440 + urlPattern: https://www.omicsdi.org/dataset/pride/{$id} + sampleId: PXD000440 + - created: 2019-06-11T14:17:38.379+0000 + deprecated: false + deprecationDate: + description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. + id: 1456 + mirId: MIR:00000516 + modified: 2019-06-11T14:17:38.379+0000 + name: Antibody Registry + namespaceEmbeddedInLui: false + pattern: ^\d{6}$ + prefix: antibodyregistry + resources: + - deprecated: false + deprecationDate: + description: Antibody Registry at University of California + id: 1458 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1457 + location: + countryCode: US + countryName: United States + name: Neuroscience Information Framework, University of California, San Diego, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100664 + name: Antibody Registry at University of California + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://antibodyregistry.org/ + sampleId: '493771' + urlPattern: http://antibodyregistry.org/AB_{$id} + sampleId: '493771' + - created: 2019-06-11T14:17:38.625+0000 + deprecated: false + deprecationDate: + description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. + id: 1459 + mirId: MIR:00000517 + modified: 2019-06-11T14:17:38.625+0000 + name: Mathematical Modelling Ontology + namespaceEmbeddedInLui: false + pattern: ^MAMO_\d{7}$ + prefix: mamo + resources: + - deprecated: false + deprecationDate: + description: MAMO through BioPortal + id: 1460 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100665 + name: MAMO through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/MAMO + sampleId: MAMO_0000026 + urlPattern: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/{$id} + - deprecated: false + deprecationDate: + description: MaMO through OLS + id: 1461 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100758 + name: MaMO through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/mamo + sampleId: MAMO_0000026 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form={$id} + sampleId: MAMO_0000026 + - created: 2019-06-11T14:17:38.985+0000 + deprecated: false + deprecationDate: + description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. + id: 1462 + mirId: MIR:00000518 + modified: 2019-06-11T14:17:38.985+0000 + name: Plant Environment Ontology + namespaceEmbeddedInLui: true + pattern: ^(P)?EO\:\d{7}$ + prefix: eo + resources: + - deprecated: false + deprecationDate: + description: Plant Environment Ontology through Gramene + id: 1463 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 556 + location: + countryCode: US + countryName: United States + name: Cold Spring Harbor Laboratory, New York + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100667 + name: Plant Environment Ontology through Gramene + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://archive.gramene.org/db/ontology/search_term?id=EO:0007359 + sampleId: '0007404' + urlPattern: http://archive.gramene.org/db/ontology/search?query=EO:{$id} + - deprecated: false + deprecationDate: + description: Plant Environment Ontology through BioPortal + id: 1464 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100668 + name: Plant Environment Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/PECO + sampleId: '0007404' + urlPattern: http://purl.bioontology.org/ontology/PECO/EO:{$id} + - deprecated: false + deprecationDate: + description: Plant Environment Ontology through OLS + id: 1465 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100669 + name: Plant Environment Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/eo + sampleId: '0007404' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=EO:{$id} + sampleId: '0007404' + - created: 2019-06-11T14:17:39.487+0000 + deprecated: false + deprecationDate: + description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. + id: 1466 + mirId: MIR:00000519 + modified: 2019-06-11T14:17:39.487+0000 + name: Identifiers.org Terms + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+$ + prefix: idot + resources: + - deprecated: false + deprecationDate: + description: IdoT via biomodels.net + id: 1467 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100670 + name: IdoT via biomodels.net + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://identifiers.org/ + sampleId: identifierPattern + urlPattern: https://biomodels.net/vocab/idot.rdf#{$id} + sampleId: identifierPattern + - created: 2019-06-11T14:17:39.906+0000 + deprecated: false + deprecationDate: + description: The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]. + id: 1470 + mirId: MIR:00000521 + modified: 2019-06-11T14:17:39.906+0000 + name: Yeast Intron Database v4.3 + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: yeastintron + resources: + - deprecated: false + deprecationDate: + description: Yeast Intron Database version 4.3 at Baskin School of Engineering + id: 1471 + institution: + description: > + UC Santa Cruz opened in 1965 with 650 students. During the + 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate + students were enrolled. + homeUrl: https://www.ucsc.edu + id: 1319 + location: + countryCode: US + countryName: United States + name: University of California, Santa Cruz + rorId: https://ror.org/03s65by71 + location: + countryCode: US + countryName: United States + mirId: MIR:00100673 + name: Yeast Intron Database version 4.3 at Baskin School of Engineering + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://intron.ucsc.edu/yeast4.3/ + sampleId: SNR17A + urlPattern: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName={$id} + sampleId: SNR17A + - created: 2019-06-11T14:17:40.104+0000 + deprecated: false + deprecationDate: + description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. + id: 1472 + mirId: MIR:00000522 + modified: 2019-06-11T14:17:40.104+0000 + name: Antibiotic Resistance Genes Database + namespaceEmbeddedInLui: false + pattern: ^[A-Z_]{3}[0-9]{4,}$ + prefix: ardb + resources: + - deprecated: false + deprecationDate: + description: ARDB at University of Maryland + id: 1474 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1473 + location: + countryCode: US + countryName: United States + name: Center for Bioinformatics and Computational Biology, University of Maryland, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100678 + name: ARDB at University of Maryland + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ardb.cbcb.umd.edu/ + sampleId: CAE46076 + urlPattern: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term={$id} + sampleId: CAE46076 + - created: 2019-06-11T14:17:40.344+0000 + deprecated: false + deprecationDate: + description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. + id: 1475 + mirId: MIR:00000524 + modified: 2019-06-11T14:17:40.344+0000 + name: ProteomicsDB Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: proteomicsdb.protein + resources: + - deprecated: false + deprecationDate: + description: Proteomics DB Protein at Center for Integrated Protein Science + id: 1477 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1476 + location: + countryCode: DE + countryName: Germany + name: Center for Integrated Protein Science, Munich, + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100680 + name: Proteomics DB Protein at Center for Integrated Protein Science + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.proteomicsdb.org/#human + sampleId: '53504' + urlPattern: https://www.proteomicsdb.org/#human/proteinDetails/{$id}/summary + sampleId: '53504' + - created: 2019-06-11T14:17:40.583+0000 + deprecated: false + deprecationDate: + description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. + id: 1478 + mirId: MIR:00000525 + modified: 2019-06-11T14:17:40.583+0000 + name: ProteomicsDB Peptide + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: proteomicsdb.peptide + resources: + - deprecated: false + deprecationDate: + description: Proteomics DB Peptide at Center for Integrated Protein Science + id: 1480 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1479 + location: + countryCode: DE + countryName: Germany + name: Center for Integrated Protein Science, Munich + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100681 + name: Proteomics DB Peptide at Center for Integrated Protein Science + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.proteomicsdb.org/#peptideSearch + sampleId: '53504' + urlPattern: https://www.proteomicsdb.org/#human/proteinDetails/{$id}/peptides/ + sampleId: '53504' + - created: 2019-06-11T14:17:40.825+0000 + deprecated: false + deprecationDate: + description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. + id: 1481 + mirId: MIR:00000526 + modified: 2019-06-11T14:17:40.825+0000 + name: Human Proteome Map Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hpm.protein + resources: + - deprecated: false + deprecationDate: + description: Human Proteome Map Protein at Institute of Bioinformatics (Bangalore) + id: 1482 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1087 + location: + countryCode: IN + countryName: India + name: Institute of Bioinformatics, International Tech Park, Bangalore + rorId: + location: + countryCode: IN + countryName: India + mirId: MIR:00100682 + name: Human Proteome Map Protein at Institute of Bioinformatics (Bangalore) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.humanproteomemap.org/index.php + sampleId: '1968' + urlPattern: http://www.humanproteomemap.org/protein.php?hpm_id={$id} + sampleId: '1968' + - created: 2019-06-11T14:17:41.032+0000 + deprecated: false + deprecationDate: + description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. + id: 1483 + mirId: MIR:00000527 + modified: 2019-06-11T14:17:41.032+0000 + name: Human Proteome Map Peptide + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hpm.peptide + resources: + - deprecated: false + deprecationDate: + description: Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore) + id: 1484 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1087 + location: + countryCode: IN + countryName: India + name: Institute of Bioinformatics, International Tech Park, Bangalore + rorId: + location: + countryCode: IN + countryName: India + mirId: MIR:00100683 + name: Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.humanproteomemap.org/index.php + sampleId: '9606117' + urlPattern: http://www.humanproteomemap.org/spectrum.php?pep_id={$id} + sampleId: '9606117' + - created: 2019-06-11T14:17:41.273+0000 + deprecated: false + deprecationDate: + description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. + id: 1485 + mirId: MIR:00000528 + modified: 2019-06-11T14:17:41.273+0000 + name: DrugBank Target v4 + namespaceEmbeddedInLui: false + pattern: ^BE\d{7}$ + prefix: drugbankv4.target + resources: + - deprecated: false + deprecationDate: + description: DrugBank Target information version 4 + id: 1487 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1486 + location: + countryCode: CA + countryName: Canada + name: Departments of Computing Science, Biological Sciences, University of Alberta + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100687 + name: DrugBank Target information version 4 + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.drugbank.ca/targets + sampleId: BE0000048 + urlPattern: http://www.drugbank.ca/biodb/bio_entities/{$id} + sampleId: BE0000048 + - created: 2019-06-11T14:17:41.559+0000 + deprecated: false + deprecationDate: + description: ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. + id: 1488 + mirId: MIR:00000529 + modified: 2019-06-11T14:17:41.559+0000 + name: ZINC + namespaceEmbeddedInLui: false + pattern: ^(ZINC)?\d+$ + prefix: zinc + resources: + - deprecated: false + deprecationDate: + description: ZINC at University of California (San Francisco) + id: 1490 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1489 + location: + countryCode: US + countryName: United States + name: Shoichet Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100688 + name: ZINC at University of California (San Francisco) + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://zinc15.docking.org/ + sampleId: ZINC1084 + urlPattern: http://zinc15.docking.org/substances/{$id} + sampleId: ZINC1084 + - created: 2019-06-11T14:17:41.796+0000 + deprecated: false + deprecationDate: + description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. + id: 1491 + mirId: MIR:00000530 + modified: 2019-06-11T14:17:41.796+0000 + name: FooDB Compound + namespaceEmbeddedInLui: false + pattern: ^FDB\d+$ + prefix: foodb.compound + resources: + - deprecated: false + deprecationDate: + description: FooDB database of food additives at University of Alberta + id: 1492 + institution: + description: The University of Alberta in Edmonton is one of Canada's top teaching and research universities, with an international reputation for excellence across the humanities, sciences, creative arts, business, engineering and health sciences. + homeUrl: https://www.ualberta.ca + id: 334 + location: + countryCode: CA + countryName: Canada + name: University of Alberta + rorId: https://ror.org/0160cpw27 + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100689 + name: FooDB database of food additives at University of Alberta + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://foodb.ca/foods + sampleId: FDB002100 + urlPattern: http://foodb.ca/compounds/{$id} + sampleId: FDB002100 + - created: 2019-06-11T14:17:41.988+0000 + deprecated: false + deprecationDate: + description: The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information. + id: 1493 + mirId: MIR:00000531 + modified: 2019-06-11T14:17:41.988+0000 + name: UNII + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: unii + resources: + - deprecated: false + deprecationDate: + description: UNII at U.S. Food and Drug Administration + id: 1494 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1238 + location: + countryCode: US + countryName: United States + name: U.S. Food and Drug Administration, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100690 + name: UNII at U.S. Food and Drug Administration + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://fdasis.nlm.nih.gov/srs/ + sampleId: 3G6A5W338E + urlPattern: http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno={$id} + sampleId: 3G6A5W338E + - created: 2019-06-11T14:17:42.194+0000 + deprecated: false + deprecationDate: + description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." + id: 1495 + mirId: MIR:00000532 + modified: 2019-06-11T14:17:42.194+0000 + name: Orphanet Rare Disease Ontology + namespaceEmbeddedInLui: false + pattern: ^Orphanet(_|:)C?\d+$ + prefix: orphanet.ordo + resources: + - deprecated: false + deprecationDate: + description: ORDO via OLS + id: 1496 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100705 + name: ORDO via OLS + official: true + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/ordo + sampleId: Orphanet_C023 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form={$id} + sampleId: Orphanet_C023 + - created: 2019-06-11T14:17:42.461+0000 + deprecated: false + deprecationDate: + description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. + id: 1497 + mirId: MIR:00000533 + modified: 2019-06-11T14:17:42.461+0000 + name: Protein Affinity Reagents + namespaceEmbeddedInLui: false + pattern: ^PAR:\d+$ + prefix: psipar + resources: + - deprecated: false + deprecationDate: + description: Protein Affinity Reagents through OLS + id: 1498 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100709 + name: Protein Affinity Reagents through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR + sampleId: PAR:0116 + urlPattern: https://www.ebi.ac.uk/ontology-lookup/?termId={$id} + sampleId: PAR:0116 + - created: 2019-06-11T14:17:42.685+0000 + deprecated: false + deprecationDate: + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. + id: 1499 + mirId: MIR:00000534 + modified: 2019-06-11T14:17:42.685+0000 + name: ClinVar Record + namespaceEmbeddedInLui: false + pattern: ^RCV\d+(\.\d+)?$ + prefix: clinvar.record + resources: + - deprecated: false + deprecationDate: + description: ClinVar Record at NCBI + id: 1501 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100710 + name: ClinVar Record at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: http://www.ncbi.nlm.nih.gov/clinvar/ + sampleId: RCV000033555.3 + urlPattern: http://www.ncbi.nlm.nih.gov/clinvar/{$id}/ + sampleId: RCV000033555.3 + - created: 2019-06-11T14:17:42.938+0000 + deprecated: false + deprecationDate: + description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. + id: 1502 + mirId: MIR:00000535 + modified: 2019-06-11T14:17:42.938+0000 + name: MGnify Project + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+$ + prefix: mgnify.proj + resources: + - deprecated: false + deprecationDate: + description: MGnify Project + id: 1503 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100711 + name: MGnify Project + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/metagenomics + sampleId: ERP004492 + urlPattern: https://www.ebi.ac.uk/metagenomics/projects/{$id} + sampleId: ERP004492 + - created: 2019-06-11T14:17:43.129+0000 + deprecated: false + deprecationDate: + description: "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population." + id: 1504 + mirId: MIR:00000536 + modified: 2019-06-11T14:17:43.129+0000 + name: EU Clinical Trials + namespaceEmbeddedInLui: false + pattern: ^\d{4}\-\d{6}\-\d{2}$ + prefix: euclinicaltrials + resources: + - deprecated: false + deprecationDate: + description: EU Clinical Trials at European Medicines Agency + id: 1506 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1505 + location: + countryCode: GB + countryName: United Kingdom + name: European Medicines Agency, London + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100712 + name: EU Clinical Trials at European Medicines Agency + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.clinicaltrialsregister.eu/ + sampleId: 2008-005144-16 + urlPattern: https://www.clinicaltrialsregister.eu/ctr-search/search?query={$id} + sampleId: 2008-005144-16 + - created: 2019-06-11T14:17:43.371+0000 + deprecated: false + deprecationDate: + description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. + id: 1507 + mirId: MIR:00000537 + modified: 2019-06-11T14:17:43.371+0000 + name: Google Patents + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}\d+([A-Z])?$ + prefix: google.patent + resources: + - deprecated: false + deprecationDate: + description: Google Patents at Google + id: 1509 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1508 + location: + countryCode: GB + countryName: United Kingdom + name: Google Incorporated + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100714 + name: Google Patents at Google + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.google.com/patents/ + sampleId: US4145692 + urlPattern: https://www.google.com/patents/{$id} + sampleId: US4145692 + - created: 2019-06-11T14:17:43.583+0000 + deprecated: false + deprecationDate: + description: The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. + id: 1510 + mirId: MIR:00000538 + modified: 2019-06-11T14:17:43.583+0000 + name: USPTO + namespaceEmbeddedInLui: false + pattern: ^(D|PP|R|T|H|X|AI)?\d+$ + prefix: uspto + resources: + - deprecated: false + deprecationDate: + description: USPTO patents at USPTO + id: 1512 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1511 + location: + countryCode: US + countryName: United States + name: United States Patent and Trademark Office + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100715 + name: USPTO patents at USPTO + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://patft.uspto.gov/netahtml/PTO/index.html + sampleId: '4145692' + urlPattern: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/{$id} + sampleId: '4145692' + - created: 2019-06-11T14:17:43.853+0000 + deprecated: false + deprecationDate: + description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. + id: 1513 + mirId: MIR:00000539 + modified: 2019-06-11T14:17:43.853+0000 + name: Cooperative Patent Classification + namespaceEmbeddedInLui: false + pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ + prefix: cpc + resources: + - deprecated: false + deprecationDate: + description: Cooperative Patent Classification at Espace + id: 1515 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1514 + location: + countryCode: US + countryName: United States + name: Espace, European Patent Office + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100716 + name: Cooperative Patent Classification at Espace + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://worldwide.espacenet.com/classification + sampleId: A01M1/026 + urlPattern: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC={$id} + sampleId: A01M1/026 + - created: 2019-06-11T14:17:44.062+0000 + deprecated: false + deprecationDate: + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. + id: 1516 + mirId: MIR:00000540 + modified: 2019-06-11T14:17:44.062+0000 + name: GWAS Central Study + namespaceEmbeddedInLui: false + pattern: ^HGVST\d+$ + prefix: gwascentral.study + resources: + - deprecated: false + deprecationDate: + description: GWAS Central Study at University of Leicester + id: 1517 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1079 + location: + countryCode: GB + countryName: United Kingdom + name: Department of Genetics, University of Leicester, Leicester + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100717 + name: GWAS Central Study at University of Leicester + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.gwascentral.org/studies + sampleId: HGVST1828 + urlPattern: https://www.gwascentral.org/study/{$id} + sampleId: HGVST1828 + - created: 2019-06-11T14:17:44.275+0000 + deprecated: false + deprecationDate: + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. + id: 1518 + mirId: MIR:00000541 + modified: 2019-06-11T14:17:44.275+0000 + name: ExAC Variant + namespaceEmbeddedInLui: false + pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ + prefix: exac.variant + resources: + - deprecated: false + deprecationDate: + description: ExAC Variant at Exome Aggregation Consortium + id: 1520 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1519 + location: + countryCode: US + countryName: United States + name: Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100718 + name: ExAC Variant at Exome Aggregation Consortium + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://exac.broadinstitute.org/ + sampleId: 22-46615880-T-C + urlPattern: http://exac.broadinstitute.org/variant/{$id} + sampleId: 22-46615880-T-C + - created: 2019-06-11T14:17:44.511+0000 + deprecated: false + deprecationDate: + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. + id: 1521 + mirId: MIR:00000542 + modified: 2019-06-11T14:17:44.511+0000 + name: GWAS Central Marker + namespaceEmbeddedInLui: false + pattern: ^HGVM\d+$ + prefix: gwascentral.marker + resources: + - deprecated: false + deprecationDate: + description: GWAS Central Marker at University of Leicester + id: 1522 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1079 + location: + countryCode: GB + countryName: United Kingdom + name: Department of Genetics, University of Leicester, Leicester + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100719 + name: GWAS Central Marker at University of Leicester + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.gwascentral.org/markers/ + sampleId: HGVM15354 + urlPattern: https://www.gwascentral.org/marker/{$id} + sampleId: HGVM15354 + - created: 2019-06-11T14:17:47.850+0000 + deprecated: false + deprecationDate: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes. + id: 1555 + mirId: MIR:00000556 + modified: 2019-06-11T14:17:47.850+0000 + name: BiGG Metabolite + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.metabolite + resources: + - deprecated: false + deprecationDate: + description: BiGG Metabolite at University of Cakifornia + id: 1556 + institution: + description: >- + is a public research university in San Diego, California. + + Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students. + homeUrl: https://ucsd.edu/ + id: 190 + location: + countryCode: US + countryName: United States + name: University of California, San Diego + rorId: https://ror.org/0168r3w48 + location: + countryCode: US + countryName: United States + mirId: MIR:00100733 + name: BiGG Metabolite at University of Cakifornia + official: false + providerCode: ucsd + resourceHomeUrl: http://bigg.ucsd.edu/universal/metabolites + sampleId: 12dgr161 + urlPattern: http://bigg.ucsd.edu/models/universal/metabolites/{$id} + sampleId: 12dgr161 + - created: 2019-06-11T14:17:44.903+0000 + deprecated: false + deprecationDate: + description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.' + id: 1525 + mirId: MIR:00000544 + modified: 2019-06-11T14:17:44.903+0000 + name: LINCS Cell + namespaceEmbeddedInLui: false + pattern: (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$) + prefix: lincs.cell + resources: + - deprecated: false + deprecationDate: + description: LINCS Portal + id: 1527 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1526 + location: + countryCode: US + countryName: United States + name: University of Miami, BD2K-LINCS DCIC + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100721 + name: LINCS Portal + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://lincsportal.ccs.miami.edu/cells/ + sampleId: LCL-2085 + urlPattern: http://lincsportal.ccs.miami.edu/cells/#/view/{$id} + sampleId: LCL-2085 + - created: 2019-06-11T14:17:45.145+0000 + deprecated: false + deprecationDate: + description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. + id: 1528 + mirId: MIR:00000545 + modified: 2019-06-11T14:17:45.145+0000 + name: LINCS Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: lincs.protein + resources: + - deprecated: false + deprecationDate: + description: LINCS Protein at Harvard Medical School + id: 1529 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1322 + location: + countryCode: US + countryName: United States + name: Harvard Medical School, Boston, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100722 + name: LINCS Protein at Harvard Medical School + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://lincs.hms.harvard.edu/db/proteins/ + sampleId: '200282' + urlPattern: http://lincs.hms.harvard.edu/db/proteins/{$id}/ + sampleId: '200282' + - created: 2019-06-11T14:17:45.396+0000 + deprecated: false + deprecationDate: + description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). + id: 1530 + mirId: MIR:00000546 + modified: 2019-06-11T14:17:45.396+0000 + name: LINCS Small Molecule + namespaceEmbeddedInLui: false + pattern: ^LSM-\d+$ + prefix: lincs.smallmolecule + resources: + - deprecated: false + deprecationDate: + description: LINCS Portal + id: 1532 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1531 + location: + countryCode: US + countryName: United States + name: University of Miami, BD2K-LINCS DCIC, USA + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100723 + name: LINCS Portal + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://lincsportal.ccs.miami.edu/SmallMolecules/ + sampleId: LSM-6306 + urlPattern: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/{$id} + sampleId: LSM-6306 + - created: 2019-06-11T14:17:45.691+0000 + deprecated: false + deprecationDate: + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. + id: 1533 + mirId: MIR:00000547 + modified: 2019-06-11T14:17:45.691+0000 + name: ExAC Transcript + namespaceEmbeddedInLui: false + pattern: ^ENST\d{11}$ + prefix: exac.transcript + resources: + - deprecated: false + deprecationDate: + description: ExAC Transcript at Exome Aggregation Consortium + id: 1534 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1519 + location: + countryCode: US + countryName: United States + name: Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100724 + name: ExAC Transcript at Exome Aggregation Consortium + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://exac.broadinstitute.org/ + sampleId: ENST00000407236 + urlPattern: http://exac.broadinstitute.org/transcript/{$id} + sampleId: ENST00000407236 + - created: 2019-06-11T14:17:45.890+0000 + deprecated: false + deprecationDate: + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. + id: 1535 + mirId: MIR:00000548 + modified: 2019-06-11T14:17:45.890+0000 + name: ExAC Gene + namespaceEmbeddedInLui: false + pattern: ^ENSG\d{11}$ + prefix: exac.gene + resources: + - deprecated: false + deprecationDate: + description: ExAC Gene at Exome Aggregation Consortium + id: 1536 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1519 + location: + countryCode: US + countryName: United States + name: Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100725 + name: ExAC Gene at Exome Aggregation Consortium + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://exac.broadinstitute.org/ + sampleId: ENSG00000169174 + urlPattern: http://exac.broadinstitute.org/gene/{$id} + sampleId: ENSG00000169174 + - created: 2019-06-11T14:17:46.612+0000 + deprecated: false + deprecationDate: + description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds. + id: 1542 + mirId: MIR:00000551 + modified: 2019-06-11T14:17:46.612+0000 + name: UniPathway Compound + namespaceEmbeddedInLui: false + pattern: ^UPC\d{5}$ + prefix: unipathway.compound + resources: + - deprecated: true + deprecationDate: 2019-10-01T12:10:54.792+0000 + description: UniPathway Compound at Swiss Institute of Bioinformatics (SIB) + id: 1544 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100728 + name: UniPathway Compound at Swiss Institute of Bioinformatics (SIB) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.grenoble.prabi.fr/obiwarehouse/unipathway + sampleId: UPC04349 + urlPattern: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid={$id} + sampleId: UPC04349 + - created: 2019-06-11T14:17:46.875+0000 + deprecated: false + deprecationDate: + description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. + id: 1545 + mirId: MIR:00000552 + modified: 2019-06-11T14:17:46.875+0000 + name: SEED Subsystem + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: seed + resources: + - deprecated: true + deprecationDate: 2019-10-08T08:49:23.021+0000 + description: SEED Subsystem at Argonne National Laboratory + id: 1547 + institution: + description: Argonne is a multidisciplinary science and engineering research center, where talented scientists and engineers work together to answer the biggest questions facing humanity, from how to obtain affordable clean energy to protecting ourselves and our environment. + homeUrl: https://www.anl.gov + id: 1546 + location: + countryCode: US + countryName: United States + name: Argonne National Laboratory + rorId: https://ror.org/05gvnxz63 + location: + countryCode: US + countryName: United States + mirId: MIR:00100729 + name: SEED Subsystem at Argonne National Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://seed-viewer.theseed.org/seedviewer.cgi + sampleId: Biotin_biosynthesis + urlPattern: https://registry.identifiers.org/deprecation/resources/MIR:00100729/{$id} + sampleId: Biotin_biosynthesis + - created: 2019-06-11T14:17:47.133+0000 + deprecated: false + deprecationDate: + description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. + id: 1548 + mirId: MIR:00000553 + modified: 2019-06-11T14:17:47.133+0000 + name: SEED Compound + namespaceEmbeddedInLui: false + pattern: ^cpd\d+$ + prefix: seed.compound + resources: + - deprecated: false + deprecationDate: + description: SEED Compound at Argonne National Laboratory + id: 1549 + institution: + description: Argonne is a multidisciplinary science and engineering research center, where talented scientists and engineers work together to answer the biggest questions facing humanity, from how to obtain affordable clean energy to protecting ourselves and our environment. + homeUrl: https://www.anl.gov + id: 1546 + location: + countryCode: US + countryName: United States + name: Argonne National Laboratory + rorId: https://ror.org/05gvnxz63 + location: + countryCode: US + countryName: United States + mirId: MIR:00100730 + name: SEED Compound at Argonne National Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://modelseed.org/ + sampleId: cpd15380 + urlPattern: http://modelseed.org/biochem/compounds/{$id} + sampleId: cpd15380 + - created: 2019-06-11T14:17:47.362+0000 + deprecated: false + deprecationDate: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. + id: 1550 + mirId: MIR:00000554 + modified: 2019-06-11T14:17:47.362+0000 + name: BiGG Model + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.model + resources: + - deprecated: false + deprecationDate: + description: BiGG Model at University of California + id: 1552 + institution: + description: >- + is a public research university in San Diego, California. + + Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students. + homeUrl: https://ucsd.edu/ + id: 190 + location: + countryCode: US + countryName: United States + name: University of California, San Diego + rorId: https://ror.org/0168r3w48 + location: + countryCode: US + countryName: United States + mirId: MIR:00100731 + name: BiGG Model at University of California + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bigg.ucsd.edu/models + sampleId: iECABU_c1320 + urlPattern: http://bigg.ucsd.edu/models/{$id} + sampleId: iECABU_c1320 + - created: 2019-06-11T14:17:47.621+0000 + deprecated: false + deprecationDate: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. + id: 1553 + mirId: MIR:00000555 + modified: 2019-06-11T14:17:47.621+0000 + name: BiGG Compartment + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z]+$ + prefix: bigg.compartment + resources: + - deprecated: false + deprecationDate: + description: BiGG Compartment at University of California + id: 1554 + institution: + description: >- + is a public research university in San Diego, California. + + Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students. + homeUrl: https://ucsd.edu/ + id: 190 + location: + countryCode: US + countryName: United States + name: University of California, San Diego + rorId: https://ror.org/0168r3w48 + location: + countryCode: US + countryName: United States + mirId: MIR:00100732 + name: BiGG Compartment at University of California + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bigg.ucsd.edu/compartments/ + sampleId: c + urlPattern: http://bigg.ucsd.edu/compartments/{$id} + sampleId: c + - created: 2019-06-11T14:17:46.087+0000 + deprecated: false + deprecationDate: + description: Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. + id: 1537 + mirId: MIR:00000549 + modified: 2020-11-30T14:15:44.647+0000 + name: Wikidata + namespaceEmbeddedInLui: false + pattern: ^(Q|P)\d+$ + prefix: wikidata + resources: + - deprecated: false + deprecationDate: + description: Wikidata at Wikimedia Foundation + id: 1538 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1111 + location: + countryCode: US + countryName: United States + name: Wikimedia Foundation, San Francisco, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100726 + name: Wikidata at Wikimedia Foundation + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.wikidata.org/ + sampleId: Q2207226 + urlPattern: http://www.wikidata.org/entity/{$id} + sampleId: Q2207226 + - created: 2019-06-11T14:17:48.059+0000 + deprecated: false + deprecationDate: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. + id: 1557 + mirId: MIR:00000557 + modified: 2019-06-11T14:17:48.059+0000 + name: BiGG Reaction + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.reaction + resources: + - deprecated: false + deprecationDate: + description: BiGG Reaction at University of California + id: 1558 + institution: + description: >- + is a public research university in San Diego, California. + + Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students. + homeUrl: https://ucsd.edu/ + id: 190 + location: + countryCode: US + countryName: United States + name: University of California, San Diego + rorId: https://ror.org/0168r3w48 + location: + countryCode: US + countryName: United States + mirId: MIR:00100734 + name: BiGG Reaction at University of California + official: false + providerCode: ucsd + resourceHomeUrl: http://bigg.ucsd.edu/universal/reactions + sampleId: 13GS + urlPattern: http://bigg.ucsd.edu/models/universal/reactions/{$id} + sampleId: 13GS + - created: 2019-06-11T14:17:48.502+0000 + deprecated: false + deprecationDate: + description: The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. + id: 1561 + mirId: MIR:00000559 + modified: 2019-06-11T14:17:48.502+0000 + name: UMLS + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: umls + resources: + - deprecated: false + deprecationDate: + description: Unified Medical Language System at LinkedLifeData + id: 1562 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 63 + location: + countryCode: BG + countryName: Bulgaria + name: Linkedlifedata, Ontotext, Sofia + rorId: + location: + countryCode: BG + countryName: Bulgaria + mirId: MIR:00100736 + name: Unified Medical Language System at LinkedLifeData + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://linkedlifedata.com/ + sampleId: C0021390 + urlPattern: http://linkedlifedata.com/resource/umls/id/{$id} + sampleId: C0021390 + - created: 2019-06-11T14:17:48.947+0000 + deprecated: false + deprecationDate: + description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. + id: 1565 + mirId: MIR:00000561 + modified: 2019-06-11T14:17:48.947+0000 + name: Electron Microscopy Data Bank + namespaceEmbeddedInLui: false + pattern: ^EMD-\d{4}$ + prefix: emdb + resources: + - deprecated: false + deprecationDate: + description: EMDB at Protein Data Bank in Europe + id: 1566 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100738 + name: EMDB at Protein Data Bank in Europe + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/pdbe/emdb/ + sampleId: EMD-1001 + urlPattern: https://www.ebi.ac.uk/pdbe/entry/emdb/{$id} + sampleId: EMD-1001 + - created: 2019-06-11T14:17:49.171+0000 + deprecated: false + deprecationDate: + description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. + id: 1567 + mirId: MIR:00000562 + modified: 2019-06-11T14:17:49.171+0000 + name: miRTarBase + namespaceEmbeddedInLui: false + pattern: ^MIRT\d{6}$ + prefix: mirtarbase + resources: + - deprecated: false + deprecationDate: + description: miRTarBase at National Chiao Tung University + id: 1569 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1568 + location: + countryCode: TW + countryName: Taiwan, Province of China + name: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu + rorId: + location: + countryCode: TW + countryName: Taiwan, Province of China + mirId: MIR:00100739 + name: miRTarBase at National Chiao Tung University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://mirtarbase.mbc.nctu.edu.tw/ + sampleId: MIRT000002 + urlPattern: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid={$id} + sampleId: MIRT000002 + - created: 2019-06-11T14:17:49.428+0000 + deprecated: false + deprecationDate: + description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). + id: 1570 + mirId: MIR:00000563 + modified: 2019-06-11T14:17:49.428+0000 + name: MedDRA + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: meddra + resources: + - deprecated: false + deprecationDate: + description: MedDRA through BioPortal + id: 1571 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100740 + name: MedDRA through BioPortal + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/MEDDRA + sampleId: '10015919' + urlPattern: http://purl.bioontology.org/ontology/MEDDRA/{$id} + sampleId: '10015919' + - created: 2019-06-11T14:17:49.634+0000 + deprecated: false + deprecationDate: + description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. + id: 1572 + mirId: MIR:00000564 + modified: 2019-06-11T14:17:49.634+0000 + name: DASHR + namespaceEmbeddedInLui: false + pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ + prefix: dashr + resources: + - deprecated: false + deprecationDate: + description: DASHR at University of Pennsylvania + id: 1574 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1573 + location: + countryCode: US + countryName: United States + name: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100741 + name: DASHR at University of Pennsylvania + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://lisanwanglab.org/DASHR/ + sampleId: hsa-mir-200a + urlPattern: http://lisanwanglab.org/DASHR/entry/{$id} + sampleId: hsa-mir-200a + - created: 2019-06-11T14:17:49.866+0000 + deprecated: false + deprecationDate: + description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. + id: 1575 + mirId: MIR:00000565 + modified: 2019-06-11T14:17:49.866+0000 + name: DASHR expression + namespaceEmbeddedInLui: false + pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ + prefix: dashr.expression + resources: + - deprecated: false + deprecationDate: + description: DASHR expression at University of Pennsylvania + id: 1576 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1573 + location: + countryCode: US + countryName: United States + name: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100742 + name: DASHR expression at University of Pennsylvania + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 + sampleId: hsa-mir-200a + urlPattern: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#{$id}#exprPerTissueTable + sampleId: hsa-mir-200a + - created: 2019-06-11T14:17:50.083+0000 + deprecated: false + deprecationDate: + description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. + id: 1577 + mirId: MIR:00000566 + modified: 2019-06-11T14:17:50.083+0000 + name: SPLASH + namespaceEmbeddedInLui: false + pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ + prefix: splash + resources: + - deprecated: false + deprecationDate: + description: Mass Bank of North America (MoNA) + id: 1579 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1578 + location: + countryCode: US + countryName: United States + name: University of Californai, Davis, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100746 + name: Mass Bank of North America (MoNA) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://mona.fiehnlab.ucdavis.edu/ + sampleId: splash10-0zq2000000-77302b0326a418630a84 + urlPattern: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/{$id} + sampleId: splash10-0zq2000000-77302b0326a418630a84 + - created: 2019-06-11T14:17:48.752+0000 + deprecated: false + deprecationDate: + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. + id: 1563 + mirId: MIR:00000560 + modified: 2020-04-21T17:40:51.334+0000 + name: MeSH + namespaceEmbeddedInLui: false + pattern: ^(C|D)\d{6,9}$ + prefix: mesh + resources: + - deprecated: false + deprecationDate: + description: MeSH Linked Data at National Library of Medicine + id: 1564 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 792 + location: + countryCode: US + countryName: United States + name: U.S. National Library of Medicine, National Institute of Health, Maryland + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100737 + name: MeSH Linked Data at National Library of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://id.nlm.nih.gov/mesh/ + sampleId: C000100 + urlPattern: http://id.nlm.nih.gov/mesh/{$id} + sampleId: C000100 + - created: 2019-06-11T14:17:50.332+0000 + deprecated: false + deprecationDate: + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. + id: 1580 + mirId: MIR:00000567 + modified: 2021-02-26T09:36:59.253+0000 + name: MetaNetX chemical + namespaceEmbeddedInLui: false + pattern: ^(MNXM\d+|BIOMASS|WATER)$ + prefix: metanetx.chemical + resources: + - deprecated: false + deprecationDate: + description: MetaNetX chemical at SIB Swiss Institute of Bioinformatics + id: 1582 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1581 + location: + countryCode: CH + countryName: Switzerland + name: Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100748 + name: MetaNetX chemical at SIB Swiss Institute of Bioinformatics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.metanetx.org/ + sampleId: MNXM1723 + urlPattern: https://www.metanetx.org/chem_info/{$id} + sampleId: MNXM1723 + - created: 2019-06-11T14:17:50.605+0000 + deprecated: false + deprecationDate: + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. + id: 1583 + mirId: MIR:00000568 + modified: 2021-02-26T09:43:13.847+0000 + name: MetaNetX reaction + namespaceEmbeddedInLui: false + pattern: ^(MNXR\d+|EMPTY)$ + prefix: metanetx.reaction + resources: + - deprecated: false + deprecationDate: + description: MetaNetX reaction at SIB Swiss Institute of Bioinformatics + id: 1584 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1581 + location: + countryCode: CH + countryName: Switzerland + name: Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100749 + name: MetaNetX reaction at SIB Swiss Institute of Bioinformatics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.metanetx.org/ + sampleId: MNXR101574 + urlPattern: https://www.metanetx.org/equa_info/{$id} + sampleId: MNXR101574 + - created: 2019-06-11T14:17:51.017+0000 + deprecated: false + deprecationDate: + description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions. + id: 1587 + mirId: MIR:00000570 + modified: 2019-06-11T14:17:51.017+0000 + name: UniPathway Reaction + namespaceEmbeddedInLui: false + pattern: ^UCR\d{5}$ + prefix: unipathway.reaction + resources: + - deprecated: true + deprecationDate: 2019-10-01T12:11:20.049+0000 + description: UniPathway Reaction at Swiss Institute of Bioinformatics (SIB) + id: 1588 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100752 + name: UniPathway Reaction at Swiss Institute of Bioinformatics (SIB) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.grenoble.prabi.fr/obiwarehouse/unipathway + sampleId: UCR00226 + urlPattern: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid={$id} + sampleId: UCR00226 + - created: 2019-06-11T14:17:51.237+0000 + deprecated: false + deprecationDate: + description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. + id: 1589 + mirId: MIR:00000571 + modified: 2019-06-11T14:17:51.237+0000 + name: Human Phenotype Ontology + namespaceEmbeddedInLui: true + pattern: ^HP:\d{7}$ + prefix: hp + resources: + - deprecated: false + deprecationDate: + description: Human Phenotype Ontology through OLS + id: 1592 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100754 + name: Human Phenotype Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/hp + sampleId: '0000118' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/hp/terms?obo_id=HP:{$id} + - deprecated: false + deprecationDate: + description: Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics + id: 1591 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1590 + location: + countryCode: DE + countryName: Germany + name: Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100753 + name: Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://human-phenotype-ontology.github.io/ + sampleId: '0000118' + urlPattern: https://hpo.jax.org/app/browse/term/HP:{$id} + sampleId: '0000118' + - created: 2019-06-11T14:17:51.650+0000 + deprecated: false + deprecationDate: + description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. + id: 1593 + mirId: MIR:00000572 + modified: 2019-06-11T14:17:51.650+0000 + name: SASBDB + namespaceEmbeddedInLui: false + pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ + prefix: sasbdb + resources: + - deprecated: false + deprecationDate: + description: SASBDB at European Molecular Biology Laboratory + id: 1595 + institution: + description: >- + EMBL is an intergovernmental organisation specialising in basic + research in the life sciences, funded by public research monies + from more than 20 member states, including much of Europe and + Israel, and two associate members, Argentina and Australia. EMBL + is led by the Director General, currently Professor Edith Heard, + appointed by the governing body, EMBL Council. The Council is + comprised of representatives of all member and associate member + states. + + Activities at EMBL Hamburg focus on state-of-the-art structural biology methods using synchrotron radiation. The unit is situated on campus of the German Synchrotron Research Centre (DESY), which hosts leading facilities for synchrotron radiation (PETRA-III) and free electron lasers (FLASH and XFEL, under construction). + homeUrl: https://www.embl-hamburg.de + id: 1594 + location: + countryCode: DE + countryName: Germany + name: European Molecular Biology Lab Hamburg Outstation + rorId: https://ror.org/050589e39 + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100763 + name: SASBDB at European Molecular Biology Laboratory + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.sasbdb.org/ + sampleId: SASDAX8 + urlPattern: http://www.sasbdb.org/data/{$id} + sampleId: SASDAX8 + - created: 2019-06-11T14:17:51.916+0000 + deprecated: false + deprecationDate: + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. + id: 1596 + mirId: MIR:00000573 + modified: 2019-06-11T14:17:51.916+0000 + name: HGNC gene family + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hgnc.genefamily + resources: + - deprecated: false + deprecationDate: + description: HGNC gene family at HUGO Genome Nomenclature Committee + id: 1597 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100765 + name: HGNC gene family at HUGO Genome Nomenclature Committee + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.genenames.org/ + sampleId: '141' + urlPattern: https://www.genenames.org/cgi-bin/genefamilies/set/{$id} + sampleId: '141' + - created: 2019-06-11T14:17:52.138+0000 + deprecated: false + deprecationDate: + description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. + id: 1598 + mirId: MIR:00000574 + modified: 2019-06-11T14:17:52.138+0000 + name: MDM + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mdm + resources: + - deprecated: false + deprecationDate: + description: MDM at University of Muenster + id: 1600 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1599 + location: + countryCode: DE + countryName: Germany + name: Institute of Medical Informatics, University of Muenster + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00100766 + name: MDM at University of Muenster + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://medical-data-models.org/ + sampleId: '4776' + urlPattern: https://medical-data-models.org/forms/{$id} + sampleId: '4776' + - created: 2019-06-11T14:17:52.483+0000 + deprecated: false + deprecationDate: + description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. + id: 1601 + mirId: MIR:00000575 + modified: 2019-06-11T14:17:52.483+0000 + name: ProbOnto + namespaceEmbeddedInLui: false + pattern: ^PROB_c\d+$ + prefix: probonto + resources: + - deprecated: false + deprecationDate: + description: ProbOnto through OLS + id: 1602 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100768 + name: ProbOnto through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/probonto + sampleId: PROB_c0000005 + urlPattern: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form={$id} + sampleId: PROB_c0000005 + - created: 2019-06-11T14:17:52.731+0000 + deprecated: false + deprecationDate: + description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. + id: 1603 + mirId: MIR:00000576 + modified: 2019-06-11T14:17:52.731+0000 + name: APID Interactomes + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ + prefix: apid.interactions + resources: + - deprecated: false + deprecationDate: + description: APID at Salamanca + id: 1605 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1604 + location: + countryCode: ES + countryName: Spain + name: Cancer Research Center (CiC-IBMCC), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca + rorId: + location: + countryCode: ES + countryName: Spain + mirId: MIR:00100769 + name: APID at Salamanca + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cicblade.dep.usal.es:8080/APID/ + sampleId: P01116 + urlPattern: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein={$id} + sampleId: P01116 + - created: 2019-06-11T14:17:53.021+0000 + deprecated: false + deprecationDate: + description: STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. + id: 1606 + mirId: MIR:00000577 + modified: 2019-06-11T14:17:53.021+0000 + name: STOREDB + namespaceEmbeddedInLui: false + pattern: ^STOREDB:(STUDY|FILE|DATASET)\d+$ + prefix: storedb + resources: + - deprecated: false + deprecationDate: + description: STOREDB at University of Cambridge + id: 1608 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1607 + location: + countryCode: GB + countryName: United Kingdom + name: University of Cambridge, Department of Physiology, Downing Street, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100771 + name: STOREDB at University of Cambridge + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.storedb.org/ + sampleId: STOREDB:STUDY1040 + urlPattern: https://www.storedb.org/?{$id} + sampleId: STOREDB:STUDY1040 + - created: 2019-06-11T14:17:53.298+0000 + deprecated: false + deprecationDate: + description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. + id: 1609 + mirId: MIR:00000578 + modified: 2019-06-11T14:17:53.298+0000 + name: Kyoto Encyclopedia of Genes and Genomes + namespaceEmbeddedInLui: false + pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ + prefix: kegg + resources: + - deprecated: false + deprecationDate: + description: KEGG at Kyoto University Bioinformatics Center + id: 1610 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 15 + location: + countryCode: JP + countryName: Japan + name: Kyoto University Bioinformatics Center + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100773 + name: KEGG at Kyoto University Bioinformatics Center + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.kegg.jp/ + sampleId: hsa00190 + urlPattern: http://www.kegg.jp/entry/{$id} + sampleId: hsa00190 + - created: 2019-06-11T14:17:53.641+0000 + deprecated: false + deprecationDate: + description: The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. + id: 1611 + mirId: MIR:00000579 + modified: 2019-06-11T14:17:53.641+0000 + name: Plant Transcription Factor Database + namespaceEmbeddedInLui: false + pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ + prefix: planttfdb + resources: + - deprecated: false + deprecationDate: + description: PlantTFDB at Peking University + id: 1613 + institution: + description: >- + Peking University is a comprehensive and national key university. + The campus, known as "Yan Yuan"（the garden of Yan）, is situated at + Haidian District in the western suburb of Beijing, with a total + area of 2,743,532 square metres (or 274 hectares). It stands near + to the Yuanmingyuan Garden and the Summer Palace. + + Peking University is proud of its outstanding faculty, including 48 members of the Chinese Academy of Sciences (CAS), 9 members of the Chinese Academy of Engineering (CAE), and 21 members of the Third World Academy of Sciences (TWAS). + homeUrl: http://english.pku.edu.cn/ + id: 1612 + location: + countryCode: CN + countryName: China + name: Peking University + rorId: + location: + countryCode: CN + countryName: China + mirId: MIR:00100772 + name: PlantTFDB at Peking University + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://planttfdb.cbi.pku.edu.cn + sampleId: Ath_AT1G01030.1 + urlPattern: http://planttfdb.cbi.pku.edu.cn/tf.php?uid={$id} + sampleId: Ath_AT1G01030.1 + - created: 2019-06-11T14:17:53.926+0000 + deprecated: false + deprecationDate: + description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. + id: 1614 + mirId: MIR:00000580 + modified: 2019-06-11T14:17:53.926+0000 + name: Mammalian Phenotype Ontology + namespaceEmbeddedInLui: true + pattern: ^MP:\d{7}$ + prefix: mp + resources: + - deprecated: false + deprecationDate: + description: Mammalian Phenotype Ontology at The Jackson Lab + id: 1615 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1278 + location: + countryCode: US + countryName: United States + name: The Jackson Laboratory, Bar Harbor, Maine + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100774 + name: Mammalian Phenotype Ontology at The Jackson Lab + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.informatics.jax.org/ + sampleId: '0005452' + urlPattern: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:{$id} + - deprecated: false + deprecationDate: + description: Mammalian Phenotype Ontology through OLS + id: 1616 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100775 + name: Mammalian Phenotype Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/mp/ + sampleId: '0005452' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/mp/terms?obo_id=MP:{$id} + - deprecated: false + deprecationDate: + description: Mammalian Phenotype Ontology through BioPortal + id: 1617 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100776 + name: Mammalian Phenotype Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: https://bioportal.bioontology.org/ontologies/MP + sampleId: '0005452' + urlPattern: https://bioportal.bioontology.org/ontologies/MP/MP:{$id} + sampleId: '0005452' + - created: 2019-06-11T14:17:54.476+0000 + deprecated: false + deprecationDate: + description: The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. + id: 1618 + mirId: MIR:00000581 + modified: 2019-06-11T14:17:54.476+0000 + name: World Register of Marine Species + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: worms + resources: + - deprecated: false + deprecationDate: + description: World Register of Marine Species + id: 1620 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1619 + location: + countryCode: BE + countryName: Belgium + name: Flanders Marine Institute, Ostend + rorId: + location: + countryCode: BE + countryName: Belgium + mirId: MIR:00100778 + name: World Register of Marine Species + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.marinespecies.org/ + sampleId: '146421' + urlPattern: http://www.marinespecies.org/aphia.php?p=taxdetails&id={$id} + sampleId: '146421' + - created: 2019-06-11T14:17:54.753+0000 + deprecated: false + deprecationDate: + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). + id: 1621 + mirId: MIR:00000582 + modified: 2019-06-11T14:17:54.753+0000 + name: MultiCellDS collection + namespaceEmbeddedInLui: false + pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.collection + resources: + - deprecated: false + deprecationDate: + description: MultiCellDScollection at Keck School of Medicine + id: 1623 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1622 + location: + countryCode: US + countryName: United States + name: Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100779 + name: MultiCellDScollection at Keck School of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://multicellds.org/MultiCellDB.php + sampleId: MCDS_C_0000000001 + urlPattern: http://multicellds.org/MultiCellDB/{$id} + sampleId: MCDS_C_0000000001 + - created: 2019-06-11T14:17:55.012+0000 + deprecated: false + deprecationDate: + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. + id: 1624 + mirId: MIR:00000583 + modified: 2019-06-11T14:17:55.012+0000 + name: MultiCellDS Digital snapshot + namespaceEmbeddedInLui: false + pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.snapshot + resources: + - deprecated: false + deprecationDate: + description: MultiCellDS snapshot at Keck School of Medicine + id: 1625 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1622 + location: + countryCode: US + countryName: United States + name: Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100780 + name: MultiCellDS snapshot at Keck School of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://multicellds.org/MultiCellDB.php + sampleId: MCDS_S_0000000001 + urlPattern: http://multicellds.org/MultiCellDB/{$id} + sampleId: MCDS_S_0000000001 + - created: 2019-06-11T14:17:55.320+0000 + deprecated: false + deprecationDate: + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. + id: 1626 + mirId: MIR:00000584 + modified: 2019-06-11T14:17:55.320+0000 + name: MultiCellDS Digital Cell Line + namespaceEmbeddedInLui: false + pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.cell_line + resources: + - deprecated: false + deprecationDate: + description: MultiCellDS Digital Cell Line at Keck School of Medicine + id: 1627 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1622 + location: + countryCode: US + countryName: United States + name: Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100781 + name: MultiCellDS Digital Cell Line at Keck School of Medicine + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://multicellds.org/MultiCellDB.php + sampleId: MCDS_L_0000000001 + urlPattern: http://multicellds.org/MultiCellDB/{$id} + sampleId: MCDS_L_0000000001 + - created: 2019-06-11T14:17:55.541+0000 + deprecated: false + deprecationDate: + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. + id: 1628 + mirId: MIR:00000585 + modified: 2019-06-11T14:17:55.541+0000 + name: E-cyanobacterium entity + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.entity + resources: + - deprecated: false + deprecationDate: + description: e-cyanobacterium entity at Masaryk University Brno + id: 1630 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1629 + location: + countryCode: CZ + countryName: Czech Republic + name: Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno + rorId: + location: + countryCode: CZ + countryName: Czech Republic + mirId: MIR:00100782 + name: e-cyanobacterium entity at Masaryk University Brno + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.e-cyanobacterium.org/bcs/entity/ + sampleId: '23' + urlPattern: http://e-cyanobacterium.org/bcs/entity/{$id}/ + sampleId: '23' + - created: 2019-06-11T14:17:55.864+0000 + deprecated: false + deprecationDate: + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. + id: 1631 + mirId: MIR:00000586 + modified: 2019-06-11T14:17:55.864+0000 + name: E-cyanobacterium model + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.model + resources: + - deprecated: false + deprecationDate: + description: e-cyanobacterium entity at Masaryk University Brno + id: 1632 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1629 + location: + countryCode: CZ + countryName: Czech Republic + name: Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno + rorId: + location: + countryCode: CZ + countryName: Czech Republic + mirId: MIR:00100783 + name: e-cyanobacterium entity at Masaryk University Brno + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://e-cyanobacterium.org/models/ + sampleId: '26' + urlPattern: http://e-cyanobacterium.org/models/model/{$id}/ + sampleId: '26' + - created: 2019-06-11T14:17:56.089+0000 + deprecated: false + deprecationDate: + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. + id: 1633 + mirId: MIR:00000587 + modified: 2019-06-11T14:17:56.089+0000 + name: E-cyanobacterium rule + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.rule + resources: + - deprecated: false + deprecationDate: + description: e-cyanobacterium entity at Masaryk University Brno + id: 1634 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1629 + location: + countryCode: CZ + countryName: Czech Republic + name: Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno + rorId: + location: + countryCode: CZ + countryName: Czech Republic + mirId: MIR:00100784 + name: e-cyanobacterium entity at Masaryk University Brno + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.e-cyanobacterium.org/bcs/rule/ + sampleId: '56' + urlPattern: http://e-cyanobacterium.org/bcs/rule/{$id}/ + sampleId: '56' + - created: 2019-06-11T14:17:56.343+0000 + deprecated: false + deprecationDate: + description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). + id: 1635 + mirId: MIR:00000588 + modified: 2019-06-11T14:17:56.343+0000 + name: LINCS Data + namespaceEmbeddedInLui: false + pattern: ^[EL]D[SG]-\d+$ + prefix: lincs.data + resources: + - deprecated: false + deprecationDate: + description: LINCS Data at University of Miami + id: 1636 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1526 + location: + countryCode: US + countryName: United States + name: University of Miami, BD2K-LINCS DCIC + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100785 + name: LINCS Data at University of Miami + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://lincsportal.ccs.miami.edu/datasets/ + sampleId: LDS-1110 + urlPattern: http://lincsportal.ccs.miami.edu/datasets/#/view/{$id} + - deprecated: false + deprecationDate: + description: Lincs through OmicsDI + id: 1637 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100856 + name: Lincs through OmicsDI + official: false + providerCode: omicsdi + resourceHomeUrl: https://www.omicsdi.org/ + sampleId: LDS-1110 + urlPattern: https://www.omicsdi.org/dataset/lincs/{$id} + sampleId: LDS-1110 + - created: 2019-06-11T14:17:56.660+0000 + deprecated: false + deprecationDate: + description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. + id: 1638 + mirId: MIR:00000589 + modified: 2019-06-11T14:17:56.660+0000 + name: AGRICOLA + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: agricola + resources: + - deprecated: false + deprecationDate: + description: AGRICOLA at National Agricultural Library + id: 1640 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1639 + location: + countryCode: US + countryName: United States + name: National Agricultural Library, United States Department of Agriculture + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100789 + name: AGRICOLA at National Agricultural Library + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://agricola.nal.usda.gov/ + sampleId: '50018' + urlPattern: http://ddr.nal.usda.gov/dspace/handle/10113/{$id} + sampleId: '50018' + - created: 2019-06-11T14:17:56.919+0000 + deprecated: false + deprecationDate: + description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. + id: 1641 + mirId: MIR:00000590 + modified: 2019-06-11T14:17:56.919+0000 + name: Mass Spectrometry Controlled Vocabulary + namespaceEmbeddedInLui: true + pattern: ^MS:\d{7}$ + prefix: ms + resources: + - deprecated: false + deprecationDate: + description: Mass Spectrometry Controlled Vocabulary through OLS + id: 1642 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100786 + name: Mass Spectrometry Controlled Vocabulary through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/ms + sampleId: '1000001' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:{$id} + - deprecated: false + deprecationDate: + description: Mass Spectrometry Controlled Vocabulary through BioPortal + id: 1643 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100787 + name: Mass Spectrometry Controlled Vocabulary through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: https://bioportal.bioontology.org/ontologies/MS + sampleId: '1000001' + urlPattern: http://purl.bioontology.org/ontology/MS/MS:{$id} + sampleId: '1000001' + - created: 2019-06-11T14:17:57.267+0000 + deprecated: false + deprecationDate: + description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. + id: 1644 + mirId: MIR:00000591 + modified: 2019-06-11T14:17:57.267+0000 + name: Environment Ontology + namespaceEmbeddedInLui: true + pattern: ^ENVO:\d{8}$ + prefix: envo + resources: + - deprecated: false + deprecationDate: + description: The Environment Ontology through OLS + id: 1645 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100790 + name: The Environment Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/envo + sampleId: '09200010' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:{$id} + - deprecated: false + deprecationDate: + description: The Environment Ontology through BioPortal + id: 1646 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100791 + name: The Environment Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://purl.bioontology.org/ontology/ENVO/ + sampleId: '09200010' + urlPattern: http://purl.bioontology.org/ontology/ENVO/ENVO:{$id} + sampleId: '09200010' + - created: 2019-06-11T14:17:57.583+0000 + deprecated: false + deprecationDate: + description: An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type. + id: 1647 + mirId: MIR:00000592 + modified: 2019-06-11T14:17:57.583+0000 + name: ARK + namespaceEmbeddedInLui: true + pattern: ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ + prefix: ark + resources: + - deprecated: false + deprecationDate: + description: ARK via the Name-to-Thing resolver. + id: 1649 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1648 + location: + countryCode: US + countryName: United States + name: California Digital Library, University of California Office of the President + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100792 + name: ARK via the Name-to-Thing resolver. + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://n2t.net/ + sampleId: /12345/fk1234 + urlPattern: http://n2t.net/ark:{$id} + sampleId: /12345/fk1234 + - created: 2019-06-11T14:17:57.806+0000 + deprecated: false + deprecationDate: + description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. + id: 1650 + mirId: MIR:00000593 + modified: 2019-06-11T14:17:57.806+0000 + name: GRID + namespaceEmbeddedInLui: false + pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ + prefix: grid + resources: + - deprecated: false + deprecationDate: + description: GRID at Digital Science & Research Ltd. + id: 1652 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1651 + location: + countryCode: GB + countryName: United Kingdom + name: Digital Science &amp; Research Ltd, London + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100793 + name: GRID at Digital Science & Research Ltd. + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.grid.ac/ + sampleId: grid.225360.0 + urlPattern: https://www.grid.ac/institutes/{$id} + sampleId: grid.225360.0 + - created: 2019-06-11T14:17:58.068+0000 + deprecated: false + deprecationDate: + description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. + id: 1653 + mirId: MIR:00000594 + modified: 2019-06-11T14:17:58.068+0000 + name: MedGen + namespaceEmbeddedInLui: false + pattern: ^[CN]*\d{4,7}$ + prefix: medgen + resources: + - deprecated: false + deprecationDate: + description: MedGen at NCBI + id: 1654 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100794 + name: MedGen at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/medgen/ + sampleId: '760050' + urlPattern: https://www.ncbi.nlm.nih.gov/medgen/{$id} + sampleId: '760050' + - created: 2019-06-11T14:17:58.273+0000 + deprecated: false + deprecationDate: + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. + id: 1655 + mirId: MIR:00000595 + modified: 2019-06-11T14:17:58.273+0000 + name: ClinVar Submission + namespaceEmbeddedInLui: false + pattern: ^SCV\d+(\.\d+)?$ + prefix: clinvar.submission + resources: + - deprecated: false + deprecationDate: + description: ClinVar Submission at NCBI + id: 1656 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100795 + name: ClinVar Submission at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: http://www.ncbi.nlm.nih.gov/clinvar/ + sampleId: SCV000151292 + urlPattern: http://www.ncbi.nlm.nih.gov/clinvar?term={$id} + sampleId: SCV000151292 + - created: 2019-06-11T14:17:58.490+0000 + deprecated: false + deprecationDate: + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. + id: 1657 + mirId: MIR:00000596 + modified: 2019-06-11T14:17:58.490+0000 + name: ClinVar Variant + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: clinvar + resources: + - deprecated: false + deprecationDate: + description: ClinVar Variant at NCBI + id: 1658 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100796 + name: ClinVar Variant at NCBI + official: false + providerCode: ncbi + resourceHomeUrl: http://www.ncbi.nlm.nih.gov/clinvar/ + sampleId: '12345' + urlPattern: https://www.ncbi.nlm.nih.gov/clinvar/variation/{$id} + sampleId: '12345' + - created: 2019-06-11T14:17:59.221+0000 + deprecated: false + deprecationDate: + description: The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources. + id: 1664 + mirId: MIR:00000599 + modified: 2019-06-11T14:17:59.221+0000 + name: Identifiers.org Registry + namespaceEmbeddedInLui: true + pattern: ^MIR:\d{8}$ + prefix: mir + resources: + - deprecated: false + deprecationDate: + description: Identifiers.org Registry through EBI + id: 1665 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100800 + name: Identifiers.org Registry through EBI + official: false + providerCode: ebi + resourceHomeUrl: https://registry.identifiers.org/registry + sampleId: '00100037' + urlPattern: https://registry.identifiers.org/registry?query="MIR:{$id}" + sampleId: '00100037' + - created: 2019-06-11T14:17:59.699+0000 + deprecated: false + deprecationDate: + description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. + id: 1669 + mirId: MIR:00000601 + modified: 2019-06-11T14:17:59.699+0000 + name: COSMIC Gene + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: cosmic + resources: + - deprecated: false + deprecationDate: + description: COSMIC Gene at Sanger + id: 1670 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1393 + location: + countryCode: GB + countryName: United Kingdom + name: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100802 + name: COSMIC Gene at Sanger + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://cancer.sanger.ac.uk/cosmic/ + sampleId: BRAF + urlPattern: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln={$id} + sampleId: BRAF + - created: 2019-06-11T14:17:59.890+0000 + deprecated: false + deprecationDate: + description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. + id: 1671 + mirId: MIR:00000602 + modified: 2019-06-11T14:17:59.890+0000 + name: dbGaP + namespaceEmbeddedInLui: false + pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ + prefix: dbgap + resources: + - deprecated: false + deprecationDate: + description: dbGaP through NCBI + id: 1672 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100803 + name: dbGaP through NCBI + official: true + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/projects/gap + sampleId: phs000768.v2.p1 + urlPattern: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id={$id} + sampleId: phs000768.v2.p1 + - created: 2019-06-11T14:18:00.081+0000 + deprecated: false + deprecationDate: + description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. + id: 1673 + mirId: MIR:00000603 + modified: 2019-06-11T14:18:00.081+0000 + name: Information Artifact Ontology + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: iao + resources: + - deprecated: false + deprecationDate: + description: IAO through Ontobee + id: 1675 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1674 + location: + countryCode: US + countryName: United States + name: University of Pennsylvania + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100804 + name: IAO through Ontobee + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ontobee.org/ontology/IAO + sampleId: '0000030' + urlPattern: http://purl.obolibrary.org/obo/IAO_{$id} + sampleId: '0000030' + - created: 2019-06-11T14:18:00.311+0000 + deprecated: false + deprecationDate: + description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. + id: 1676 + mirId: MIR:00000604 + modified: 2019-06-11T14:18:00.311+0000 + name: Genomic Data Commons Data Portal + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ + prefix: gdc + resources: + - deprecated: false + deprecationDate: + description: Genomic Data Commons + id: 1678 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1677 + location: + countryCode: US + countryName: United States + name: National Cancer Institute Genomic Data Commons, NIH + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100805 + name: Genomic Data Commons + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://gdc.cancer.gov + sampleId: ae8c77fe-e6c8-44d5-8265-4a38c637bbef + urlPattern: https://portal.gdc.cancer.gov/cases/{$id} + sampleId: ae8c77fe-e6c8-44d5-8265-4a38c637bbef + - created: 2019-06-11T14:18:00.566+0000 + deprecated: false + deprecationDate: + description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). + id: 1679 + mirId: MIR:00000605 + modified: 2019-06-11T14:18:00.566+0000 + name: OMIT + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: omit + resources: + - deprecated: false + deprecationDate: + description: Ontology for miRNA Target (OMIT) through OLS + id: 1680 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100806 + name: Ontology for miRNA Target (OMIT) through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/omit/ + sampleId: '0005506' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_{$id} + sampleId: '0005506' + - created: 2019-06-11T14:18:00.782+0000 + deprecated: false + deprecationDate: + description: The coding sequence or protein identifiers as maintained in INSDC. + id: 1681 + mirId: MIR:00000606 + modified: 2019-06-11T14:18:00.782+0000 + name: INSDC CDS + namespaceEmbeddedInLui: false + pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ + prefix: insdc.cds + resources: + - deprecated: false + deprecationDate: + description: INSDC CDS through DDBJ + id: 1684 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 121 + location: + countryCode: JP + countryName: Japan + name: DNA Data Bank of Japan, Mishima, Shizuoka + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100809 + name: INSDC CDS through DDBJ + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://getentry.ddbj.nig.ac.jp + sampleId: AAA35559 + urlPattern: http://getentry.ddbj.nig.ac.jp/getentry/dad/{$id} + - deprecated: false + deprecationDate: + description: INSDC CDS through ENA + id: 1682 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100807 + name: INSDC CDS through ENA + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.ebi.ac.uk/ena + sampleId: AAA35559 + urlPattern: https://www.ebi.ac.uk/ena/data/view/{$id} + - deprecated: false + deprecationDate: + description: INSDC CDS through NCBI + id: 1683 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100808 + name: INSDC CDS through NCBI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/protein/ + sampleId: AAA35559 + urlPattern: https://www.ncbi.nlm.nih.gov/protein/{$id} + sampleId: AAA35559 + - created: 2019-06-11T14:18:01.543+0000 + deprecated: false + deprecationDate: + description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. + id: 1688 + mirId: MIR:00000608 + modified: 2019-06-11T14:18:01.543+0000 + name: GlyTouCan + namespaceEmbeddedInLui: false + pattern: ^G[0-9]{5}[A-Z]{2}$ + prefix: glytoucan + resources: + - 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MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. + id: 1691 + mirId: MIR:00000609 + modified: 2019-06-11T14:18:01.783+0000 + name: MetaCyc Compound + namespaceEmbeddedInLui: false + pattern: ^CPD-\d{5}$ + prefix: metacyc.compound + resources: + - deprecated: false + deprecationDate: + description: MetaCyc Metabolic Pathway Database + id: 1693 + institution: + description: SRI is an independent, nonprofit research center that works with clients to take the most advanced R&D from the laboratory to the marketplace. + homeUrl: https://www.sri.com/ + id: 1692 + location: + countryCode: US + countryName: United States + name: SRI International + rorId: https://ror.org/05s570m15 + location: + countryCode: US + countryName: United States + mirId: MIR:00100813 + name: MetaCyc Metabolic Pathway Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://metacyc.org + sampleId: CPD-10330 + urlPattern: https://metacyc.org/compound?orgid=META&id={$id} + sampleId: CPD-10330 + - created: 2019-06-11T14:18:02.043+0000 + deprecated: false + deprecationDate: + description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. + id: 1694 + mirId: MIR:00000610 + modified: 2019-06-11T14:18:02.043+0000 + name: MetaCyc Reaction + namespaceEmbeddedInLui: false + pattern: ^RXN-\d{5}$ + prefix: metacyc.reaction + resources: + - deprecated: false + deprecationDate: + description: MetaCyc Metabolic Pathway Database - Reaction + id: 1695 + institution: + description: SRI is an independent, nonprofit research center that works with clients to take the most advanced R&D from the laboratory to the marketplace. + homeUrl: https://www.sri.com/ + id: 1692 + location: + countryCode: US + countryName: United States + name: SRI International + rorId: https://ror.org/05s570m15 + location: + countryCode: US + countryName: United States + mirId: MIR:00100814 + name: MetaCyc Metabolic Pathway Database - Reaction + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://metacyc.org + sampleId: RXN-14904 + urlPattern: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object={$id} + sampleId: RXN-14904 + - 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deprecated: false + deprecationDate: + description: AOPWiki + id: 1714 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1713 + location: + countryCode: US + countryName: United States + name: European Commision - DG Joint Research Centre and U.S Environmental Protection Agency + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100821 + name: AOPWiki + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://aopwiki.org/ + sampleId: '98' + urlPattern: https://aopwiki.org/aops/{$id} + sampleId: '98' + - created: 2019-06-11T14:18:03.826+0000 + deprecated: false + deprecationDate: + description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. + id: 1715 + mirId: MIR:00000618 + modified: 2019-06-11T14:18:03.826+0000 + name: NASA GeneLab + namespaceEmbeddedInLui: false + pattern: ^GLDS-\d+$ + prefix: ngl + resources: + - 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We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. + id: 1699 + mirId: MIR:00000612 + modified: 2021-02-01T16:12:25.234+0000 + name: CATH Protein Structural Domain Superfamily + namespaceEmbeddedInLui: false + pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ + prefix: cath + resources: + - deprecated: false + deprecationDate: + description: CATH Node through UCL + id: 1701 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1700 + location: + countryCode: GB + countryName: United Kingdom + name: University College London + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100816 + name: CATH Node through UCL + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.cathdb.info + sampleId: 1.10.8.10 + urlPattern: http://www.cathdb.info/cathnode/{$id} + sampleId: 1.10.8.10 + - created: 2019-06-11T14:17:59.000+0000 + deprecated: false + deprecationDate: + description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' + id: 1662 + mirId: MIR:00000598 + modified: 2021-02-01T16:38:40.925+0000 + name: Cellosaurus + namespaceEmbeddedInLui: false + pattern: ^CVCL_[A-Z0-9]{4}$ + prefix: cellosaurus + resources: + - deprecated: false + deprecationDate: + description: Cellosaurus through SIB + id: 1663 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100799 + name: Cellosaurus through SIB + official: false + providerCode: sib + resourceHomeUrl: https://web.expasy.org/cellosaurus/ + sampleId: CVCL_0030 + urlPattern: https://web.expasy.org/cellosaurus/{$id} + sampleId: CVCL_0030 + - created: 2019-06-11T14:18:04.072+0000 + deprecated: false + deprecationDate: + description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. + id: 1718 + mirId: MIR:00000619 + modified: 2019-06-11T14:18:04.072+0000 + name: Human Endogenous Retrovirus Database + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\-\_]+$ + prefix: erv + resources: + - deprecated: false + deprecationDate: + description: Human Endogenous Retrovirus Database + id: 1720 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1719 + location: + countryCode: CZ + countryName: Czech Republic + name: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic + rorId: + location: + countryCode: CZ + countryName: Czech Republic + mirId: MIR:00100823 + name: Human Endogenous Retrovirus Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://herv.img.cas.cz/ + sampleId: THE1B + urlPattern: https://herv.img.cas.cz/s/{$id} + sampleId: THE1B + - created: 2019-06-11T14:18:04.316+0000 + deprecated: false + deprecationDate: + description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). + id: 1721 + mirId: MIR:00000620 + modified: 2019-06-11T14:18:04.316+0000 + name: Natural Product-Drug Interaction Research Data Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: napdi + resources: + - deprecated: false + deprecationDate: + description: Natural Product-Drug Interaction Research Data Repository + id: 1723 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1722 + location: + countryCode: US + countryName: United States + name: National Center for Complementary and Integrative Health, National Institutes of Health, Washington D.C. + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100824 + name: Natural Product-Drug Interaction Research Data Repository + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://repo.napdi.org/ + sampleId: '28' + urlPattern: https://repo.napdi.org/study/{$id} + sampleId: '28' + - created: 2019-06-11T14:18:04.557+0000 + deprecated: false + deprecationDate: + description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. + id: 1724 + mirId: MIR:00000621 + modified: 2019-06-11T14:18:04.557+0000 + name: ArrayMap + namespaceEmbeddedInLui: false + pattern: ^[\w\-:,]{3,64}$ + prefix: arraymap + resources: + - deprecated: false + deprecationDate: + description: ArrayMap + id: 1725 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1385 + location: + countryCode: CH + countryName: Switzerland + name: Institute of Molecular Life Sciences, University of Zurich, Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100825 + name: ArrayMap + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.arraymap.org + sampleId: icdom:8500_3 + urlPattern: https://www.arraymap.org/pgx:{$id} + sampleId: icdom:8500_3 + - created: 2019-06-11T14:18:04.748+0000 + deprecated: false + deprecationDate: + description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. 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The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies. + id: 1732 + mirId: MIR:00000624 + modified: 2019-06-11T14:18:05.215+0000 + name: SISu + namespaceEmbeddedInLui: false + pattern: ^[0-9]+:[0-9]+$ + prefix: sisu + resources: + - deprecated: false + deprecationDate: + description: SISu + id: 1734 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1733 + location: + countryCode: FI + countryName: Finland + name: Sequencing Initiative Suomi project (SISu), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki + rorId: + location: + countryCode: FI + countryName: Finland + mirId: MIR:00100828 + name: SISu + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.sisuproject.fi/ + sampleId: 17:41223048 + urlPattern: http://search.sisuproject.fi/#/variant/{$id} + sampleId: 17:41223048 + - created: 2019-06-11T14:18:05.468+0000 + deprecated: false + deprecationDate: + description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. + id: 1735 + mirId: MIR:00000625 + modified: 2019-06-11T14:18:05.468+0000 + name: Universal Spectrum Identifier + namespaceEmbeddedInLui: true + pattern: ^mzspec:.+$ + prefix: mzspec + resources: + - deprecated: false + deprecationDate: + description: Universal Spectrum Identifier through Peptide Atlas + id: 1737 + institution: + description: ISB was created in 2000 as the first-ever institute dedicated to systems biology. + homeUrl: https://isbscience.org/ + id: 193 + location: + countryCode: US + countryName: United States + name: Institute for Systems Biology + rorId: https://ror.org/02tpgw303 + location: + countryCode: US + countryName: United States + mirId: MIR:00100829 + name: Universal Spectrum Identifier through Peptide Atlas + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum + sampleId: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 + urlPattern: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:{$id} + - deprecated: false + deprecationDate: + description: Institute for Systems Biology (ISB), Seattle, USA is an independent research institute focusing on systems biology. + id: 2394 + institution: + description: ISB was created in 2000 as the first-ever institute dedicated to systems biology. + homeUrl: https://isbscience.org/ + id: 193 + location: + countryCode: US + countryName: United States + name: Institute for Systems Biology + rorId: https://ror.org/02tpgw303 + location: + countryCode: US + countryName: United States + mirId: MIR:00000771 + name: Institute for Systems Biology, Seattle, USA + official: true + providerCode: pc + resourceHomeUrl: http://proteomecentral.proteomexchange.org/ + sampleId: PXD000865:00603_F01_P004608_B00F_A00_R1:scan:14453:SSLLDVLAAR/2 + urlPattern: http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:{$id} + sampleId: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 + - created: 2019-06-11T14:18:05.694+0000 + deprecated: false + deprecationDate: + description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. + id: 1738 + mirId: MIR:00000626 + modified: 2019-06-11T14:18:05.694+0000 + name: CRISPRdb + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: crisprdb + resources: + - deprecated: false + deprecationDate: + description: CRISPRdb + id: 1740 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1739 + location: + countryCode: FR + countryName: France + name: Université Paris-Sud, Institut de Génétique et Microbiologie, Orsay, + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100830 + name: CRISPRdb + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://crispr.i2bc.paris-saclay.fr/ + sampleId: '551115' + urlPattern: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]={$id} + sampleId: '551115' + - created: 2019-06-11T14:18:05.948+0000 + deprecated: false + deprecationDate: + description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. + id: 1741 + mirId: MIR:00000627 + modified: 2019-06-11T14:18:05.948+0000 + name: GnpIS + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: gnpis + resources: + - deprecated: false + deprecationDate: + description: GnpIS + id: 1743 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1742 + location: + countryCode: FR + countryName: France + name: URGI (Research Unit in Genomics-Info), INRA de Versailles, Route de Saint-Cyr, Versailles + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100831 + name: GnpIS + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://urgi.versailles.inra.fr/gnpis/ + sampleId: AY109603 + urlPattern: https://urgi.versailles.inra.fr/gnpis/#result/term={$id} + sampleId: AY109603 + - created: 2019-06-11T14:18:06.185+0000 + deprecated: false + deprecationDate: + description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. + id: 1744 + mirId: MIR:00000628 + modified: 2019-06-11T14:18:06.185+0000 + name: LiceBase + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\-\/]+$ + prefix: licebase + resources: + - deprecated: false + deprecationDate: + description: LiceBase + id: 1746 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1745 + location: + countryCode: NO + countryName: Norway + name: Sea Lice Research Centre (SLRC), University of Bergen + rorId: + location: + countryCode: NO + countryName: Norway + mirId: MIR:00100832 + name: LiceBase + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://licebase.org + sampleId: EMLSAT00000003403 + urlPattern: https://licebase.org/?q={$id} + sampleId: EMLSAT00000003403 + - created: 2019-06-11T14:18:06.412+0000 + deprecated: false + deprecationDate: + description: The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands. + id: 1747 + mirId: MIR:00000629 + modified: 2019-06-11T14:18:06.412+0000 + name: SugarBind + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+\/[0-9]+$ + prefix: sugarbind + resources: + - deprecated: false + deprecationDate: + description: SugarBind + id: 1749 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1748 + location: + countryCode: CH + countryName: Switzerland + name: Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100833 + name: SugarBind + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://sugarbind.expasy.org/ + sampleId: lectins/172 + urlPattern: http://sugarbind.expasy.org/{$id} + sampleId: lectins/172 + - created: 2019-06-11T14:18:06.653+0000 + deprecated: false + deprecationDate: + description: RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. + id: 1750 + mirId: MIR:00000630 + modified: 2019-06-11T14:18:06.653+0000 + name: RNAcentral + namespaceEmbeddedInLui: false + pattern: ^URS[0-9A-F]{10}(\_\d+)?$ + prefix: rnacentral + resources: + - deprecated: false + deprecationDate: + description: RNAcentral through EMBL-EBI + id: 1751 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100834 + name: RNAcentral through EMBL-EBI + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://rnacentral.org/ + sampleId: URS0000759CF4 + urlPattern: https://rnacentral.org/rna/{$id} + sampleId: URS0000759CF4 + - created: 2019-06-11T14:18:06.853+0000 + deprecated: false + deprecationDate: + description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. + id: 1752 + mirId: MIR:00000631 + modified: 2019-06-11T14:18:06.853+0000 + name: MicroScope + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: microscope + resources: + - deprecated: false + deprecationDate: + description: MicroScope + id: 1754 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1753 + location: + countryCode: FR + countryName: France + name: Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Evry + rorId: + location: + countryCode: FR + countryName: France + mirId: MIR:00100836 + name: MicroScope + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genoscope.cns.fr/agc/microscope + sampleId: '5601141' + urlPattern: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id={$id} + sampleId: '5601141' + - created: 2019-06-11T14:18:07.113+0000 + deprecated: false + deprecationDate: + description: A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. + id: 1755 + mirId: MIR:00000632 + modified: 2019-06-11T14:18:07.113+0000 + name: SwissRegulon + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: swissregulon + resources: + - deprecated: false + deprecationDate: + description: SwissRegulon + id: 1756 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100837 + name: SwissRegulon + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://swissregulon.unibas.ch + sampleId: AHR + urlPattern: http://swissregulon.unibas.ch/query/{$id} + sampleId: AHR + - created: 2019-06-11T14:18:07.321+0000 + deprecated: false + deprecationDate: + description: Database of validation results for ligands and non-standard residues in the Protein Data Bank. + id: 1757 + mirId: MIR:00000633 + modified: 2019-06-11T14:18:07.321+0000 + name: ValidatorDB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\/]+$ + prefix: validatordb + resources: + - deprecated: false + deprecationDate: + description: ValidatorDB + id: 1759 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1758 + location: + countryCode: CZ + countryName: Czech Republic + name: Central European Institute of Technology + rorId: + location: + countryCode: CZ + countryName: Czech Republic + mirId: MIR:00100838 + name: ValidatorDB + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ + sampleId: ByStructure/2h6o + urlPattern: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/{$id} + sampleId: ByStructure/2h6o + - created: 2019-06-11T14:18:07.548+0000 + deprecated: false + deprecationDate: + description: Database of the dielectric properties of biological tissues. + id: 1760 + mirId: MIR:00000634 + modified: 2019-06-11T14:18:07.548+0000 + name: Bio-MINDER Tissue Database + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\-]+$ + prefix: biominder + resources: + - deprecated: false + deprecationDate: + description: Bio-MINDER Tissue Database + id: 1762 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1761 + location: + countryCode: IE + countryName: Ireland + name: RWTH Aachen University / NUIG Galway + rorId: + location: + countryCode: IE + countryName: Ireland + mirId: MIR:00100839 + name: Bio-MINDER Tissue Database + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://datalab.rwth-aachen.de/MINDER + sampleId: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 + urlPattern: https://datalab.rwth-aachen.de/MINDER/resource/{$id} + sampleId: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 + - created: 2019-06-11T14:18:07.777+0000 + deprecated: false + deprecationDate: + description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images. + id: 1763 + mirId: MIR:00000635 + modified: 2019-06-11T14:18:07.777+0000 + name: NeuroVault Collection + namespaceEmbeddedInLui: false + pattern: ^[1-9][0-9]*$ + prefix: neurovault.collection + resources: + - deprecated: false + deprecationDate: + description: NeuroVault Collection + id: 1764 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 98 + location: + countryCode: US + countryName: United States + name: Stanford University + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100840 + name: NeuroVault Collection + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://neurovault.org + sampleId: '3304' + urlPattern: https://neurovault.org/collections/{$id} + sampleId: '3304' + - created: 2019-06-11T14:18:07.981+0000 + deprecated: false + deprecationDate: + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + id: 1765 + mirId: MIR:00000636 + modified: 2019-06-11T14:18:07.981+0000 + name: VMH metabolite + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9_\(\_\)\[\]]+' + prefix: vmhmetabolite + resources: + - deprecated: false + deprecationDate: + description: VMH metabolite + id: 1767 + institution: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/03bea9k73' with Wikidata IDs [Q644478], and ISNI IDs [0000 0004 0488 0789] + homeUrl: http://www.nuigalway.ie/ + id: 2496 + location: + countryCode: IE + countryName: Ireland + name: National University of Ireland, Galway + rorId: + location: + countryCode: IE + countryName: Ireland + mirId: MIR:00100841 + name: VMH metabolite + official: false + providerCode: NUI + resourceHomeUrl: https://www.vmh.life/ + sampleId: h2o + urlPattern: https://www.vmh.life/#metabolite/{$id} + sampleId: h2o + - created: 2019-06-11T14:18:08.710+0000 + deprecated: false + deprecationDate: + description: nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. + id: 1773 + mirId: MIR:00000639 + modified: 2019-06-11T14:18:08.710+0000 + name: Nuclear Magnetic Resonance Controlled Vocabulary + namespaceEmbeddedInLui: true + pattern: ^NMR:\d+$ + prefix: nmr + resources: + - deprecated: false + deprecationDate: + description: NMR through OLS + id: 1774 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100844 + name: NMR through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/nmrcv + sampleId: '1000003' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:{$id} + sampleId: '1000003' + - created: 2019-06-11T14:18:08.921+0000 + deprecated: false + deprecationDate: + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + id: 1775 + mirId: MIR:00000640 + modified: 2019-06-11T14:18:08.921+0000 + name: VMH reaction + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9_\(\_\)\[\]]+' + prefix: vmhreaction + resources: + - deprecated: false + deprecationDate: + description: VMH reaction + id: 1776 + institution: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/03bea9k73' with Wikidata IDs [Q644478], and ISNI IDs [0000 0004 0488 0789] + homeUrl: http://www.nuigalway.ie/ + id: 2496 + location: + countryCode: IE + countryName: Ireland + name: National University of Ireland, Galway + rorId: + location: + countryCode: IE + countryName: Ireland + mirId: MIR:00100845 + name: VMH reaction + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.vmh.life/ + sampleId: HEX1 + urlPattern: https://www.vmh.life/#reaction/{$id} + sampleId: HEX1 + - created: 2019-06-11T14:18:09.136+0000 + deprecated: false + deprecationDate: + description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). + id: 1777 + mirId: MIR:00000641 + modified: 2019-06-11T14:18:09.136+0000 + name: Astrophysics Source Code Library + namespaceEmbeddedInLui: false + pattern: ^[0-9\.]+$ + prefix: ascl + resources: + - deprecated: false + deprecationDate: + description: Astrophysics Source Code Library + id: 1779 + institution: + description: The Astrophysics Source Code Library (ASCL), founded in 1999 by Robert Nemiroff and John Wallin, takes an active approach to sharing astrophysical source code. + homeUrl: http://ascl.net/ + id: 1778 + location: + countryCode: US + countryName: United States + name: Astrophysics Source Code Library + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100846 + name: Astrophysics Source Code Library + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://ascl.net/ + sampleId: '1801.012' + urlPattern: http://ascl.net/{$id} + sampleId: '1801.012' + - created: 2019-06-11T14:18:09.365+0000 + deprecated: false + deprecationDate: + description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. + id: 1780 + mirId: MIR:00000642 + modified: 2019-06-11T14:18:09.365+0000 + name: FaceBase Data Repository + namespaceEmbeddedInLui: false + pattern: ^FB\d{8}$ + prefix: facebase + resources: + - deprecated: false + deprecationDate: + description: FaceBase Data Repository + id: 1782 + institution: + description: The University of Southern California is a leading private research university located in Los Angeles — a global center for arts, technology and international business. It is home to the College of Letters, Arts and Sciences and 21 exceptional academic schools and units. USC’s Health Sciences campus houses renowned specialized care and research in cancer, stem cell and regenerative medicine, orthopedics and sports medicine. The university is the largest private sector employer in the city of Los Angeles, responsible for $8 billion annually in economic activity in the region. + homeUrl: https://www.usc.edu/ + id: 1781 + location: + countryCode: US + countryName: United States + name: University of Southern California + rorId: https://ror.org/03taz7m60 + location: + countryCode: US + countryName: United States + mirId: MIR:00100847 + name: FaceBase Data Repository + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.facebase.org + sampleId: FB00000917 + urlPattern: https://www.facebase.org/data/record/#1/isa:dataset/accession={$id} + sampleId: FB00000917 + - created: 2019-06-11T14:18:09.598+0000 + deprecated: false + deprecationDate: + description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. + id: 1783 + mirId: MIR:00000643 + modified: 2019-06-11T14:18:09.598+0000 + name: GUDMAP + namespaceEmbeddedInLui: false + pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ + prefix: gudmap + resources: + - deprecated: false + deprecationDate: + description: GUDMAP + id: 1785 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1784 + location: + countryCode: US + countryName: United States + name: GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100848 + name: GUDMAP + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.gudmap.org/ + sampleId: Q-2958 + urlPattern: https://gudmap.org/id/{$id} + sampleId: Q-2958 + - created: 2019-06-11T14:18:09.859+0000 + deprecated: false + deprecationDate: + description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. + id: 1786 + mirId: MIR:00000644 + modified: 2019-06-11T14:18:09.859+0000 + name: JRC Data Catalogue + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\-_]+$ + prefix: eu89h + resources: + - deprecated: false + deprecationDate: + description: JRC Data Catalogue + id: 1788 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1787 + location: + countryCode: BE + countryName: Belgium + name: European Commission, Joint Research Centre (JRC) + rorId: + location: + countryCode: BE + countryName: Belgium + mirId: MIR:00100849 + name: JRC Data Catalogue + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://data.jrc.ec.europa.eu/ + sampleId: jrc-eurl-ecvam-chemagora + urlPattern: http://data.europa.eu/89h/{$id} + sampleId: jrc-eurl-ecvam-chemagora + - created: 2019-06-11T14:18:10.316+0000 + deprecated: false + deprecationDate: + description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). + id: 1792 + mirId: MIR:00000646 + modified: 2019-06-11T14:18:10.316+0000 + name: Metabolomics Workbench Study + namespaceEmbeddedInLui: false + pattern: ^ST[0-9]{6}$ + prefix: mw.study + resources: + - 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It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. + id: 1834 + mirId: MIR:00000661 + modified: 2019-06-11T14:18:14.340+0000 + name: FoodOn Food Ontology + namespaceEmbeddedInLui: true + pattern: ^FOODON:[0-9]{8}$ + prefix: foodon + resources: + - deprecated: false + deprecationDate: + description: FoodOn Food Ontology through OLS + id: 1835 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100879 + name: FoodOn Food Ontology through OLS + official: false + providerCode: ebi + resourceHomeUrl: https://foodon.org + sampleId: '03307879' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:{$id} + sampleId: '03307879' + - created: 2019-06-11T14:18:14.565+0000 + deprecated: false + deprecationDate: + description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. + id: 1836 + mirId: MIR:00000662 + modified: 2019-06-11T14:18:14.565+0000 + name: 'ENCODE: Encyclopedia of DNA Elements' + namespaceEmbeddedInLui: false + pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ + prefix: encode + resources: + - deprecated: false + deprecationDate: + description: 'ENCODE: Encyclopedia of DNA Elements' + id: 1838 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1837 + location: + countryCode: US + countryName: United States + name: ENCODE Consortium + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100880 + name: 'ENCODE: Encyclopedia of DNA Elements' + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: www.encodeproject.org + sampleId: ENCSR163RYW + urlPattern: https://www.encodeproject.org/{$id} + sampleId: ENCSR163RYW + - created: 2019-06-11T14:18:14.830+0000 + deprecated: false + deprecationDate: + description: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. + id: 1839 + mirId: MIR:00000663 + modified: 2019-06-11T14:18:14.830+0000 + name: GTEx + namespaceEmbeddedInLui: false + pattern: ^\w.+$ + prefix: gtex + resources: + - deprecated: false + deprecationDate: + description: The GTEx Project + id: 1841 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1840 + location: + countryCode: US + countryName: United States + name: The Broad Institute of MIT and Harvard + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100881 + name: The GTEx Project + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.gtexportal.org + sampleId: BRIP1 + urlPattern: https://www.gtexportal.org/home/gene/{$id} + sampleId: BRIP1 + - created: 2019-06-11T14:18:15.139+0000 + deprecated: false + deprecationDate: + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. 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The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception. + id: 1904 + mirId: MIR:00000687 + modified: 2019-06-11T14:18:20.855+0000 + name: SPDX License List + namespaceEmbeddedInLui: false + pattern: ^[0-9A-Za-z\-.]+$ + prefix: spdx + resources: + - deprecated: false + deprecationDate: + description: SPDX License List + id: 1906 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1905 + location: + countryCode: US + countryName: United States + name: SPDX Workgroup a Linux Foundation Project + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100918 + name: SPDX License List + official: true + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://spdx.org + sampleId: CC-BY-1.0 + urlPattern: https://spdx.org/licenses/{$id} + sampleId: CC-BY-1.0 + - created: 2019-06-11T14:18:21.119+0000 + deprecated: false + deprecationDate: + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. 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The database can accept a wide range of types of studies described via a simple format. 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The university stands out for its innovative + education model, international character and multidisciplinary + approach to research and education. + + Thanks to its high-quality research and study programmes as well as a strong focus on social engagement, UM has quickly built up a solid reputation. Today it is considered one of the best young universities in the world. + homeUrl: https://www.maastrichtuniversity.nl + id: 283 + location: + countryCode: NL + countryName: Netherlands + name: Maastricht University + rorId: https://ror.org/02jz4aj89 + location: + countryCode: NL + countryName: Netherlands + mirId: MIR:00000711 + name: European Registry of Materials + official: true + providerCode: erm + resourceHomeUrl: https://nanocommons.github.io/identifiers/ + sampleId: ERM00000044 + urlPattern: https://nanocommons.github.io/identifiers/registry#{$id} + sampleId: ERM00000044 + - created: 2019-09-05T11:46:36.162+0000 + deprecated: false + deprecationDate: + description: ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API. + id: 1977 + mirId: MIR:00000770 + modified: 2019-09-05T11:46:36.162+0000 + name: ClassyFire + namespaceEmbeddedInLui: false + pattern: ^C[0-9]{7}$ + prefix: classyfire + resources: + - deprecated: false + deprecationDate: + description: Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT). 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Some of his lab's most significant contributions have been in the area of protein chemical shift analysis and the prediction of protein structure. + homeUrl: http://www.wishartlab.com/ + id: 1976 + location: + countryCode: CA + countryName: Canada + name: The Wishart Research Group, University of Alberta, Edmonton, Alberta, Canada + rorId: + location: + countryCode: CA + countryName: Canada + mirId: MIR:00000710 + name: The Wishart Research Group, University of Alberta, Edmonton, Alberta, Canada + official: true + providerCode: classyfire + resourceHomeUrl: http://classyfire.wishartlab.com/ + sampleId: C0004828 + urlPattern: http://classyfire.wishartlab.com/tax_nodes/{$id} + sampleId: C0004828 + - created: 2019-09-10T09:27:59.693+0000 + deprecated: false + deprecationDate: + description: "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology." + id: 1989 + mirId: MIR:00000738 + modified: 2019-09-10T09:27:59.693+0000 + name: Ontology Concept Identifiers + namespaceEmbeddedInLui: true + pattern: ocid:[0-9]{12} + prefix: ocid + resources: + - deprecated: false + deprecationDate: + description: SciWalker is an open access ontology based search tool for annotated data and extracted knowledge from scientific databases, patents and scientific documents. + id: 1990 + institution: + description: OntoChem develops and uses ontologies and semantic NLP software to annotate, analyze, extract and predict knowledge from scientific databases, patents, scientific articles or general private documents. + homeUrl: https://www.ontochem.com + id: 1988 + location: + countryCode: DE + countryName: Germany + name: OntoChem GmbH + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00000706 + name: SciWalker Open Data + official: true + providerCode: oc + resourceHomeUrl: https://www.sciwalker.com + sampleId: '190000021540' + urlPattern: https://www.sciwalker.com/sciwalker/faces/ociddata.xhtml?ocid={$id} + sampleId: '190000021540' + - created: 2019-09-10T10:50:49.547+0000 + deprecated: false + deprecationDate: + description: MarFun is manually curated database for marine fungi which is a part of the MAR databases. + id: 1997 + mirId: MIR:00000729 + modified: 2019-09-10T10:50:49.547+0000 + name: MarFun + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.fun + resources: + - deprecated: false + deprecationDate: + description: MarFun through SfB + id: 1998 + institution: + description: The Centre for bioinformatics at UiT is a part of ELIXIR Norway dedicated to services. + homeUrl: https://uit.no + id: 1996 + location: + countryCode: NO + countryName: Norway + name: Centre for bioinformatics (SfB), UiT The Arctic university of Norway + rorId: + location: + countryCode: NO + countryName: Norway + mirId: MIR:00000713 + name: MarFun through SfB + official: true + providerCode: mmp + resourceHomeUrl: https://mmp.sfb.uit.no/databases/marfun + sampleId: MMP3888430 + urlPattern: https://mmp.sfb.uit.no/databases/marfun/#/records/{$id} + sampleId: MMP3888430 + - created: 2019-09-10T12:51:24.637+0000 + deprecated: false + deprecationDate: + description: E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments. + id: 2003 + mirId: MIR:00000760 + modified: 2019-09-10T12:51:24.637+0000 + name: E-cyanobacterium Experimental Data + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.experiment + resources: + - deprecated: false + deprecationDate: + description: E-cyanobacterium is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations. It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references wet-lab experiments. + id: 2004 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1629 + location: + countryCode: CZ + countryName: Czech Republic + name: Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno + rorId: + location: + countryCode: CZ + countryName: Czech Republic + mirId: MIR:00000754 + name: E-cyanobacterium + official: true + providerCode: ecyano + resourceHomeUrl: https://www.e-cyanobacterium.org/experiments-repository/ + sampleId: '18' + urlPattern: https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id={$id} + sampleId: '18' + - created: 2019-09-24T11:03:08.927+0000 + deprecated: false + deprecationDate: + description: DOULIX lab-tested standard biological parts, in this case, full length constructs. + id: 2022 + mirId: MIR:00000742 + modified: 2019-09-24T11:03:08.927+0000 + name: Circular double stranded DNA sequences composed + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]{6,7}$ + prefix: dlxc + resources: + - deprecated: false + deprecationDate: + description: Doulix DNA repository provides a FAIR-compliant database of DNA sequences for synthetic biology. Doulix allows user to retrieve, inspect and manipulate DNA sequences while ensuring data traceability and integrity. + id: 2023 + institution: + description: 'Double Helix Technologies (DOULIX) is currently an operative unit of Explora Biotech (https://www.explora-biotech). ' + homeUrl: https://doulix.com + id: 2021 + location: + countryCode: IT + countryName: Italy + name: Double Helix Technologies (DOULIX) + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00000734 + name: Doulix DNA repository + official: true + providerCode: dlxc + resourceHomeUrl: https://doulix.com + sampleId: M77F7JM + urlPattern: https://doulix.com/constructs/{$id}/ + sampleId: M77F7JM + - created: 2019-10-01T11:40:36.666+0000 + deprecated: false + deprecationDate: + description: DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences. + id: 2026 + mirId: MIR:00000747 + modified: 2019-10-01T11:40:36.666+0000 + name: Linear double stranded DNA sequences + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]{6,7}$ + prefix: dlxb + resources: + - deprecated: false + deprecationDate: + description: Doulix DNA repository provides a FAIR-compliant database of DNA sequences for synthetic biology. Doulix allows user to retrieve, inspect and manipulate DNA sequences while ensuring data traceability and integrity. + id: 2027 + institution: + description: 'Double Helix Technologies (DOULIX) is currently an operative unit of Explora Biotech (https://www.explora-biotech.com). ' + homeUrl: https://doulix.com + id: 2025 + location: + countryCode: IT + countryName: Italy + name: Doulix Helix Technologies (DOULIX) + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00000717 + name: Doulix DNA repository + official: true + providerCode: dlxb + resourceHomeUrl: https://doulix.com + sampleId: 6VDC956 + urlPattern: https://doulix.com/biomodules/{$id}/ + sampleId: 6VDC956 + - created: 2019-06-11T14:18:04.976+0000 + deprecated: false + deprecationDate: + description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. + id: 1729 + mirId: MIR:00000623 + modified: 2019-10-01T11:46:06.302+0000 + name: CAMEO + namespaceEmbeddedInLui: false + pattern: ^[0-9\-_]+$ + prefix: cameo + resources: + - deprecated: false + deprecationDate: + description: CAMEO + id: 1731 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100827 + name: CAMEO + official: false + providerCode: sib + resourceHomeUrl: https://cameo3d.org + sampleId: 2019-08-03_00000089_1 + urlPattern: https://www.cameo3d.org/sp/targets/target/{$id} + sampleId: 2019-08-03_00000089_1 + - created: 2019-09-19T13:46:35.999+0000 + deprecated: false + deprecationDate: + description: This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects. + id: 2013 + mirId: MIR:00000744 + modified: 2019-10-02T08:18:15.555+0000 + name: Neuroscience Multi-Omic BRAIN Initiative Data + namespaceEmbeddedInLui: false + pattern: '[a-z]{3}-[a-km-z0-9]{7}' + prefix: nemo + resources: + - deprecated: false + deprecationDate: + description: The Neuroscience Multi-Omic Archive (NeMO Archive) is a data repository specifically focused on the storage and dissemination of omic data generated from the BRAIN Initiative and related brain research projects. + id: 2014 + institution: + description: Formed in May 2007, the Institute for Genome Sciences (IGS) is part of the University of Maryland School of Medicine and is on the University of Maryland Baltimore campus. Members of the IGS team have helped revolutionize genomic discoveries in medicine, agriculture, environmental science and biodefense. + homeUrl: http://www.igs.umaryland.edu + id: 2012 + location: + countryCode: US + countryName: United States + name: The Institute for Genome Sciences + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000790 + name: The NeMO Archive + official: true + providerCode: igs + resourceHomeUrl: https://www.nemoarchive.org + sampleId: smp-m3w9hbe + urlPattern: https://assets.nemoarchive.org/{$id} + sampleId: smp-m3w9hbe + - created: 2019-11-07T10:59:42.032+0000 + deprecated: false + deprecationDate: + description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways. + id: 2037 + mirId: MIR:00000726 + modified: 2019-11-07T10:59:42.032+0000 + name: Signaling Pathways Project + namespaceEmbeddedInLui: false + pattern: ^10.\w{4}/\w{10}$ + prefix: spp + resources: + - deprecated: false + deprecationDate: + description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways. + id: 2038 + institution: + description: Baylor College of Medicine is a health sciences university that creates knowledge and applies science and discoveries to further education, healthcare and community service locally and globally. + homeUrl: https://www.bcm.edu + id: 485 + location: + countryCode: US + countryName: United States + name: Baylor College of Medicine + rorId: https://ror.org/02pttbw34 + location: + countryCode: US + countryName: United States + mirId: MIR:00000730 + name: Signaling Pathways Project + official: true + providerCode: spp + resourceHomeUrl: https://www.signalingpathways.org/index.jsf + sampleId: 10.1621/vwN2g2HaX3 + urlPattern: https://www.signalingpathways.org/datasets/dataset.jsf?doi={$id} + sampleId: 10.1621/vwN2g2HaX3 + - created: 2019-12-09T15:05:02.665+0000 + deprecated: false + deprecationDate: + description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. + id: 2055 + mirId: MIR:00000716 + modified: 2019-12-09T15:05:02.665+0000 + name: Biological Magnetic Resonance Data Bank + namespaceEmbeddedInLui: false + pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$ + prefix: bmrb + resources: + - deprecated: false + deprecationDate: + description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. + id: 2056 + institution: + description: >- + The University of Wisconsin–Madison is a public research + university in Madison, Wisconsin. Founded when Wisconsin achieved + statehood in 1848, UW–Madison is the official state university of + Wisconsin, and the flagship campus of the University of Wisconsin + System. + + It was the first public university established in Wisconsin and remains the oldest and largest public university in the state. It became a land-grant institution in 1866. + + The 933-acre (378 ha) main campus, located on the shores of Lake Mendota, includes four National Historic Landmarks. + + The University also owns and operates a historic 1,200-acre (486 ha) arboretum established in 1932, located 4 miles (6.4 km) south of the main campus. + homeUrl: https://www.wisc.edu/ + id: 2054 + location: + countryCode: US + countryName: United States + name: University of Wisconsin-Madison + rorId: https://ror.org/01y2jtd41 + location: + countryCode: US + countryName: United States + mirId: MIR:00000735 + name: Biological Magnetic Resonance Data Bank + official: true + providerCode: bmrb + resourceHomeUrl: http://www.bmrb.wisc.edu/ + sampleId: '15000' + urlPattern: http://rest.bmrb.wisc.edu/bmrb/{$id}/html + sampleId: '15000' + - created: 2019-12-09T15:18:31.130+0000 + deprecated: false + deprecationDate: + description: DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature. + id: 2061 + mirId: MIR:00000745 + modified: 2019-12-09T15:18:31.130+0000 + name: DisProt region + namespaceEmbeddedInLui: false + pattern: ^DP\d{5}r\d{3}$ + prefix: disprot.region + resources: + - deprecated: false + deprecationDate: + description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. + id: 2062 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1769 + location: + countryCode: IT + countryName: Italy + name: University of Padua + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00000756 + name: DisProt region + official: true + providerCode: disprot.region + resourceHomeUrl: https://www.disprot.org + sampleId: DP00086r013 + urlPattern: https://www.disprot.org/{$id} + sampleId: DP00086r013 + - created: 2020-01-24T13:57:43.399+0000 + deprecated: false + deprecationDate: + description: "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. " + id: 2072 + mirId: MIR:00000723 + modified: 2020-01-24T13:57:43.399+0000 + name: VegBank + namespaceEmbeddedInLui: false + pattern: ^VB\.[A-Za-z][A-Za-z]\..*$ + prefix: vegbank + resources: + - deprecated: false + deprecationDate: + description: VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. + id: 2073 + institution: + description: NCEAS works to accelerate scientific discoveries that will enhance our understanding of the world and benefit people and nature, as well as to transform the scientific culture to be more open, efficient, and collaborative. + homeUrl: https://nceas.ucsb.edu/ + id: 2071 + location: + countryCode: US + countryName: United States + name: National Center for Ecological Analysis and Synthesis + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000751 + name: VegBank + official: true + providerCode: vegbank + resourceHomeUrl: http://vegbank.org/ + sampleId: VB.Ob.3736.GRSM125 + urlPattern: http://vegbank.org/cite/{$id} + sampleId: VB.Ob.3736.GRSM125 + - created: 2020-02-25T11:14:38.686+0000 + deprecated: false + deprecationDate: + description: 'Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ' + id: 2085 + mirId: MIR:00000707 + modified: 2020-02-28T10:24:36.137+0000 + name: MINID Test + namespaceEmbeddedInLui: false + pattern: '[A-Za-z0-9]+$' + prefix: minid.test + resources: + - deprecated: false + deprecationDate: + description: FAIR Research is a collaboration of the Informatics Systems Research Division at the Information Sciences Institute of University of Southern California and the Computational Systems Division at the University of Chicago. + id: 2086 + institution: + description: The University of Southern California is a leading private research university located in Los Angeles — a global center for arts, technology and international business. It is home to the College of Letters, Arts and Sciences and 21 exceptional academic schools and units. USC’s Health Sciences campus houses renowned specialized care and research in cancer, stem cell and regenerative medicine, orthopedics and sports medicine. The university is the largest private sector employer in the city of Los Angeles, responsible for $8 billion annually in economic activity in the region. + homeUrl: https://www.usc.edu/ + id: 1781 + location: + countryCode: US + countryName: United States + name: University of Southern California + rorId: https://ror.org/03taz7m60 + location: + countryCode: US + countryName: United States + mirId: MIR:00000724 + name: FAIR Research + official: true + providerCode: fair + resourceHomeUrl: https://fair-research.org + sampleId: 3SBPLMKKVEVR + urlPattern: https://hdl.handle.net/hdl:20.500.12633/{$id} + sampleId: 3SBPLMKKVEVR + - created: 2020-03-02T17:27:03.688+0000 + deprecated: false + deprecationDate: + description: Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools. + id: 2108 + mirId: MIR:00000743 + modified: 2020-03-02T17:27:03.688+0000 + name: Image Data Resource + namespaceEmbeddedInLui: false + pattern: ^[0-9]{4}$ + prefix: idr + resources: + - deprecated: false + deprecationDate: + description: OME is a consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data. + id: 2109 + institution: + description: The University of Dundee is a public research university in Dundee, Scotland. Founded in 1881 the institution was, for most of its early existence, a constituent college of the University of St Andrews alongside United College and St Mary's College located in the town of St Andrews itself. Following significant expansion, the University of Dundee gained independent university status in 1967 while retaining much of its ancient heritage and governance structure. + homeUrl: https://www.dundee.ac.uk/ + id: 2107 + location: + countryCode: GB + countryName: United Kingdom + name: University of Dundee + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00000705 + name: Open Microscopy Environment + official: true + providerCode: ome + resourceHomeUrl: https://idr.openmicroscopy.org + sampleId: '0001' + urlPattern: https://idr.openmicroscopy.org/search/?query=Name:idr{$id} + sampleId: '0001' + - created: 2020-02-28T10:48:52.126+0000 + deprecated: false + deprecationDate: + description: The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes. + id: 2096 + mirId: MIR:00000736 + modified: 2020-03-03T05:45:40.200+0000 + name: TranSyT + namespaceEmbeddedInLui: false + pattern: T[A-Z]\d{7} + prefix: transyt + resources: + - deprecated: false + deprecationDate: + description: The BIOSYSTEMS Research Group is a research group at CEB, using competences in systems biotechnology and bioengineering to foster the development of a knowledge-based bio-economy, leading to new added-value products and processes. + id: 2097 + institution: + description: 'The Centre of Biological Engineering (CEB), designated as “Excellent” by FCT, is a research unit located at University of Minho (ROR:037wpkx04) that develops its activities on interdisciplinary thrust areas covering molecular, cellular and process scales, corresponding to 4 thematic strands: Industrial, Food, Environmental, and Health Biotechnology and Bioengineering.' + homeUrl: https://www.ceb.uminho.pt + id: 2095 + location: + countryCode: PT + countryName: Portugal + name: Centre of Biological Engineering + rorId: + location: + countryCode: PT + countryName: Portugal + mirId: MIR:00000731 + name: BIOSYSTEMS Research Group + official: true + providerCode: transyt + resourceHomeUrl: https://www.bio.di.uminho.pt/ + sampleId: TR0000001 + urlPattern: https://transyt.bio.di.uminho.pt/reactions/{$id} + sampleId: TR0000001 + - created: 2019-06-11T14:18:01.236+0000 + deprecated: false + deprecationDate: + description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. + id: 1685 + mirId: MIR:00000607 + modified: 2020-03-31T12:32:16.941+0000 + name: Genome assembly database + namespaceEmbeddedInLui: false + pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$ + prefix: insdc.gca + resources: + - deprecated: false + deprecationDate: + description: Genome assembly database through ENA + id: 1686 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100810 + name: Genome assembly database through ENA + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.ebi.ac.uk/ena/browse/genome-assembly-database + sampleId: GCA_000155495.1 + urlPattern: https://www.ebi.ac.uk/ena/data/view/{$id} + - deprecated: false + deprecationDate: + description: Genome assembly database NCBI + id: 1687 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100811 + name: Genome assembly database NCBI + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/assembly/ + sampleId: GCA_000155495.1 + urlPattern: https://www.ncbi.nlm.nih.gov/assembly/{$id} + sampleId: GCA_000155495.1 + - created: 2019-06-11T14:17:46.314+0000 + deprecated: false + deprecationDate: + description: SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. + id: 1539 + mirId: MIR:00000550 + modified: 2020-05-01T09:59:44.482+0000 + name: SwissLipids + namespaceEmbeddedInLui: true + pattern: ^SLM:\d+$ + prefix: slm + resources: + - deprecated: false + deprecationDate: + description: SwissLipids at Swiss Institute of Bioinformatics + id: 1541 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100727 + name: SwissLipids at Swiss Institute of Bioinformatics + official: false + providerCode: sib + resourceHomeUrl: http://www.swisslipids.org/#/ + sampleId: '000048885' + urlPattern: http://www.swisslipids.org/#/entity/SLM:{$id}/ + sampleId: '000048885' + - created: 2020-05-12T14:08:31.024+0000 + deprecated: false + deprecationDate: + description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. + id: 2222 + mirId: MIR:00000765 + modified: 2020-05-12T14:08:31.024+0000 + name: VGNC + namespaceEmbeddedInLui: false + pattern: ^((VGNC|vgnc):)?\d{1,9}$ + prefix: vgnc + resources: + - deprecated: false + deprecationDate: + description: 'The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. ' + id: 2223 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00000752 + name: VGNC + official: true + providerCode: vgnc + resourceHomeUrl: https://vertebrate.genenames.org + sampleId: VGNC:3792 + urlPattern: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/{$id} + sampleId: VGNC:3792 + - created: 2020-05-22T09:04:15.866+0000 + deprecated: false + deprecationDate: + description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. + id: 2248 + mirId: MIR:00000718 + modified: 2020-05-22T09:04:15.866+0000 + name: Datanator Metabolite + namespaceEmbeddedInLui: false + pattern: ^[A-Z\-]+$ + prefix: datanator.metabolite + resources: + - deprecated: false + deprecationDate: + description: The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes eight hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. + id: 2249 + institution: + description: The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes eight hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. + homeUrl: https://icahn.mssm.edu/ + id: 2247 + location: + countryCode: US + countryName: United States + name: Icahn School of Medicine at Mount Sinai + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000772 + name: Icahn School of Medicine at Mount Sinai + official: true + providerCode: icahn + resourceHomeUrl: https://datanator.info/ + sampleId: OUYCCCASQSFEME-MRVPVSSYSA-N + urlPattern: https://www.datanator.info/metabolite/{$id} + sampleId: OUYCCCASQSFEME-MRVPVSSYSA-N + - created: 2019-06-11T14:17:48.275+0000 + deprecated: false + deprecationDate: + description: "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch." + id: 1559 + mirId: MIR:00000558 + modified: 2020-03-11T14:52:15.242+0000 + name: RRID + namespaceEmbeddedInLui: true + pattern: ^RRID:[a-zA-Z]+.+$ + prefix: rrid + resources: + - deprecated: false + deprecationDate: + description: RRID at SciCrunch + id: 1560 + institution: + description: >- + is a public research university in San Diego, California. + + Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students. + homeUrl: https://ucsd.edu/ + id: 190 + location: + countryCode: US + countryName: United States + name: University of California, San Diego + rorId: https://ror.org/0168r3w48 + location: + countryCode: US + countryName: United States + mirId: MIR:00100735 + name: RRID at SciCrunch + official: false + providerCode: ucsd + resourceHomeUrl: https://scicrunch.org/resolver + sampleId: AB_262044 + urlPattern: https://scicrunch.org/resolver/RRID:{$id} + sampleId: AB_262044 + - created: 2019-06-11T14:16:11.083+0000 + deprecated: false + deprecationDate: + description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. + id: 447 + mirId: MIR:00000141 + modified: 2020-03-16T08:35:08.949+0000 + name: Protein Ontology + namespaceEmbeddedInLui: true + pattern: ^PR:P?\d+$ + prefix: pr + resources: + - deprecated: false + deprecationDate: + description: Protein Ontology at Georgetown + id: 448 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 173 + location: + countryCode: US + countryName: United States + name: Georgetown University Medical Center, Washington + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100184 + name: Protein Ontology at Georgetown + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://proconsortium.org/ + sampleId: '000000024' + urlPattern: https://proconsortium.org/app/entry/PR:{$id} + - deprecated: false + deprecationDate: + description: Protein Ontology through BioPortal + id: 449 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100240 + name: Protein Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/PR + sampleId: '000000024' + urlPattern: http://purl.bioontology.org/ontology/PR/PR:{$id} + - deprecated: false + deprecationDate: + description: Protein Ontology through OLS + id: 450 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100755 + name: Protein Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/pr + sampleId: '000000024' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/pr/terms?obo_id=PR:{$id} + sampleId: '000000024' + - created: 2020-03-17T08:03:56.077+0000 + deprecated: false + deprecationDate: + description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.' + id: 2129 + mirId: MIR:00000733 + modified: 2020-03-17T08:03:56.077+0000 + name: Genomes OnLine Database (GOLD) + namespaceEmbeddedInLui: false + pattern: ^[A-Z][a-z][0-9]+$ + prefix: gold + resources: + - deprecated: false + deprecationDate: + description: >- + The Genomes OnLine Database (GOLD) is a centralized resource for + cataloguing genome and metagenome sequencing projects from around + the world, along with their associated metadata. Information in GOLD + is organized into four levels: Study, Biosample/Organism, Sequencing + Project and Analysis Project. + + Study is an umbrella Project that broadly defines the overall goal of a research proposal. It consists of sequencing projects along with corresponding organism or Biosample information as well as any analysis done on the sequencing projects. + + E.g., Gs0016050: Human Microbiome Project (HMP), Gs0000008: A Genomic Encyclopedia of Bacteria and Archaea (GEBA) study. + + Biosample is the description of the environment from where the DNA/RNA sample was collected. Currently GOLD Biosample entities are defined for all metagenome and metatranscriptomes projects, i.e. for non-isolate genomes. E.g., Gb0055733 + + Organism is an individual living thing. It can be a bacterium, plant, fungus etc. In GOLD, all isolate or single cell genome sequencing projects are associated with an organism. Additionally, GOLD Organisms are also created for genomes assembled from metagenome sequences(MAGs). E.g., Go0003442 + + Sequencing Project represents the procedures undertaken for generating sequencing output from an individual Organism or Biosample. An individual genome project may be composed of more than one sequencing reactions and/or sequencing technologies. A Sequencing Project may be an isolate genome, or a metagenome, transcriptome, or metatranscriptome etc. + + E.g., Gp0003442 + + Analysis Project represents the computational processing of sequencing data generated by a sequencing project. It describes how the assembly and annotation of a Sequencing Project were performed. + + E.g., Ga0027275 + id: 2130 + institution: + description: The mission of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility of Lawrence Berkeley National Laboratory (Berkeley Lab) and part of the Biosciences Area, is to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. + homeUrl: https://gold.jgi.doe.gov/ + id: 2128 + location: + countryCode: US + countryName: United States + name: Joint Genome Institute + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000757 + name: Genomes OnLine Database (GOLD) + official: true + providerCode: jgi + resourceHomeUrl: https://gold.jgi.doe.gov/ + sampleId: Gs0000008 + urlPattern: https://gold.jgi.doe.gov/resolver?id={$id} + sampleId: Gs0000008 + - created: 2020-03-17T12:41:40.413+0000 + deprecated: false + deprecationDate: + description: NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. + id: 2140 + mirId: MIR:00000748 + modified: 2020-03-17T12:43:18.460+0000 + name: NMR Shift Database + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: nmrshiftdb2 + resources: + - deprecated: false + deprecationDate: + description: NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. + id: 2141 + institution: + description: The University of Cologne is one of the oldest and largest universities in Europe. Due to its outstanding scientific achievements and the high quality and diversity of its degree programmes, it enjoys an excellent international reputation. + homeUrl: https://www.portal.uni-koeln.de/uoc_home.html?&L=1 + id: 2139 + location: + countryCode: DE + countryName: Germany + name: University of Cologne + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00000719 + name: NMRShiftDB + official: true + providerCode: uoc + resourceHomeUrl: https://nmrshiftdb.nmr.uni-koeln.de + sampleId: '234' + urlPattern: https://nmrshiftdb.nmr.uni-koeln.de/molecule/{$id} + sampleId: '234' + - created: 2019-06-11T14:18:10.091+0000 + deprecated: false + deprecationDate: + description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. + id: 1789 + mirId: MIR:00000645 + modified: 2020-03-20T09:37:38.029+0000 + name: Minimal Viable Identifier + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: minid + resources: + - deprecated: false + deprecationDate: + description: FAIR Research is a collaboration of the Informatics Systems Research Division at the Information Sciences Institute of University of Southern California and the Computational Systems Division at the University of Chicago. + id: 1791 + institution: + description: The University of Southern California is a leading private research university located in Los Angeles — a global center for arts, technology and international business. It is home to the College of Letters, Arts and Sciences and 21 exceptional academic schools and units. USC’s Health Sciences campus houses renowned specialized care and research in cancer, stem cell and regenerative medicine, orthopedics and sports medicine. The university is the largest private sector employer in the city of Los Angeles, responsible for $8 billion annually in economic activity in the region. + homeUrl: https://www.usc.edu/ + id: 1781 + location: + countryCode: US + countryName: United States + name: University of Southern California + rorId: https://ror.org/03taz7m60 + location: + countryCode: US + countryName: United States + mirId: MIR:00100850 + name: FAIR Research + official: false + providerCode: fair + resourceHomeUrl: https://fair-research.org + sampleId: r8059v + urlPattern: https://hdl.handle.net/hdl:20.500.12582/{$id} + sampleId: b97957 + - created: 2020-03-20T12:58:53.045+0000 + deprecated: false + deprecationDate: + description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome. + id: 2152 + mirId: MIR:00000766 + modified: 2020-03-20T12:58:53.045+0000 + name: SNP2TFBS + namespaceEmbeddedInLui: false + pattern: ^rs[0-9]+$ + prefix: snp2tfbs + resources: + - deprecated: false + deprecationDate: + description: SNP2TFBS is a Web interface aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome. + id: 2153 + institution: + description: SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide. + homeUrl: https://www.sib.swiss + id: 1730 + location: + countryCode: CH + countryName: Switzerland + name: SIB Swiss Institute of Bioinformatics + rorId: https://ror.org/002n09z45 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00000737 + name: SNP2TFBS + official: true + providerCode: sib + resourceHomeUrl: https://ccg.epfl.ch/snp2tfbs/ + sampleId: rs11603840 + urlPattern: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid={$id} + sampleId: rs11603840 + - created: 2020-03-20T15:04:54.734+0000 + deprecated: false + deprecationDate: + description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. + id: 2160 + mirId: MIR:00000782 + modified: 2020-03-20T15:04:54.734+0000 + name: BioLink Model + namespaceEmbeddedInLui: false + pattern: ^\S+$ + prefix: biolink + resources: + - deprecated: false + deprecationDate: + description: This resource is not backed by a physical institution. The resource is managed and deployed on GitHub, and is maintained by a broad community of develops + id: 2161 + institution: + description: This resource is not backed by a physical institution. The resource is managed and deployed on GitHub, and is maintained by a broad community of develops + homeUrl: https://biolink.github.io/biolink-model + id: 2159 + location: + countryCode: US + countryName: United States + name: BioLink GitHub Organization + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000778 + name: BioLink GitHub Organization + official: true + providerCode: biolinkgithub + resourceHomeUrl: https://biolink.github.io/biolink-model + sampleId: Gene + urlPattern: https://w3id.org/biolink/vocab/{$id} + sampleId: Gene + - created: 2020-03-24T05:11:19.658+0000 + deprecated: false + deprecationDate: + description: >- + DANDI works with BICCN and other BRAIN Initiative awardees to curate + data using community data standards such as NWB and BIDS, and to make + data and software for cellular neurophysiology FAIR (Findable, + Accessible, Interoperable, and Reusable). + + DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. + + These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders. + id: 2168 + mirId: MIR:00000786 + modified: 2020-03-24T05:11:19.658+0000 + name: 'DANDI: Distributed Archives for Neurophysiology Data Integration' + namespaceEmbeddedInLui: false + pattern: ^\d{6}(/\d+\.\d+\.\d+)?$ + prefix: dandi + resources: + - deprecated: false + deprecationDate: + description: 'DANDI is a Web platform for scientists to share, collaborate, and process data from cellular neurophysiology experiments. DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI will store electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. DANDI will provide: 1) A cloud platform for neurophysiology data storage for the purposes of collaboration and dissemination of data; 2) Easy to use tools for neurophysiology data submission, visualization, and access in the archive; and 3) Standardized applications for data ingestion, visualization and processing, which facilitate adoption of NWB and other standards. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.' + id: 2169 + institution: + description: Founded to accelerate the nation’s industrial revolution, MIT is profoundly American. With ingenuity and drive, our graduates have invented fundamental technologies, launched new industries, and created millions of American jobs. At the same time, and without the slightest sense of contradiction, MIT is profoundly global(opens in new window). Our community gains tremendous strength as a magnet for talent from around the world. Through teaching, research, and innovation, MIT’s exceptional community pursues its mission of service to the nation and the world. + homeUrl: http://web.mit.edu/ + id: 2167 + location: + countryCode: US + countryName: United States + name: Massachusetts Institute of Technology + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000750 + name: 'DANDI: Distributed Archives for Neurophysiology Data Integration' + official: true + providerCode: dandi + resourceHomeUrl: https://dandiarchive.org/ + sampleId: '000017' + urlPattern: https://dandiarchive.org/dandiset/{$id} + sampleId: '000017' + - created: 2020-03-24T06:40:28.546+0000 + deprecated: false + deprecationDate: + description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB. + id: 2184 + mirId: MIR:00000762 + modified: 2020-03-24T06:40:28.546+0000 + name: RAP-DB Transcript + namespaceEmbeddedInLui: false + pattern: ^Os\S+t\d{7}-\d{2}$ + prefix: rapdb.transcript + resources: + - deprecated: false + deprecationDate: + description: The Rice Annotation Project (RAP) was conceptualized in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. + id: 2185 + institution: + description: The National Agriculture and Food Research Organization or NARO is the core institute in Japan for conducting research and development on agriculture and food. + homeUrl: http://www.naro.affrc.go.jp/english/index.html + id: 2183 + location: + countryCode: JP + countryName: Japan + name: The National Agriculture and Food Research Organization (NARO) + rorId: https://ror.org/023v4bd62 + location: + countryCode: JP + countryName: Japan + mirId: MIR:00000773 + name: RAP-DB + official: true + providerCode: rapdb + resourceHomeUrl: https://rapdb.dna.affrc.go.jp/ + sampleId: Os01t0883800-02 + urlPattern: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name={$id} + sampleId: Os01t0883800-02 + - created: 2020-03-24T06:41:41.433+0000 + deprecated: false + deprecationDate: + description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB. + id: 2187 + mirId: MIR:00000702 + modified: 2020-03-24T06:41:41.433+0000 + name: RAP-DB Locus + namespaceEmbeddedInLui: false + pattern: ^Os\S+g\d{7}$ + prefix: rapdb.locus + resources: + - deprecated: false + deprecationDate: + description: The Rice Annotation Project (RAP) was conceptualized in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. + id: 2188 + institution: + description: The National Agriculture and Food Research Organization or NARO is the core institute in Japan for conducting research and development on agriculture and food. + homeUrl: http://www.naro.affrc.go.jp/english/index.html + id: 2183 + location: + countryCode: JP + countryName: Japan + name: The National Agriculture and Food Research Organization (NARO) + rorId: https://ror.org/023v4bd62 + location: + countryCode: JP + countryName: Japan + mirId: MIR:00000741 + name: RAP-DB, Rice Annotation Project Database + official: true + providerCode: rapdb + resourceHomeUrl: https://rapdb.dna.affrc.go.jp/ + sampleId: Os01g0883800 + urlPattern: https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name={$id} + sampleId: Os01g0883800 + - created: 2020-03-24T07:50:16.285+0000 + deprecated: false + deprecationDate: + description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. + id: 2198 + mirId: MIR:00000727 + modified: 2020-03-24T07:50:16.285+0000 + name: enviPath + namespaceEmbeddedInLui: false + pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ + prefix: envipath + resources: + - deprecated: false + deprecationDate: + description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. + id: 2199 + institution: + description: We currently have no more details on this institution / organization, for more information, please see https://envipath.com/imprint/ + homeUrl: https://envipath.org/ + id: 2197 + location: + countryCode: DE + countryName: Germany + name: enviPath UG & Co. KG + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00000776 + name: enviPath + official: true + providerCode: envipathug + resourceHomeUrl: https://envipath.org/ + sampleId: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea + urlPattern: https://envipath.org/package/{$id} + sampleId: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea + - created: 2019-06-11T14:17:12.564+0000 + deprecated: false + deprecationDate: + description: >- + - DEPRECATION NOTE - + + Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. + + + The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples. + id: 1167 + mirId: MIR:00000402 + modified: 2020-03-26T09:38:38.398+0000 + name: GOLD metadata + namespaceEmbeddedInLui: false + pattern: ^Gm\d+$ + prefix: gold.meta + resources: + - deprecated: false + deprecationDate: + description: GOLD metadata at Department of Energy Joint Genome Institute + id: 1168 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1165 + location: + countryCode: US + countryName: United States + name: Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100522 + name: GOLD metadata at Department of Energy Joint Genome Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi + sampleId: Gm00047 + urlPattern: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp={$id} + sampleId: Gm00047 + - created: 2019-06-11T14:15:43.085+0000 + deprecated: false + deprecationDate: + description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. + id: 153 + mirId: MIR:00000039 + modified: 2020-03-31T09:55:28.774+0000 + name: RefSeq + namespaceEmbeddedInLui: false + pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$ + prefix: refseq + resources: + - deprecated: false + deprecationDate: + description: The NCBI Reference Sequence database + id: 155 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00100067 + name: The NCBI Reference Sequence database + official: false + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/projects/RefSeq/ + sampleId: NP_012345 + urlPattern: https://www.ncbi.nlm.nih.gov/protein/{$id} + sampleId: NP_012345 + - created: 2019-06-11T14:17:12.343+0000 + deprecated: false + deprecationDate: + description: >- + - DEPRECATION NOTE - + + Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. + + + The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes. + id: 1164 + mirId: MIR:00000401 + modified: 2020-03-26T09:37:26.767+0000 + name: GOLD genome + namespaceEmbeddedInLui: false + pattern: ^(Gi|Gc)\d+$ + prefix: gold.genome + resources: + - deprecated: false + deprecationDate: + description: GOLD genome at Department of Energy Joint Genome Institute + id: 1166 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1165 + location: + countryCode: US + countryName: United States + name: Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100521 + name: GOLD genome at Department of Energy Joint Genome Institute + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi + sampleId: Gi07796 + urlPattern: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp={$id} + sampleId: Gi07796 + - created: 2019-06-11T14:16:41.635+0000 + deprecated: false + deprecationDate: + description: |- + KNApSAcK provides information on metabolites and the + taxonomic class with which they are associated. + id: 794 + mirId: MIR:00000271 + modified: 2020-04-22T09:28:07.963+0000 + name: KNApSAcK + namespaceEmbeddedInLui: false + pattern: ^C\d{8} + prefix: knapsack + resources: + - deprecated: false + deprecationDate: + description: KNApSAcK at NAIST + id: 796 + institution: + description: 'Nara Institute of Science and Technology (NAIST) is a Japanese national university located in Kansai Science City, a border region between Nara, Osaka, and Kyoto. Founded in 1991, NAIST consisted of graduate schools in three integrated areas: information science, biological sciences, and materials science.' + homeUrl: https://www.naist.jp/en/ + id: 795 + location: + countryCode: JP + countryName: Japan + name: Nara Institute of Science and Technology + rorId: https://ror.org/05bhada84 + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100350 + name: KNApSAcK at NAIST + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.knapsackfamily.com/KNApSAcK/ + sampleId: C00000001 + urlPattern: http://www.knapsackfamily.com/knapsack_core/information.php?word={$id} + sampleId: C00000001 + - created: 2020-04-22T09:46:18.729+0000 + deprecated: false + deprecationDate: + description: The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation. + id: 2215 + mirId: MIR:00000753 + modified: 2020-04-22T09:46:18.729+0000 + name: Polygenic Score Catalog + namespaceEmbeddedInLui: false + pattern: ^PGS[0-9]{6}$ + prefix: pgs + resources: + - deprecated: false + deprecationDate: + description: >- + The Polygenic Score (PGS) Catalog is an open database of PGS and the + relevant metadata required for accurate application and evaluation. + + + Developed in collaboration with the NHGRI-EBI GWAS Catalog and Health Data Research UK/ + id: 2216 + institution: + description: The University of Cambridge is a collegiate public research university in Cambridge, United Kingdom. Founded in 1209 and granted a royal charter by King Henry III in 1231, Cambridge is the second-oldest university in the English-speaking world and the world's fourth-oldest surviving university. + homeUrl: https://www.cam.ac.uk/ + id: 2214 + location: + countryCode: GB + countryName: United Kingdom + name: University of Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00000755 + name: PGS Catalog + official: true + providerCode: pgs + resourceHomeUrl: http://pgscatalog.org + sampleId: PGS000018 + urlPattern: https://www.pgscatalog.org/pgs/{$id}/ + sampleId: PGS000018 + - created: 2020-05-22T09:05:34.813+0000 + deprecated: false + deprecationDate: + description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. + id: 2251 + mirId: MIR:00000720 + modified: 2020-05-22T09:05:34.813+0000 + name: Datanator Gene + namespaceEmbeddedInLui: false + pattern: ^K[0-9]+$ + prefix: datanator.gene + resources: + - deprecated: false + deprecationDate: + description: The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes eight hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. + id: 2252 + institution: + description: The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes eight hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. + homeUrl: https://icahn.mssm.edu/ + id: 2247 + location: + countryCode: US + countryName: United States + name: Icahn School of Medicine at Mount Sinai + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000740 + name: Icahn School of Medicine at Mount Sinai + official: true + providerCode: icahn + resourceHomeUrl: https://datanator.info/ + sampleId: K00973 + urlPattern: https://www.datanator.info/gene/{$id} + sampleId: K00973 + - created: 2019-06-11T14:17:05.115+0000 + deprecated: false + deprecationDate: + description: A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. + id: 1078 + mirId: MIR:00000376 + modified: 2020-05-22T10:35:39.544+0000 + name: Locus Reference Genomic + namespaceEmbeddedInLui: false + pattern: ^LRG_\d+$ + prefix: lrg + resources: + - deprecated: false + deprecationDate: + description: Locus Reference Genomic through Ensembl + id: 1082 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1081 + location: + countryCode: GB + countryName: United Kingdom + name: EnSembl, Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100627 + name: Locus Reference Genomic through Ensembl + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.ensembl.org/ + sampleId: LRG_1 + urlPattern: http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg={$id} + - deprecated: false + deprecationDate: + description: Locus Reference Genomic through Ensembl mirror (asia) + id: 1083 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1081 + location: + countryCode: GB + countryName: United Kingdom + name: EnSembl, Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge + rorId: + location: + countryCode: SG + countryName: Singapore + mirId: MIR:00100629 + name: Locus Reference Genomic through Ensembl mirror (asia) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://asia.ensembl.org/ + sampleId: LRG_1 + urlPattern: http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg={$id} + - deprecated: false + deprecationDate: + description: Locus Reference Genomic through Ensembl mirror (US west) + id: 1084 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1081 + location: + countryCode: GB + countryName: United Kingdom + name: EnSembl, Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100630 + name: Locus Reference Genomic through Ensembl mirror (US west) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://uswest.ensembl.org/ + sampleId: LRG_1 + urlPattern: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg={$id} + - deprecated: false + deprecationDate: + description: Locus Reference Genomic through Ensembl mirror (US east) + id: 1085 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1081 + location: + countryCode: GB + countryName: United Kingdom + name: EnSembl, Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100631 + name: Locus Reference Genomic through Ensembl mirror (US east) + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://useast.ensembl.org/ + sampleId: LRG_1 + urlPattern: http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg={$id} + - deprecated: false + deprecationDate: + description: Locus Reference Genomic + id: 1080 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100478 + name: Locus Reference Genomic + official: true + providerCode: ebi + resourceHomeUrl: http://www.lrg-sequence.org/ + sampleId: LRG_1 + urlPattern: ftp://ftp.ebi.ac.uk/pub/databases/lrgex/{$id}.xml + sampleId: LRG_1 + - created: 2019-06-11T14:15:31.442+0000 + deprecated: true + deprecationDate: 2020-06-04T11:17:21.453+0000 + description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. + id: 41 + mirId: MIR:00000008 + modified: 2020-06-04T11:17:21.456+0000 + name: MIRIAM Registry collection + namespaceEmbeddedInLui: false + pattern: ^MIR:000\d{5}$ + prefix: miriam.collection + resources: + - deprecated: true + deprecationDate: 2020-06-04T10:00:30.300+0000 + description: MIRIAM Resources (data collection) + id: 42 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100005 + name: MIRIAM Resources (data collection) + official: false + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/miriam/ + sampleId: MIR:00000008 + urlPattern: https://registry.identifiers.org/deprecation/resources/MIR:00100005/{$id} + sampleId: MIR:00000008 + - created: 2019-06-11T14:16:21.651+0000 + deprecated: false + deprecationDate: + description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. + id: 567 + mirId: MIR:00000186 + modified: 2020-06-09T19:30:57.158+0000 + name: Xenbase + namespaceEmbeddedInLui: false + pattern: ^XB\-\w+\-\d+$ + prefix: xenbase + resources: + - deprecated: false + deprecationDate: + description: Xenbase at University of Calgary + id: 569 + institution: + description: The University of Calgary is one of Canada’s top comprehensive research universities, combining the best of university tradition with the city of Calgary’s vibrant energy and diversity. + homeUrl: https://www.ucalgary.ca/ + id: 568 + location: + countryCode: CA + countryName: Canada + name: University of Calgary + rorId: https://ror.org/03yjb2x39 + location: + countryCode: CA + countryName: Canada + mirId: MIR:00100232 + name: Xenbase at University of Calgary + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.xenbase.org/ + sampleId: XB-GENE-922462 + urlPattern: https://www.xenbase.org/common/xsearch.do?exactSearch=true&searchIn=7&searchValue={$id} + sampleId: XB-GENE-922462 + - created: 2020-06-09T20:12:07.077+0000 + deprecated: false + deprecationDate: + description: This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein. + id: 2265 + mirId: MIR:00000739 + modified: 2020-06-26T08:48:10.292+0000 + name: UniProt Chain + namespaceEmbeddedInLui: false + pattern: ^PRO_[0-9]{10}$ + prefix: uniprot.chain + resources: + - deprecated: false + deprecationDate: + description: > + The UniProt Knowledgebase (UniProtKB) is a comprehensive resource + for protein sequence and functional information with extensive + cross-references to more than 120 external databases. This + collection is a subset of UniProtKB that provides a means to + reference the proteolytic cleavage products of a precursor protein. + id: 2266 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 24 + location: + countryCode: GB + countryName: United Kingdom + name: UniProt Consortium + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000728 + name: UniProt Chain through Universal Protein Resource + official: true + providerCode: upr + resourceHomeUrl: https://www.uniprot.org + sampleId: PRO_0000016681 + urlPattern: http://purl.uniprot.org/annotation/{$id} + sampleId: PRO_0000016681 + - created: 2019-06-11T14:16:01.860+0000 + deprecated: false + deprecationDate: + description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. + id: 350 + mirId: MIR:00000109 + modified: 2020-06-26T10:17:31.752+0000 + name: Molecular Interactions Ontology + namespaceEmbeddedInLui: true + pattern: ^MI:\d{4}$ + prefix: mi + resources: + - deprecated: false + deprecationDate: + description: Molecular Interactions Ontology through OLS + id: 351 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100142 + name: Molecular Interactions Ontology through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/mi + sampleId: '0308' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:{$id} + sampleId: '0308' + - created: 2020-07-03T09:30:53.125+0000 + deprecated: false + deprecationDate: + description: 'MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ' + id: 2277 + mirId: MIR:00000768 + modified: 2020-07-03T09:30:53.125+0000 + name: MolMeDB + namespaceEmbeddedInLui: false + pattern: ^[m,M]{2}[0-9]{5}[0-9]*$ + prefix: molmedb + resources: + - deprecated: false + deprecationDate: + description: Palacký University Olomouc is a university with long-standing tradition. Founded in the 16th century, it is the oldest university in Moravia and the second-oldest university in the Czech Republic. Today it is a modern higher education facility with a wide range of study programmes and copious scientific and research activities. In 2019, more than 22 000 students studied in accredited study programmes, exchange programmes and lifelong learning programmes at eight faculties. Palacký University Olomouc is one of the very top Czech universities, and ranks among the best universities in the world, according to international rankings. + id: 2278 + institution: + description: Palacký University Olomouc is a university with long-standing tradition. Founded in the 16th century, it is the oldest university in Moravia and the second-oldest university in the Czech Republic. Today it is a modern higher education facility with a wide range of study programmes and copious scientific and research activities. In 2019, more than 22 000 students studied in accredited study programmes, exchange programmes and lifelong learning programmes at eight faculties. Palacký University Olomouc is one of the very top Czech universities, and ranks among the best universities in the world, according to international rankings. + homeUrl: http://www.upol.cz/en/ + id: 2276 + location: + countryCode: CZ + countryName: Czech Republic + name: Palacký University, Olomouc + rorId: + location: + countryCode: CZ + countryName: Czech Republic + mirId: MIR:00000749 + name: Palacký University, Olomouc + official: true + providerCode: upol + resourceHomeUrl: http://www.upol.cz/en/ + sampleId: MM00040 + urlPattern: https://molmedb.upol.cz/mol/{$id} + sampleId: MM00040 + - created: 2020-07-08T15:12:19.317+0000 + deprecated: false + deprecationDate: + description: Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed. + id: 2293 + mirId: MIR:00000722 + modified: 2020-07-08T15:12:19.317+0000 + name: Open Data for Access and Mining + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: odam + resources: + - deprecated: false + deprecationDate: + description: Bordeaux Metabolome Facility provides equipments and expertise for the study of metabolome, lipidome and metabolic fluxes. + id: 2294 + institution: + description: INRAE is France's new National Research Institute for Agriculture, Food and Environment, created on January 1, 2020, It was formed by the merger of INRA, the National Institute for Agricultural Research, and IRSTEA, the National Research Institute of Science and Technology for the Environment and Agriculture. + homeUrl: https://www.inrae.fr/ + id: 2292 + location: + countryCode: FR + countryName: France + name: National Research Institute for Agriculture, Food and Environment + rorId: https://ror.org/003vg9w96 + location: + countryCode: FR + countryName: France + mirId: MIR:00000759 + name: INRA + official: true + providerCode: bmf + resourceHomeUrl: https://metabolome.cgfb.u-bordeaux.fr/ + sampleId: frim1 + urlPattern: http://pmb-bordeaux.fr/getdata/json/{$id}/datapackage?links=1 + sampleId: frim1 + - created: 2019-06-11T14:17:39.700+0000 + deprecated: true + deprecationDate: 2020-07-16T06:11:33.734+0000 + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol. + id: 1468 + mirId: MIR:00000520 + modified: 2020-07-16T06:11:33.736+0000 + name: HGNC Family + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9-]+(#[A-Z0-9-]+)?$ + prefix: hgnc.family + resources: + - deprecated: true + deprecationDate: 2020-07-16T06:11:29.395+0000 + description: HGNC Family at HUGO Genome Nomenclature Committee + id: 1469 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100671 + name: HGNC Family at HUGO Genome Nomenclature Committee + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.genenames.org/ + sampleId: PADI + urlPattern: https://registry.identifiers.org/deprecation/resources/MIR:00100671/{$id} + sampleId: PADI + - created: 2020-07-16T06:20:43.698+0000 + deprecated: false + deprecationDate: + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. + id: 2306 + mirId: MIR:00000709 + modified: 2020-07-16T06:20:43.698+0000 + name: HGNC Gene Group + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hgnc.genegroup + resources: + - deprecated: false + deprecationDate: + description: HGNC Gene Group at HUGO Genome Nomenclature Committee + id: 2307 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00000703 + name: HGNC Gene Group at HUGO Genome Nomenclature Committee + official: true + providerCode: ebi + resourceHomeUrl: https://www.genenames.org + sampleId: '141' + urlPattern: https://www.genenames.org/cgi-bin/genefamilies/set/{$id} + sampleId: '141' + - created: 2019-06-11T14:16:32.719+0000 + deprecated: false + deprecationDate: + description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. + id: 689 + mirId: MIR:00000233 + modified: 2020-07-20T14:34:20.285+0000 + name: Human Disease Ontology + namespaceEmbeddedInLui: true + pattern: ^DOID:\d+$ + prefix: doid + resources: + - deprecated: false + deprecationDate: + description: Human Disease Ontology through BioPortal + id: 690 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 571 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford University + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100292 + name: Human Disease Ontology through BioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/DOID + sampleId: '11337' + urlPattern: http://purl.bioontology.org/ontology/DOID/DOID:{$id} + - deprecated: false + deprecationDate: + description: Human Disease Ontology at Northwestern University + id: 693 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 692 + location: + countryCode: US + countryName: United States + name: University of Maryland (Maryland) and Northwestern University (Illinois) + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100297 + name: Human Disease Ontology at Northwestern University + official: false + providerCode: hdo + resourceHomeUrl: http://disease-ontology.org/ + sampleId: '11337' + urlPattern: http://disease-ontology.org/term/DOID:{$id} + - deprecated: false + deprecationDate: + description: Human Disease Ontology through OLS + id: 691 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100293 + name: Human Disease Ontology through OLS + official: true + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/doid + sampleId: '11337' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:{$id} + sampleId: '11337' + - created: 2019-06-11T14:17:23.452+0000 + deprecated: false + deprecationDate: + description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. + id: 1292 + mirId: MIR:00000450 + modified: 2020-07-30T07:27:34.233+0000 + name: Gene Ontology Reference + namespaceEmbeddedInLui: true + pattern: ^GO_REF:\d{7}$ + prefix: go_ref + resources: + - deprecated: false + deprecationDate: + description: Gene Ontology Reference at The Gene Ontology Consortium + id: 1293 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 89 + location: + countryCode: US + countryName: United States + name: The Gene Ontology Consortium + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100584 + name: Gene Ontology Reference at The Gene Ontology Consortium + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.geneontology.org/cgi-bin/references.cgi + sampleId: '0000041' + urlPattern: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-{$id}.md + sampleId: '0000041' + - created: 2019-06-17T12:55:17.868+0000 + deprecated: false + deprecationDate: + description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. + id: 1934 + mirId: MIR:00000715 + modified: 2020-09-23T11:03:41.882+0000 + name: GWAS Catalog + namespaceEmbeddedInLui: false + pattern: ^GCST\d{6}\d*$ + prefix: gcst + resources: + - deprecated: false + deprecationDate: + description: The European Bioinformatics Institute (EMBL-EBI) helps scientists realise the potential of 'big data' in biology, exploiting complex information to make discoveries that benefit humankind. + id: 1935 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00000775 + name: European Bioinformatics Institute + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk + sampleId: GCST000035 + urlPattern: https://www.ebi.ac.uk/gwas/studies/{$id} + sampleId: GCST000035 + - created: 2020-10-07T10:25:14.491+0000 + deprecated: false + deprecationDate: + description: 'PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ' + id: 2370 + mirId: MIR:00000708 + modified: 2020-10-07T10:25:14.491+0000 + name: PK-DB + namespaceEmbeddedInLui: false + pattern: ^PKDB[0-9]{5}$ + prefix: pkdb + resources: + - deprecated: false + deprecationDate: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/01hcx6992' with Wikidata IDs [Q152087], and ISNI IDs [0000 0001 2248 7639] + id: 2371 + institution: + description: Humboldt University of Berlin is a university in the central borough of Mitte in Berlin, Germany. It was established by Frederick William III on the initiative of Wilhelm von Humboldt, Johann Gottlieb Fichte and Friedrich Ernst Daniel Schleiermacher as the University of Berlin (Universität zu Berlin) in 1809, and opened in 1810. + homeUrl: https://www.hu-berlin.de/?set_language=en&cl=en + id: 2369 + location: + countryCode: DE + countryName: Germany + name: Humboldt University of Berlin + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00000714 + name: Humboldt University of Berlin + official: true + providerCode: pkdb + resourceHomeUrl: https://www.hu-berlin.de/?set_language=en&cl=en + sampleId: PKDB00198 + urlPattern: https://pk-db.com/data/{$id} + sampleId: PKDB00198 + - created: 2020-10-07T10:43:05.918+0000 + deprecated: false + deprecationDate: + description: > + The Morpheus model repository is an open-access data resource to store, + search and retrieve unpublished and published computational models of + spatio-temporal and multicellular biological systems, encoded in the + MorpheusML language and readily executable with the Morpheus software. + id: 2377 + mirId: MIR:00000725 + modified: 2020-10-07T10:43:05.918+0000 + name: Morpheus model repository + namespaceEmbeddedInLui: false + pattern: ^M[0-9]{4,}$ + prefix: morpheus + resources: + - deprecated: false + deprecationDate: + description: >- + Morpheus.lab is affiliated with the Center for Information Services + and High Performance Computing (ZIH) + + at Technische Universität Dresden, Germany. Morpheus.lab develops and maintains the open-source software Morpheus, the domain-specific language MorpheusML, online courses, a user forum and the model repository. + id: 2378 + institution: + description: The Technische Universität Dresden (TUD) is one of the largest “Technische Universitäten” in Germany and one of the leading and most dynamic universities in Germany. As a full-curriculum university with 17 faculties in five schools it offers a broad variety of 124 disciplines and covers a wide research spectrum. Its focuses Health Sciences, Biomedicine & Bioengineering, Information Technology & Microelectronics, Smart Materials & Structures, Energy, Mobility & Environment as well as Culture & Societal Change are considered exemplary in Germany and throughout Europe. + homeUrl: https://tu-dresden.de/?set_language=en + id: 2376 + location: + countryCode: DE + countryName: Germany + name: TU Dresden + rorId: + location: + countryCode: DE + countryName: Germany + mirId: MIR:00000700 + name: Morpheus.lab + official: true + providerCode: morpheus.lab + resourceHomeUrl: https://morpheus.gitlab.io/ + sampleId: M0001 + urlPattern: https://morpheus.gitlab.io/models/{$id} + sampleId: M0001 + - created: 2020-10-08T09:25:59.424+0000 + deprecated: false + deprecationDate: + description: GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines. + id: 2384 + mirId: MIR:00000721 + modified: 2020-10-08T09:25:59.424+0000 + name: GlycoPOST + namespaceEmbeddedInLui: false + pattern: ^GPST[0-9]{6}$ + prefix: glycopost + resources: + - deprecated: false + deprecationDate: + description: Niigata University has a long institutional history, with origins going back some 150 years. Since its inauguration as a national university in 1949 under the new university system, it has played an important role in higher education and research in Japan. Over the years, it has grown into a large-scale comprehensive university offering bachelor's, master's, and doctoral degree programs under ten faculties and five graduate schools in a wide range of disciplines spanning the humanities, education, law, economics, science, engineering, agriculture, medicine, health sciences, and dentistry. With a student body of approximately 13,000 and 3,000 academic and administrative staff members, and as a research-oriented university, it boasts several world-leading research institutes, including the Brain Research Institute and the Research Institute for Natural Hazards and Disaster Recovery as well as a university hospital providing high-level medical care as an advanced treatment hospital for the region. + id: 2385 + institution: + description: Niigata University has a long institutional history, with origins going back some 150 years. Since its inauguration as a national university in 1949 under the new university system, it has played an important role in higher education and research in Japan. Over the years, it has grown into a large-scale comprehensive university offering bachelor's, master's, and doctoral degree programs under ten faculties and five graduate schools in a wide range of disciplines spanning the humanities, education, law, economics, science, engineering, agriculture, medicine, health sciences, and dentistry. With a student body of approximately 13,000 and 3,000 academic and administrative staff members, and as a research-oriented university, it boasts several world-leading research institutes, including the Brain Research Institute and the Research Institute for Natural Hazards and Disaster Recovery as well as a university hospital providing high-level medical care as an advanced treatment hospital for the region. + homeUrl: https://www.niigata-u.ac.jp/ + id: 2383 + location: + countryCode: JP + countryName: Japan + name: Niigata University + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00000704 + name: Niigata University + official: true + providerCode: glycopost + resourceHomeUrl: https://glycopost.glycosmos.org + sampleId: GPST000024 + urlPattern: https://glycopost.glycosmos.org/entry/{$id} + sampleId: GPST000024 + - created: 2019-06-11T14:17:22.433+0000 + deprecated: false + deprecationDate: + description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. + id: 1280 + mirId: MIR:00000446 + modified: 2021-02-27T10:19:43.666+0000 + name: UBERON + namespaceEmbeddedInLui: true + pattern: ^UBERON:\d+$ + prefix: uberon + resources: + - deprecated: false + deprecationDate: + description: UBERON through bioPortal + id: 1281 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 5 + location: + countryCode: US + countryName: United States + name: National Center for Biomedical Ontology, Stanford + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00100579 + name: UBERON through bioPortal + official: false + providerCode: bptl + resourceHomeUrl: http://bioportal.bioontology.org/ontologies/UBERON + sampleId: '0008203' + urlPattern: http://purl.bioontology.org/ontology/UBERON/UBERON:{$id} + - deprecated: false + deprecationDate: + description: UBERON through OLS + id: 1282 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100580 + name: UBERON through OLS + official: false + providerCode: ols + resourceHomeUrl: https://www.ebi.ac.uk/ols/ontologies/uberon + sampleId: '0008203' + urlPattern: https://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=UBERON:{$id} + sampleId: '0008203' + - created: 2021-02-17T18:06:52.762+0000 + deprecated: false + deprecationDate: + description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. + id: 2524 + mirId: MIR:00000795 + modified: 2021-02-17T18:06:52.762+0000 + name: Protein Ensemble Database ensemble + namespaceEmbeddedInLui: false + pattern: ^PED\d{5}e\d{3}$ + prefix: ped.ensemble + resources: + - deprecated: false + deprecationDate: + description: The Protein Ensemble Database (PED) is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. + id: 2525 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1769 + location: + countryCode: IT + countryName: Italy + name: University of Padua + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00000791 + name: PED - Protein Ensemble Database + official: true + providerCode: ped.ensemble + resourceHomeUrl: https://proteinensemble.org/ + sampleId: PED00017e001 + urlPattern: https://proteinensemble.org/{$id} + sampleId: PED00017e001 + - created: 2021-02-17T18:09:04.420+0000 + deprecated: false + deprecationDate: + description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. + id: 2527 + mirId: MIR:00000764 + modified: 2021-02-17T18:09:04.420+0000 + name: RepeatsDB Structure + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$ + prefix: repeatsdb.structure + resources: + - deprecated: false + deprecationDate: + description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. + id: 2528 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1769 + location: + countryCode: IT + countryName: Italy + name: University of Padua + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00000780 + name: RepeatsDB + official: true + providerCode: repeatsdb.structure + resourceHomeUrl: https://repeatsdb.org/ + sampleId: 2gc4E + urlPattern: https://repeatsdb.org/structure/{$id} + sampleId: 2gc4E + - created: 2020-10-22T01:16:20.744+0000 + deprecated: false + deprecationDate: + description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML). + id: 2416 + mirId: MIR:00000767 + modified: 2020-10-22T01:16:20.744+0000 + name: BioSimulators + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9-_]+' + prefix: biosimulators + resources: + - deprecated: false + deprecationDate: + description: The BioSimulators project aims to make it easier for the research community to reuse biosimulation tools through standards and a registry of simulation tools. + id: 2417 + institution: + description: The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes eight hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. + homeUrl: https://icahn.mssm.edu/ + id: 2247 + location: + countryCode: US + countryName: United States + name: Icahn School of Medicine at Mount Sinai + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000746 + name: BioSimulators + official: true + providerCode: icahn + resourceHomeUrl: https://biosimulators.org/ + sampleId: vcell + urlPattern: https://biosimulators.org/simulators/{$id} + sampleId: vcell + - created: 2020-11-05T10:42:17.722+0000 + deprecated: false + deprecationDate: + description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. + id: 2423 + mirId: MIR:00000712 + modified: 2020-11-05T10:59:53.808+0000 + name: Gender, Sex, and Sexual Orientation (GSSO) Ontology + namespaceEmbeddedInLui: true + pattern: ^GSSO:\d{6}$ + prefix: gsso + resources: + - deprecated: false + deprecationDate: + description: One of the National Centers for Biomedical Computing, and is funded by the NIH. Among the goals of the NCBO are to provide tools for discovery and access of biomedical ontologies, which are a type of controlled vocabulary designed to allow the expression of complex relationships in machine-readable form. + id: 2424 + institution: + description: UC is a public research university with an enrollment of more than 46,000 students and has been named "Among the top tier of the Best National Universities," according to U.S. News & World Report. + homeUrl: https://www.uc.edu/ + id: 2422 + location: + countryCode: US + countryName: United States + name: University of Cincinnati + rorId: https://ror.org/01e3m7079 + location: + countryCode: US + countryName: United States + mirId: MIR:00000758 + name: National Center for Biomedical Ontology (NCBO) BioPortal + official: true + providerCode: bioportal + resourceHomeUrl: https://bioportal.bioontology.org/ + sampleId: '002368' + urlPattern: http://purl.obolibrary.org/obo/GSSO_{$id} + sampleId: '002368' + - created: 2019-06-11T14:17:28.979+0000 + deprecated: false + deprecationDate: + description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. + id: 1357 + mirId: MIR:00000477 + modified: 2020-11-20T10:55:30.526+0000 + name: LigandBox + namespaceEmbeddedInLui: false + pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$ + prefix: ligandbox + resources: + - deprecated: false + deprecationDate: + description: LigandBox at N2PC + id: 1359 + institution: + description: https://www.natprodchem.jp/files/english.pdf + homeUrl: https://www.natprodchem.jp/ + id: 1358 + location: + countryCode: JP + countryName: Japan + name: Next generation Natural Products Chemistry + rorId: + location: + countryCode: JP + countryName: Japan + mirId: MIR:00100612 + name: LigandBox at N2PC + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en + sampleId: D00001 + urlPattern: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id={$id} + sampleId: D00001 + - created: 2019-06-11T14:17:59.445+0000 + deprecated: false + deprecationDate: + description: The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt "neoplasm" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs. + id: 1666 + mirId: MIR:00000600 + modified: 2020-11-25T15:01:33.103+0000 + name: Progenetix + namespaceEmbeddedInLui: false + pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$ + prefix: pgx + resources: + - deprecated: false + deprecationDate: + description: Progenetix + id: 1668 + institution: + description: No description available + homeUrl: https://www.uzh.ch/en.html + id: 1667 + location: + countryCode: CH + countryName: Switzerland + name: University of Zurich + rorId: https://ror.org/02crff812 + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100801 + name: Progenetix + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://progenetix.org/ + sampleId: pgxbs-kftva5zv + urlPattern: https://progenetix.org/services/ids/{$id} + sampleId: pgxbs-kftva5zv + - created: 2020-12-14T12:49:56.333+0000 + deprecated: false + deprecationDate: + description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease. + id: 2477 + mirId: MIR:00000789 + modified: 2020-12-14T12:49:56.333+0000 + name: SARS-CoV-2 + namespaceEmbeddedInLui: false + pattern: ^\w+_COVID19_[-\w]+$ + prefix: covid19 + resources: + - deprecated: false + deprecationDate: + description: Elixir@UiT is the local branch of ELIXIR-NO node based at UiT. + id: 2478 + institution: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/00wge5k78' with Wikidata IDs [Q279724], and ISNI IDs [0000000122595234] + homeUrl: https://uit.no/startsida + id: 2476 + location: + countryCode: NO + countryName: Norway + name: University of Tromsø - The Arctic University of Norway + rorId: + location: + countryCode: NO + countryName: Norway + mirId: MIR:00000787 + name: Elixir@UiT + official: true + providerCode: sfb + resourceHomeUrl: https://covid19.sfb.uit.no + sampleId: SFB_COVID19_MW286762 + urlPattern: https://covid19.sfb.uit.no/api/records/{$id} + sampleId: SFB_COVID19_MW286762 + - created: 2020-12-14T12:57:54.560+0000 + deprecated: false + deprecationDate: + description: 'Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ' + id: 2484 + mirId: MIR:00000785 + modified: 2020-12-14T12:57:54.560+0000 + name: OMA HOGs + namespaceEmbeddedInLui: true + pattern: ^HOG:[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ + prefix: oma.hog + resources: + - deprecated: false + deprecationDate: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/05a28rw58' with Wikidata IDs [Q11942], and ISNI IDs [0000 0001 2156 2780] + id: 2485 + institution: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/05a28rw58' with Wikidata IDs [Q11942], and ISNI IDs [0000 0001 2156 2780] + homeUrl: https://ethz.ch/en.html + id: 2483 + location: + countryCode: CH + countryName: Switzerland + name: ETH Zurich + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00000761 + name: ETH Zurich + official: true + providerCode: oma + resourceHomeUrl: https://omabrowser.org + sampleId: HOG:0459895 + urlPattern: https://omabrowser.org/oma/hog/resolve/HOG:{$id}/ + sampleId: HOG:0459895 + - created: 2021-02-01T15:47:59.756+0000 + deprecated: false + deprecationDate: + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + id: 2497 + mirId: MIR:00000774 + modified: 2021-02-01T15:47:59.756+0000 + name: VMH Gene + namespaceEmbeddedInLui: false + pattern: ^[0-9]+\.[0-9]+ + prefix: vmhgene + resources: + - deprecated: false + deprecationDate: + description: >- + VMH Gene, provided by Thiele Group, NUI Galway. + + The VMH database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data. + id: 2498 + institution: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/03bea9k73' with Wikidata IDs [Q644478], and ISNI IDs [0000 0004 0488 0789] + homeUrl: http://www.nuigalway.ie/ + id: 2496 + location: + countryCode: IE + countryName: Ireland + name: National University of Ireland, Galway + rorId: + location: + countryCode: IE + countryName: Ireland + mirId: MIR:00000794 + name: VMH Gene + official: true + providerCode: NUI + resourceHomeUrl: https://www.vmh.life/ + sampleId: '8639.1' + urlPattern: https://www.vmh.life/#gene/{$id} + sampleId: '8639.1' + - created: 2019-06-11T14:17:44.698+0000 + deprecated: false + deprecationDate: + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. + id: 1523 + mirId: MIR:00000543 + modified: 2021-02-01T16:43:30.697+0000 + name: GWAS Central Phenotype + namespaceEmbeddedInLui: false + pattern: ^HGVPM\d+$ + prefix: gwascentral.phenotype + resources: + - deprecated: false + deprecationDate: + description: GWAS Central Phenotype at University of Leicester + id: 1524 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1079 + location: + countryCode: GB + countryName: United Kingdom + name: Department of Genetics, University of Leicester, Leicester + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00100720 + name: GWAS Central Phenotype at University of Leicester + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.gwascentral.org/phenotypes + sampleId: HGVPM623 + urlPattern: https://www.gwascentral.org/phenotype/{$id} + sampleId: HGVPM623 + - created: 2021-02-17T17:56:14.329+0000 + deprecated: false + deprecationDate: + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs). + id: 2518 + mirId: MIR:00000769 + modified: 2021-02-17T17:56:14.329+0000 + name: ClinVar Submitter + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: clinvar.submitter + resources: + - deprecated: false + deprecationDate: + description: ClinVar Submitter ids are assigned by NCBI for all authorized submitters of clinvar submissions (SCVs) + id: 2519 + institution: + description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. + homeUrl: https://www.ncbi.nlm.nih.gov/ + id: 26 + location: + countryCode: US + countryName: United States + name: National Center for Biotechnology Information + rorId: https://ror.org/02meqm098 + location: + countryCode: US + countryName: United States + mirId: MIR:00000783 + name: ClinVar Submitter at NCBI + official: true + providerCode: ncbi + resourceHomeUrl: https://www.ncbi.nlm.nih.gov/clinvar/ + sampleId: '26957' + urlPattern: https://www.ncbi.nlm.nih.gov/clinvar/submitters/{$id} + sampleId: '26957' + - created: 2021-02-17T18:02:05.160+0000 + deprecated: false + deprecationDate: + description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. + id: 2521 + mirId: MIR:00000777 + modified: 2021-02-17T18:02:05.160+0000 + name: Protein Ensemble Database + namespaceEmbeddedInLui: false + pattern: ^PED\d{5}$ + prefix: ped + resources: + - deprecated: false + deprecationDate: + description: The Protein Ensemble Database (PED) is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. + id: 2522 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1769 + location: + countryCode: IT + countryName: Italy + name: University of Padua + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00000784 + name: PED - Protein Ensemble Database + official: true + providerCode: ped + resourceHomeUrl: https://proteinensemble.org/ + sampleId: PED00037 + urlPattern: https://proteinensemble.org/{$id} + sampleId: PED00037 + - created: 2021-02-17T18:11:07.592+0000 + deprecated: false + deprecationDate: + description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database. + id: 2532 + mirId: MIR:00000792 + modified: 2021-02-17T18:11:07.592+0000 + name: RepeatsDB Protein + namespaceEmbeddedInLui: false + pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$ + prefix: repeatsdb.protein + resources: + - deprecated: false + deprecationDate: + description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. + id: 2533 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1769 + location: + countryCode: IT + countryName: Italy + name: University of Padua + rorId: + location: + countryCode: IT + countryName: Italy + mirId: MIR:00000699 + name: RepeatsDB + official: true + providerCode: '' + resourceHomeUrl: https://repeatsdb.org/ + sampleId: P29894 + urlPattern: https://repeatsdb.org/protein/{$id} + sampleId: P29894 + - created: 2021-02-26T07:35:34.234+0000 + deprecated: false + deprecationDate: + description: The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access. + id: 2548 + mirId: MIR:00000796 + modified: 2021-02-26T07:35:34.234+0000 + name: gateway + namespaceEmbeddedInLui: false + pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ + prefix: gateway + resources: + - deprecated: false + deprecationDate: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/04rtjaj74' with no Wikidata information, and no ISNI information + id: 2549 + institution: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/04rtjaj74' with no Wikidata information, and no ISNI information + homeUrl: https://www.hdruk.ac.uk + id: 2547 + location: + countryCode: GB + countryName: United Kingdom + name: Health Data Research UK + rorId: + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00000697 + name: Health Data Research UK + official: true + providerCode: hdruk + resourceHomeUrl: https://www.hdruk.ac.uk + sampleId: fd8d0743-344a-4758-bb97-f8ad84a37357 + urlPattern: https://web.www.healthdatagateway.org/dataset/{$id} + sampleId: fd8d0743-344a-4758-bb97-f8ad84a37357 + - created: 2019-06-11T14:17:50.805+0000 + deprecated: false + deprecationDate: + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. + id: 1585 + mirId: MIR:00000569 + modified: 2021-02-26T09:49:03.051+0000 + name: MetaNetX compartment + namespaceEmbeddedInLui: false + pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$ + prefix: metanetx.compartment + resources: + - deprecated: false + deprecationDate: + description: MetaNetX compartment at SIB Swiss Institute of Bioinformatics + id: 1586 + institution: + description: CURATOR_REVIEW + homeUrl: CURATOR_REVIEW + id: 1581 + location: + countryCode: CH + countryName: Switzerland + name: Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne + rorId: + location: + countryCode: CH + countryName: Switzerland + mirId: MIR:00100750 + name: MetaNetX compartment at SIB Swiss Institute of Bioinformatics + official: false + providerCode: CURATOR_REVIEW + resourceHomeUrl: https://www.metanetx.org/ + sampleId: MNXC15 + urlPattern: https://www.metanetx.org/comp_info/{$id} + sampleId: MNXC15 + - created: 2021-02-26T10:27:01.032+0000 + deprecated: false + deprecationDate: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent. + id: 2559 + mirId: MIR:00000798 + modified: 2021-02-26T10:27:01.032+0000 + name: Animal Genome QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: qtldb + resources: + - deprecated: false + deprecationDate: + description: Animal QTL DB at Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University + id: 2560 + institution: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/04rswrd78' with Wikidata IDs [Q1136919], and ISNI IDs [0000 0004 1936 7312] + homeUrl: https://www.iastate.edu/ + id: 2558 + location: + countryCode: US + countryName: United States + name: Iowa State University + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000797 + name: Animal QTL DB at Iowa State University + official: true + providerCode: iastate + resourceHomeUrl: https://www.animalgenome.org/QTLdb + sampleId: '4685' + urlPattern: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:{$id} + sampleId: '4685' + - created: 2021-02-28T15:53:07.380+0000 + deprecated: false + deprecationDate: + description: runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive. + id: 2565 + mirId: MIR:00000897 + modified: 2021-02-28T15:53:07.380+0000 + name: runBioSimulations + namespaceEmbeddedInLui: false + pattern: '[0-9a-z]{24,24}' + prefix: runbiosimulations + resources: + - deprecated: false + deprecationDate: + description: Organization information obtained from ROR API using ROR ID 'https://ror.org/04a9tmd77' with Wikidata IDs [Q1950740], and ISNI IDs [0000 0001 0670 2351] + id: 2566 + institution: + description: The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes eight hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. + homeUrl: https://icahn.mssm.edu/ + id: 2247 + location: + countryCode: US + countryName: United States + name: Icahn School of Medicine at Mount Sinai + rorId: + location: + countryCode: US + countryName: United States + mirId: MIR:00000898 + name: Icahn School of Medicine at Mount Sinai + official: true + providerCode: icahn + resourceHomeUrl: https://icahn.mssm.edu/ + sampleId: 5fde96bdc5f1aa9ff0cce18a + urlPattern: https://run.biosimulations.org/simulations/{$id} + sampleId: 5fde96bdc5f1aa9ff0cce18a + - created: 2021-02-28T16:13:04.331+0000 + deprecated: false + deprecationDate: + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + id: 2571 + mirId: MIR:00000799 + modified: 2021-02-28T16:13:04.331+0000 + name: ChEMBL + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl + resources: + - deprecated: false + deprecationDate: + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + id: 2572 + institution: + description: >- + At EMBL-EBI, we make the world’s public biological data freely + available to the scientific community via a range of services and + tools, perform basic research and provide professional training in + bioinformatics. + + We are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states. + homeUrl: https://www.ebi.ac.uk + id: 2 + location: + countryCode: GB + countryName: United Kingdom + name: European Bioinformatics Institute + rorId: https://ror.org/02catss52 + location: + countryCode: GB + countryName: United Kingdom + mirId: MIR:00000800 + name: European Bioinformatics Institute + official: true + providerCode: ebi + resourceHomeUrl: https://www.ebi.ac.uk/chembl + sampleId: CHEMBL4303805 + urlPattern: 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"schema:storageRequirements" - }, - "streetAddress": { - "@id": "schema:streetAddress" - }, - "strengthUnit": { - "@id": "schema:strengthUnit" - }, - "strengthValue": { - "@id": "schema:strengthValue" - }, - "structuralClass": { - "@id": "schema:structuralClass" - }, - "study": { - "@id": "schema:study" - }, - "studyDesign": { - "@id": "schema:studyDesign" - }, - "studyLocation": { - "@id": "schema:studyLocation" - }, - "studySubject": { - "@id": "schema:studySubject" - }, - "stupidProperty": { - "@id": "schema:stupidProperty" - }, - "subEvent": { - "@id": "schema:subEvent" - }, - "subEvents": { - "@id": "schema:subEvents" - }, - "subOrganization": { - "@id": "schema:subOrganization" - }, - "subReservation": { - "@id": "schema:subReservation" - }, - "subStageSuffix": { - "@id": "schema:subStageSuffix" - }, - "subStructure": { - "@id": "schema:subStructure" - }, - "subTest": { - "@id": "schema:subTest" - }, - "subTrip": { - "@id": "schema:subTrip" - }, - "subjectOf": { - "@id": "schema:subjectOf" - }, - "subtitleLanguage": { - "@id": "schema:subtitleLanguage" - }, - "successorOf": { - "@id": "schema:successorOf" - }, - "sugarContent": { - "@id": "schema:sugarContent" - }, - "suggestedAnswer": { - "@id": "schema:suggestedAnswer" - }, - "suggestedGender": { - "@id": "schema:suggestedGender" - }, - "suggestedMaxAge": { - "@id": "schema:suggestedMaxAge" - }, - "suggestedMinAge": { - "@id": "schema:suggestedMinAge" - }, - "suitableForDiet": { - "@id": "schema:suitableForDiet" - }, - "superEvent": { - "@id": "schema:superEvent" - }, - "supersededBy": { - "@id": "schema:supersededBy" - }, - "supply": { - "@id": "schema:supply" - }, - "supplyTo": { - "@id": "schema:supplyTo" - }, - "supportingData": { - "@id": "schema:supportingData" - }, - "surface": { - "@id": "schema:surface" - }, - "target": { - "@id": "schema:target" - }, - "targetCollection": { - "@id": "schema:targetCollection" - }, - "targetDescription": { - "@id": "schema:targetDescription" - }, - "targetName": { - "@id": "schema:targetName" - }, - "targetPlatform": { - "@id": "schema:targetPlatform" - }, - "targetPopulation": { - "@id": "schema:targetPopulation" - }, - "targetProduct": { - "@id": "schema:targetProduct" - }, - "targetUrl": { - "@id": "schema:targetUrl", - "@type": "@id" - }, - "taxID": { - "@id": "schema:taxID" - }, - "teaches": { - "@id": "schema:teaches" - }, - "telephone": { - "@id": "schema:telephone" - }, - "temporal": { - "@id": "schema:temporal" - }, - "temporalCoverage": { - "@id": "schema:temporalCoverage" - }, - "termCode": { - "@id": "schema:termCode" - }, - "termDuration": { - "@id": "schema:termDuration" - }, - "termsOfService": { - "@id": "schema:termsOfService" - }, - "termsPerYear": { - "@id": "schema:termsPerYear" - }, - "text": { - "@id": "schema:text" - }, - "textValue": { - "@id": "schema:textValue" - }, - "thumbnail": { - "@id": "schema:thumbnail" - }, - "thumbnailUrl": { - "@id": "schema:thumbnailUrl", - "@type": "@id" - }, - "tickerSymbol": { - "@id": "schema:tickerSymbol" - }, - "ticketNumber": { - "@id": "schema:ticketNumber" - }, - "ticketToken": { - "@id": "schema:ticketToken" - }, - "ticketedSeat": { - "@id": "schema:ticketedSeat" - }, - "timeOfDay": { - "@id": "schema:timeOfDay" - }, - "timeRequired": { - "@id": "schema:timeRequired" - }, - "timeToComplete": { - "@id": "schema:timeToComplete" - }, - "tissueSample": { - "@id": "schema:tissueSample" - }, - "title": { - "@id": "schema:title" - }, - "titleEIDR": { - "@id": "schema:titleEIDR" - }, - "toLocation": { - "@id": "schema:toLocation" - }, - "toRecipient": { - "@id": "schema:toRecipient" - }, - "tongueWeight": { - "@id": "schema:tongueWeight" - }, - "tool": { - "@id": "schema:tool" - }, - "torque": { - "@id": "schema:torque" - }, - "totalJobOpenings": { - "@id": "schema:totalJobOpenings" - }, - "totalPaymentDue": { - "@id": "schema:totalPaymentDue" - }, - "totalPrice": { - "@id": "schema:totalPrice" - }, - "totalTime": { - "@id": "schema:totalTime" - }, - "tourBookingPage": { - "@id": "schema:tourBookingPage", - "@type": "@id" - }, - "touristType": { - "@id": "schema:touristType" - }, - "track": { - "@id": "schema:track" - }, - "trackingNumber": { - "@id": "schema:trackingNumber" - }, - "trackingUrl": { - "@id": "schema:trackingUrl", - "@type": "@id" - }, - "tracks": { - "@id": "schema:tracks" - }, - "trailer": { - "@id": "schema:trailer" - }, - "trailerWeight": { - "@id": "schema:trailerWeight" - }, - "trainName": { - "@id": "schema:trainName" - }, - "trainNumber": { - "@id": "schema:trainNumber" - }, - "trainingSalary": { - "@id": "schema:trainingSalary" - }, - "transFatContent": { - "@id": "schema:transFatContent" - }, - "transcript": { - "@id": "schema:transcript" - }, - "transitTime": { - "@id": "schema:transitTime" - }, - "transitTimeLabel": { - "@id": "schema:transitTimeLabel" - }, - "translationOfWork": { - "@id": "schema:translationOfWork" - }, - "translator": { - "@id": "schema:translator" - }, - "transmissionMethod": { - "@id": "schema:transmissionMethod" - }, - "travelBans": { - "@id": "schema:travelBans", - "@type": "@id" - }, - "trialDesign": { - "@id": "schema:trialDesign" - }, - "tributary": { - "@id": "schema:tributary" - }, - "type": "@type", - "typeOfBed": { - "@id": "schema:typeOfBed" - }, - "typeOfGood": { - "@id": "schema:typeOfGood" - }, - "typicalAgeRange": { - "@id": "schema:typicalAgeRange" - }, - "typicalCreditsPerTerm": { - "@id": "schema:typicalCreditsPerTerm" - }, - "typicalTest": { - "@id": "schema:typicalTest" - }, - "underName": { - "@id": "schema:underName" - }, - "unitCode": { - "@id": "schema:unitCode" - }, - "unitText": { - "@id": "schema:unitText" - }, - "unnamedSourcesPolicy": { - "@id": "schema:unnamedSourcesPolicy", - "@type": "@id" - }, - "unsaturatedFatContent": { - "@id": "schema:unsaturatedFatContent" - }, - "uploadDate": { - "@id": "schema:uploadDate", - "@type": "Date" - }, - "upvoteCount": { - "@id": "schema:upvoteCount" - }, - "url": { - "@id": "schema:url", - "@type": "@id" - }, - "urlTemplate": { - "@id": "schema:urlTemplate" - }, - "usageInfo": { - "@id": "schema:usageInfo", - "@type": "@id" - }, - "usedToDiagnose": { - "@id": "schema:usedToDiagnose" - }, - "userInteractionCount": { - "@id": "schema:userInteractionCount" - }, - "usesDevice": { - "@id": "schema:usesDevice" - }, - "usesHealthPlanIdStandard": { - "@id": "schema:usesHealthPlanIdStandard" - }, - "validFor": { - "@id": "schema:validFor" - }, - "validFrom": { - "@id": "schema:validFrom", - "@type": "Date" - }, - "validIn": { - "@id": "schema:validIn" - }, - "validThrough": { - "@id": "schema:validThrough", - "@type": "Date" - }, - "validUntil": { - "@id": "schema:validUntil", - "@type": "Date" - }, - "value": { - "@id": "schema:value" - }, - "valueAddedTaxIncluded": { - "@id": "schema:valueAddedTaxIncluded" - }, - "valueMaxLength": { - "@id": "schema:valueMaxLength" - }, - "valueMinLength": { - "@id": "schema:valueMinLength" - }, - "valueName": { - "@id": "schema:valueName" - }, - "valuePattern": { - "@id": "schema:valuePattern" - }, - "valueReference": { - "@id": "schema:valueReference" - }, - "valueRequired": { - "@id": "schema:valueRequired" - }, - "variableMeasured": { - "@id": "schema:variableMeasured" - }, - "variablesMeasured": { - "@id": "schema:variablesMeasured" - }, - "variantCover": { - "@id": "schema:variantCover" - }, - "variesBy": { - "@id": "schema:variesBy" - }, - "vatID": { - "@id": "schema:vatID" - }, - "vehicleConfiguration": { - "@id": "schema:vehicleConfiguration" - }, - "vehicleEngine": { - "@id": "schema:vehicleEngine" - }, - "vehicleIdentificationNumber": { - "@id": "schema:vehicleIdentificationNumber" - }, - "vehicleInteriorColor": { - "@id": "schema:vehicleInteriorColor" - }, - "vehicleInteriorType": { - "@id": "schema:vehicleInteriorType" - }, - "vehicleModelDate": { - "@id": "schema:vehicleModelDate", - "@type": "Date" - }, - "vehicleSeatingCapacity": { - "@id": "schema:vehicleSeatingCapacity" - }, - "vehicleSpecialUsage": { - "@id": "schema:vehicleSpecialUsage" - }, - "vehicleTransmission": { - "@id": "schema:vehicleTransmission" - }, - "vendor": { - "@id": "schema:vendor" - }, - "verificationFactCheckingPolicy": { - "@id": "schema:verificationFactCheckingPolicy", - "@type": "@id" - }, - "version": { - "@id": "schema:version" - }, - "video": { - "@id": "schema:video" - }, - "videoFormat": { - "@id": "schema:videoFormat" - }, - "videoFrameSize": { - "@id": "schema:videoFrameSize" - }, - "videoQuality": { - "@id": "schema:videoQuality" - }, - "void": "http://rdfs.org/ns/void#", - "volumeNumber": { - "@id": "schema:volumeNumber" - }, - "warning": { - "@id": "schema:warning" - }, - "warranty": { - "@id": "schema:warranty" - }, - "warrantyPromise": { - "@id": "schema:warrantyPromise" - }, - "warrantyScope": { - "@id": "schema:warrantyScope" - }, - "webCheckinTime": { - "@id": "schema:webCheckinTime", - "@type": "DateTime" - }, - "webFeed": { - "@id": "schema:webFeed", - "@type": "@id" - }, - "weight": { - "@id": "schema:weight" - }, - "weightTotal": { - "@id": "schema:weightTotal" - }, - "wheelbase": { - "@id": "schema:wheelbase" - }, - "width": { - "@id": "schema:width" - }, - "winner": { - "@id": "schema:winner" - }, - "wordCount": { - "@id": "schema:wordCount" - }, - "workExample": { - "@id": "schema:workExample" - }, - "workFeatured": { - "@id": "schema:workFeatured" - }, - "workHours": { - "@id": "schema:workHours" - }, - "workLocation": { - "@id": "schema:workLocation" - }, - "workPerformed": { - "@id": "schema:workPerformed" - }, - "workPresented": { - "@id": "schema:workPresented" - }, - "workTranslation": { - "@id": "schema:workTranslation" - }, - "workload": { - "@id": "schema:workload" - }, - "worksFor": { - "@id": "schema:worksFor" - }, - "worstRating": { - "@id": "schema:worstRating" - }, - "xml": "http://www.w3.org/XML/1998/namespace", - "xpath": { - "@id": "schema:xpath" - }, - "xsd": "http://www.w3.org/2001/XMLSchema#", - "yearBuilt": { - "@id": "schema:yearBuilt" - }, - "yearlyRevenue": { - "@id": "schema:yearlyRevenue" - }, - "yearsInOperation": { - "@id": "schema:yearsInOperation" - }, - "yield": { - "@id": "schema:yield" - } - } -} diff --git a/fuji_server/data/jsonldcontext.yaml b/fuji_server/data/jsonldcontext.yaml new file mode 100644 index 00000000..2a2e9c01 --- /dev/null +++ b/fuji_server/data/jsonldcontext.yaml @@ -0,0 +1,5377 @@ +'@context': + 3DModel: + '@id': schema:3DModel + '@vocab': http://schema.org/ + AMRadioChannel: + '@id': schema:AMRadioChannel + APIReference: + '@id': schema:APIReference + Abdomen: + '@id': schema:Abdomen + AboutPage: + '@id': schema:AboutPage + AcceptAction: + '@id': schema:AcceptAction + Accommodation: + '@id': schema:Accommodation + AccountingService: + '@id': schema:AccountingService + AchieveAction: + '@id': schema:AchieveAction + Action: + '@id': schema:Action + ActionAccessSpecification: + '@id': schema:ActionAccessSpecification + ActionStatusType: + '@id': schema:ActionStatusType + ActivateAction: + '@id': schema:ActivateAction + ActiveActionStatus: + '@id': schema:ActiveActionStatus + ActiveNotRecruiting: + '@id': schema:ActiveNotRecruiting + AddAction: + '@id': schema:AddAction + AdministrativeArea: + '@id': schema:AdministrativeArea + AdultEntertainment: + '@id': schema:AdultEntertainment + AdvertiserContentArticle: + '@id': schema:AdvertiserContentArticle + AerobicActivity: + '@id': schema:AerobicActivity + AggregateOffer: + '@id': schema:AggregateOffer + AggregateRating: + '@id': schema:AggregateRating + AgreeAction: + '@id': schema:AgreeAction + Airline: + '@id': schema:Airline + Airport: + '@id': schema:Airport + AlbumRelease: + '@id': schema:AlbumRelease + AlignmentObject: + '@id': schema:AlignmentObject + AllWheelDriveConfiguration: + '@id': schema:AllWheelDriveConfiguration + AllocateAction: + '@id': schema:AllocateAction + AmusementPark: + '@id': schema:AmusementPark + AnaerobicActivity: + '@id': schema:AnaerobicActivity + AnalysisNewsArticle: + '@id': schema:AnalysisNewsArticle + AnatomicalStructure: + '@id': schema:AnatomicalStructure + AnatomicalSystem: + '@id': schema:AnatomicalSystem + Anesthesia: + '@id': schema:Anesthesia + AnimalShelter: + '@id': schema:AnimalShelter + Answer: + '@id': schema:Answer + Apartment: + '@id': schema:Apartment + ApartmentComplex: + '@id': schema:ApartmentComplex + Appearance: + '@id': schema:Appearance + AppendAction: + '@id': schema:AppendAction + ApplyAction: + '@id': schema:ApplyAction + ApprovedIndication: + '@id': schema:ApprovedIndication + Aquarium: + '@id': schema:Aquarium + ArchiveComponent: + '@id': schema:ArchiveComponent + ArchiveOrganization: + '@id': schema:ArchiveOrganization + ArriveAction: + '@id': schema:ArriveAction + ArtGallery: + '@id': schema:ArtGallery + Artery: + '@id': schema:Artery + Article: + '@id': schema:Article + AskAction: + '@id': schema:AskAction + AskPublicNewsArticle: + '@id': schema:AskPublicNewsArticle + AssessAction: + '@id': schema:AssessAction + AssignAction: + '@id': schema:AssignAction + Atlas: + '@id': schema:Atlas + Attorney: + '@id': schema:Attorney + Audience: + '@id': schema:Audience + AudioObject: + '@id': schema:AudioObject + Audiobook: + '@id': schema:Audiobook + AudiobookFormat: + '@id': schema:AudiobookFormat + AuthenticContent: + '@id': schema:AuthenticContent + AuthoritativeLegalValue: + '@id': schema:AuthoritativeLegalValue + AuthorizeAction: + '@id': schema:AuthorizeAction + AutoBodyShop: + '@id': schema:AutoBodyShop + AutoDealer: + '@id': schema:AutoDealer + AutoPartsStore: + '@id': schema:AutoPartsStore + AutoRental: + '@id': schema:AutoRental + AutoRepair: + '@id': schema:AutoRepair + AutoWash: + '@id': schema:AutoWash + AutomatedTeller: + '@id': schema:AutomatedTeller + AutomotiveBusiness: + '@id': schema:AutomotiveBusiness + Ayurvedic: + '@id': schema:Ayurvedic + BackgroundNewsArticle: + '@id': schema:BackgroundNewsArticle + Bacteria: + '@id': schema:Bacteria + Bakery: + '@id': schema:Bakery + Balance: + '@id': schema:Balance + BankAccount: + '@id': schema:BankAccount + BankOrCreditUnion: + '@id': schema:BankOrCreditUnion + BarOrPub: + '@id': schema:BarOrPub + Barcode: + '@id': schema:Barcode + BasicIncome: + '@id': schema:BasicIncome + Beach: + '@id': schema:Beach + BeautySalon: + '@id': schema:BeautySalon + BedAndBreakfast: + '@id': schema:BedAndBreakfast + BedDetails: + '@id': schema:BedDetails + BedType: + '@id': schema:BedType + BefriendAction: + '@id': schema:BefriendAction + BenefitsHealthAspect: + '@id': schema:BenefitsHealthAspect + BikeStore: + '@id': schema:BikeStore + Blog: + '@id': schema:Blog + BlogPosting: + '@id': schema:BlogPosting + BloodTest: + '@id': schema:BloodTest + BoardingPolicyType: + '@id': schema:BoardingPolicyType + BoatReservation: + '@id': schema:BoatReservation + BoatTerminal: + '@id': schema:BoatTerminal + BoatTrip: + '@id': schema:BoatTrip + BodyOfWater: + '@id': schema:BodyOfWater + Bone: + '@id': schema:Bone + Book: + '@id': schema:Book + BookFormatType: + '@id': schema:BookFormatType + BookSeries: + '@id': schema:BookSeries + BookStore: + '@id': schema:BookStore + BookmarkAction: + '@id': schema:BookmarkAction + Boolean: + '@id': schema:Boolean + BorrowAction: + '@id': schema:BorrowAction + BowlingAlley: + '@id': schema:BowlingAlley + BrainStructure: + '@id': schema:BrainStructure + Brand: + '@id': schema:Brand + BreadcrumbList: + '@id': schema:BreadcrumbList + Brewery: + '@id': schema:Brewery + Bridge: + '@id': schema:Bridge + BroadcastChannel: + '@id': schema:BroadcastChannel + BroadcastEvent: + '@id': schema:BroadcastEvent + BroadcastFrequencySpecification: + '@id': schema:BroadcastFrequencySpecification + BroadcastRelease: + '@id': schema:BroadcastRelease + BroadcastService: + '@id': schema:BroadcastService + BrokerageAccount: + '@id': schema:BrokerageAccount + BuddhistTemple: + '@id': schema:BuddhistTemple + BusOrCoach: + '@id': schema:BusOrCoach + BusReservation: + '@id': schema:BusReservation + BusStation: + '@id': schema:BusStation + BusStop: + '@id': schema:BusStop + BusTrip: + '@id': schema:BusTrip + BusinessAudience: + '@id': schema:BusinessAudience + BusinessEntityType: + '@id': schema:BusinessEntityType + BusinessEvent: + '@id': schema:BusinessEvent + BusinessFunction: + '@id': schema:BusinessFunction + BusinessSupport: + '@id': schema:BusinessSupport + BuyAction: + '@id': schema:BuyAction + CDCPMDRecord: + '@id': schema:CDCPMDRecord + CDFormat: + '@id': schema:CDFormat + CT: + '@id': schema:CT + CableOrSatelliteService: + '@id': schema:CableOrSatelliteService + CafeOrCoffeeShop: + '@id': schema:CafeOrCoffeeShop + Campground: + '@id': schema:Campground + CampingPitch: + '@id': schema:CampingPitch + Canal: + '@id': schema:Canal + CancelAction: + '@id': schema:CancelAction + Car: + '@id': schema:Car + CarUsageType: + '@id': schema:CarUsageType + Cardiovascular: + '@id': schema:Cardiovascular + CardiovascularExam: + '@id': schema:CardiovascularExam + CaseSeries: + '@id': schema:CaseSeries + Casino: + '@id': schema:Casino + CassetteFormat: + '@id': schema:CassetteFormat + CategoryCode: + '@id': schema:CategoryCode + CategoryCodeSet: + '@id': schema:CategoryCodeSet + CatholicChurch: + '@id': schema:CatholicChurch + CausesHealthAspect: + '@id': schema:CausesHealthAspect + Cemetery: + '@id': schema:Cemetery + Chapter: + '@id': schema:Chapter + CharitableIncorporatedOrganization: + '@id': schema:CharitableIncorporatedOrganization + CheckAction: + '@id': schema:CheckAction + CheckInAction: + '@id': schema:CheckInAction + CheckOutAction: + '@id': schema:CheckOutAction + CheckoutPage: + '@id': schema:CheckoutPage + ChildCare: + '@id': schema:ChildCare + ChildrensEvent: + '@id': schema:ChildrensEvent + Chiropractic: + '@id': schema:Chiropractic + ChooseAction: + '@id': schema:ChooseAction + Church: + '@id': schema:Church + City: + '@id': schema:City + CityHall: + '@id': schema:CityHall + CivicStructure: + '@id': schema:CivicStructure + Claim: + '@id': schema:Claim + ClaimReview: + '@id': schema:ClaimReview + Class: + '@id': schema:Class + Clinician: + '@id': schema:Clinician + Clip: + '@id': schema:Clip + ClothingStore: + '@id': schema:ClothingStore + CoOp: + '@id': schema:CoOp + Code: + '@id': schema:Code + CohortStudy: + '@id': schema:CohortStudy + Collection: + '@id': schema:Collection + CollectionPage: + '@id': schema:CollectionPage + CollegeOrUniversity: + '@id': schema:CollegeOrUniversity + ComedyClub: + '@id': schema:ComedyClub + ComedyEvent: + '@id': schema:ComedyEvent + ComicCoverArt: + '@id': schema:ComicCoverArt + ComicIssue: + '@id': schema:ComicIssue + ComicSeries: + '@id': schema:ComicSeries + ComicStory: + '@id': schema:ComicStory + Comment: + '@id': schema:Comment + CommentAction: + '@id': schema:CommentAction + CommentPermission: + '@id': schema:CommentPermission + CommunicateAction: + '@id': schema:CommunicateAction + CommunityHealth: + '@id': schema:CommunityHealth + CompilationAlbum: + '@id': schema:CompilationAlbum + CompleteDataFeed: + '@id': schema:CompleteDataFeed + Completed: + '@id': schema:Completed + CompletedActionStatus: + '@id': schema:CompletedActionStatus + CompoundPriceSpecification: + '@id': schema:CompoundPriceSpecification + ComputerLanguage: + '@id': schema:ComputerLanguage + ComputerStore: + '@id': schema:ComputerStore + ConfirmAction: + '@id': schema:ConfirmAction + Consortium: + '@id': schema:Consortium + ConsumeAction: + '@id': schema:ConsumeAction + ContactPage: + '@id': schema:ContactPage + ContactPoint: + '@id': schema:ContactPoint + ContactPointOption: + '@id': schema:ContactPointOption + ContagiousnessHealthAspect: + '@id': schema:ContagiousnessHealthAspect + Continent: + '@id': schema:Continent + ControlAction: + '@id': schema:ControlAction + ConvenienceStore: + '@id': schema:ConvenienceStore + Conversation: + '@id': schema:Conversation + CookAction: + '@id': schema:CookAction + Corporation: + '@id': schema:Corporation + CorrectionComment: + '@id': schema:CorrectionComment + Country: + '@id': schema:Country + Course: + '@id': schema:Course + CourseInstance: + '@id': schema:CourseInstance + Courthouse: + '@id': schema:Courthouse + CoverArt: + '@id': schema:CoverArt + CovidTestingFacility: + '@id': schema:CovidTestingFacility + CreateAction: + '@id': schema:CreateAction + CreativeWork: + '@id': schema:CreativeWork + CreativeWorkSeason: + '@id': schema:CreativeWorkSeason + CreativeWorkSeries: + '@id': schema:CreativeWorkSeries + CreditCard: + '@id': schema:CreditCard + Crematorium: + '@id': schema:Crematorium + CriticReview: + '@id': schema:CriticReview + CrossSectional: + '@id': schema:CrossSectional + CssSelectorType: + '@id': schema:CssSelectorType + CurrencyConversionService: + '@id': schema:CurrencyConversionService + DDxElement: + '@id': schema:DDxElement + DJMixAlbum: + '@id': schema:DJMixAlbum + DVDFormat: + '@id': schema:DVDFormat + DamagedCondition: + '@id': schema:DamagedCondition + DanceEvent: + '@id': schema:DanceEvent + DanceGroup: + '@id': schema:DanceGroup + DataCatalog: + '@id': schema:DataCatalog + DataDownload: + '@id': schema:DataDownload + DataFeed: + '@id': schema:DataFeed + DataFeedItem: + '@id': schema:DataFeedItem + DataType: + '@id': schema:DataType + Dataset: + '@id': schema:Dataset + Date: + '@id': schema:Date + DateTime: + '@id': schema:DateTime + DatedMoneySpecification: + '@id': schema:DatedMoneySpecification + DayOfWeek: + '@id': schema:DayOfWeek + DaySpa: + '@id': schema:DaySpa + DeactivateAction: + '@id': schema:DeactivateAction + DefenceEstablishment: + '@id': schema:DefenceEstablishment + DefinedRegion: + '@id': schema:DefinedRegion + DefinedTerm: + '@id': schema:DefinedTerm + DefinedTermSet: + '@id': schema:DefinedTermSet + DefinitiveLegalValue: + '@id': schema:DefinitiveLegalValue + DeleteAction: + '@id': schema:DeleteAction + DeliveryChargeSpecification: + '@id': schema:DeliveryChargeSpecification + DeliveryEvent: + '@id': schema:DeliveryEvent + DeliveryMethod: + '@id': schema:DeliveryMethod + DeliveryTimeSettings: + '@id': schema:DeliveryTimeSettings + Demand: + '@id': schema:Demand + DemoAlbum: + '@id': schema:DemoAlbum + Dentist: + '@id': schema:Dentist + Dentistry: + '@id': schema:Dentistry + DepartAction: + '@id': schema:DepartAction + DepartmentStore: + '@id': schema:DepartmentStore + DepositAccount: + '@id': schema:DepositAccount + Dermatologic: + '@id': schema:Dermatologic + Dermatology: + '@id': schema:Dermatology + DiabeticDiet: + '@id': schema:DiabeticDiet + Diagnostic: + '@id': schema:Diagnostic + DiagnosticLab: + '@id': schema:DiagnosticLab + DiagnosticProcedure: + '@id': schema:DiagnosticProcedure + Diet: + '@id': schema:Diet + DietNutrition: + '@id': schema:DietNutrition + DietarySupplement: + '@id': schema:DietarySupplement + DigitalAudioTapeFormat: + '@id': schema:DigitalAudioTapeFormat + DigitalDocument: + '@id': schema:DigitalDocument + DigitalDocumentPermission: + '@id': schema:DigitalDocumentPermission + DigitalDocumentPermissionType: + '@id': schema:DigitalDocumentPermissionType + DigitalFormat: + '@id': schema:DigitalFormat + DisabilitySupport: + '@id': schema:DisabilitySupport + DisagreeAction: + '@id': schema:DisagreeAction + Discontinued: + '@id': schema:Discontinued + DiscoverAction: + '@id': schema:DiscoverAction + DiscussionForumPosting: + '@id': schema:DiscussionForumPosting + DislikeAction: + '@id': schema:DislikeAction + Distance: + '@id': schema:Distance + Distillery: + '@id': schema:Distillery + DonateAction: + '@id': schema:DonateAction + DoseSchedule: + '@id': schema:DoseSchedule + DoubleBlindedTrial: + '@id': schema:DoubleBlindedTrial + DownloadAction: + '@id': schema:DownloadAction + DrawAction: + '@id': schema:DrawAction + Drawing: + '@id': schema:Drawing + DrinkAction: + '@id': schema:DrinkAction + DriveWheelConfigurationValue: + '@id': schema:DriveWheelConfigurationValue + DrivingSchoolVehicleUsage: + '@id': schema:DrivingSchoolVehicleUsage + Drug: + '@id': schema:Drug + DrugClass: + '@id': schema:DrugClass + DrugCost: + '@id': schema:DrugCost + DrugCostCategory: + '@id': schema:DrugCostCategory + DrugLegalStatus: + '@id': schema:DrugLegalStatus + DrugPregnancyCategory: + '@id': schema:DrugPregnancyCategory + DrugPrescriptionStatus: + '@id': schema:DrugPrescriptionStatus + DrugStrength: + '@id': schema:DrugStrength + DryCleaningOrLaundry: + '@id': schema:DryCleaningOrLaundry + Duration: + '@id': schema:Duration + EBook: + '@id': schema:EBook + EPRelease: + '@id': schema:EPRelease + EUEnergyEfficiencyCategoryA: + '@id': schema:EUEnergyEfficiencyCategoryA + EUEnergyEfficiencyCategoryA1Plus: + '@id': schema:EUEnergyEfficiencyCategoryA1Plus + EUEnergyEfficiencyCategoryA2Plus: + '@id': schema:EUEnergyEfficiencyCategoryA2Plus + EUEnergyEfficiencyCategoryA3Plus: + '@id': schema:EUEnergyEfficiencyCategoryA3Plus + EUEnergyEfficiencyCategoryB: + '@id': schema:EUEnergyEfficiencyCategoryB + EUEnergyEfficiencyCategoryC: + '@id': schema:EUEnergyEfficiencyCategoryC + EUEnergyEfficiencyCategoryD: + '@id': schema:EUEnergyEfficiencyCategoryD + EUEnergyEfficiencyCategoryE: + '@id': schema:EUEnergyEfficiencyCategoryE + EUEnergyEfficiencyCategoryF: + '@id': schema:EUEnergyEfficiencyCategoryF + EUEnergyEfficiencyCategoryG: + '@id': schema:EUEnergyEfficiencyCategoryG + EUEnergyEfficiencyEnumeration: + '@id': schema:EUEnergyEfficiencyEnumeration + Ear: + '@id': schema:Ear + EatAction: + '@id': schema:EatAction + EducationEvent: + '@id': schema:EducationEvent + EducationalAudience: + '@id': schema:EducationalAudience + EducationalOccupationalCredential: + '@id': schema:EducationalOccupationalCredential + EducationalOccupationalProgram: + '@id': schema:EducationalOccupationalProgram + EducationalOrganization: + '@id': schema:EducationalOrganization + Electrician: + '@id': schema:Electrician + ElectronicsStore: + '@id': schema:ElectronicsStore + ElementarySchool: + '@id': schema:ElementarySchool + EmailMessage: + '@id': schema:EmailMessage + Embassy: + '@id': schema:Embassy + Emergency: + '@id': schema:Emergency + EmergencyService: + '@id': schema:EmergencyService + EmployeeRole: + '@id': schema:EmployeeRole + EmployerAggregateRating: + '@id': schema:EmployerAggregateRating + EmployerReview: + '@id': schema:EmployerReview + EmploymentAgency: + '@id': schema:EmploymentAgency + Endocrine: + '@id': schema:Endocrine + EndorseAction: + '@id': schema:EndorseAction + EndorsementRating: + '@id': schema:EndorsementRating + Energy: + '@id': schema:Energy + EnergyConsumptionDetails: + '@id': schema:EnergyConsumptionDetails + EnergyEfficiencyEnumeration: + '@id': schema:EnergyEfficiencyEnumeration + EnergyStarCertified: + '@id': schema:EnergyStarCertified + EnergyStarEnergyEfficiencyEnumeration: + '@id': schema:EnergyStarEnergyEfficiencyEnumeration + EngineSpecification: + '@id': schema:EngineSpecification + EnrollingByInvitation: + '@id': schema:EnrollingByInvitation + EntertainmentBusiness: + '@id': schema:EntertainmentBusiness + EntryPoint: + '@id': schema:EntryPoint + Enumeration: + '@id': schema:Enumeration + Episode: + '@id': schema:Episode + Event: + '@id': schema:Event + EventAttendanceModeEnumeration: + '@id': schema:EventAttendanceModeEnumeration + EventCancelled: + '@id': schema:EventCancelled + EventMovedOnline: + '@id': schema:EventMovedOnline + EventPostponed: + '@id': schema:EventPostponed + EventRescheduled: + '@id': schema:EventRescheduled + EventReservation: + '@id': schema:EventReservation + EventScheduled: + '@id': schema:EventScheduled + EventSeries: + '@id': schema:EventSeries + EventStatusType: + '@id': schema:EventStatusType + EventVenue: + '@id': schema:EventVenue + EvidenceLevelA: + '@id': schema:EvidenceLevelA + EvidenceLevelB: + '@id': schema:EvidenceLevelB + EvidenceLevelC: + '@id': schema:EvidenceLevelC + ExchangeRateSpecification: + '@id': schema:ExchangeRateSpecification + ExchangeRefund: + '@id': schema:ExchangeRefund + ExerciseAction: + '@id': schema:ExerciseAction + ExerciseGym: + '@id': schema:ExerciseGym + ExercisePlan: + '@id': schema:ExercisePlan + ExhibitionEvent: + '@id': schema:ExhibitionEvent + Eye: + '@id': schema:Eye + FAQPage: + '@id': schema:FAQPage + FDAcategoryA: + '@id': schema:FDAcategoryA + FDAcategoryB: + '@id': schema:FDAcategoryB + FDAcategoryC: + '@id': schema:FDAcategoryC + FDAcategoryD: + '@id': schema:FDAcategoryD + FDAcategoryX: + '@id': schema:FDAcategoryX + FDAnotEvaluated: + '@id': schema:FDAnotEvaluated + FMRadioChannel: + '@id': schema:FMRadioChannel + FailedActionStatus: + '@id': schema:FailedActionStatus + 'False': + '@id': schema:False + FastFoodRestaurant: + '@id': schema:FastFoodRestaurant + Female: + '@id': schema:Female + Festival: + '@id': schema:Festival + FilmAction: + '@id': schema:FilmAction + FinancialProduct: + '@id': schema:FinancialProduct + FinancialService: + '@id': schema:FinancialService + FindAction: + '@id': schema:FindAction + FireStation: + '@id': schema:FireStation + Flexibility: + '@id': schema:Flexibility + Flight: + '@id': schema:Flight + FlightReservation: + '@id': schema:FlightReservation + Float: + '@id': schema:Float + FloorPlan: + '@id': schema:FloorPlan + Florist: + '@id': schema:Florist + FollowAction: + '@id': schema:FollowAction + FoodEstablishment: + '@id': schema:FoodEstablishment + FoodEstablishmentReservation: + '@id': schema:FoodEstablishmentReservation + FoodEvent: + '@id': schema:FoodEvent + FoodService: + '@id': schema:FoodService + FourWheelDriveConfiguration: + '@id': schema:FourWheelDriveConfiguration + Friday: + '@id': schema:Friday + FrontWheelDriveConfiguration: + '@id': schema:FrontWheelDriveConfiguration + FullRefund: + '@id': schema:FullRefund + FundingAgency: + '@id': schema:FundingAgency + FundingScheme: + '@id': schema:FundingScheme + Fungus: + '@id': schema:Fungus + FurnitureStore: + '@id': schema:FurnitureStore + Game: + '@id': schema:Game + GamePlayMode: + '@id': schema:GamePlayMode + GameServer: + '@id': schema:GameServer + GameServerStatus: + '@id': schema:GameServerStatus + GardenStore: + '@id': schema:GardenStore + GasStation: + '@id': schema:GasStation + Gastroenterologic: + '@id': schema:Gastroenterologic + GatedResidenceCommunity: + '@id': schema:GatedResidenceCommunity + GenderType: + '@id': schema:GenderType + GeneralContractor: + '@id': schema:GeneralContractor + Genetic: + '@id': schema:Genetic + Genitourinary: + '@id': schema:Genitourinary + GeoCircle: + '@id': schema:GeoCircle + GeoCoordinates: + '@id': schema:GeoCoordinates + GeoShape: + '@id': schema:GeoShape + GeospatialGeometry: + '@id': schema:GeospatialGeometry + Geriatric: + '@id': schema:Geriatric + GiveAction: + '@id': schema:GiveAction + GlutenFreeDiet: + '@id': schema:GlutenFreeDiet + GolfCourse: + '@id': schema:GolfCourse + GovernmentBenefitsType: + '@id': schema:GovernmentBenefitsType + GovernmentBuilding: + '@id': schema:GovernmentBuilding + GovernmentOffice: + '@id': schema:GovernmentOffice + GovernmentOrganization: + '@id': schema:GovernmentOrganization + GovernmentPermit: + '@id': schema:GovernmentPermit + GovernmentService: + '@id': schema:GovernmentService + Grant: + '@id': schema:Grant + GraphicNovel: + '@id': schema:GraphicNovel + GroceryStore: + '@id': schema:GroceryStore + GroupBoardingPolicy: + '@id': schema:GroupBoardingPolicy + Guide: + '@id': schema:Guide + Gynecologic: + '@id': schema:Gynecologic + HTML: + '@id': rdf:HTML + HVACBusiness: + '@id': schema:HVACBusiness + Hackathon: + '@id': schema:Hackathon + HairSalon: + '@id': schema:HairSalon + HalalDiet: + '@id': schema:HalalDiet + Hardcover: + '@id': schema:Hardcover + HardwareStore: + '@id': schema:HardwareStore + Head: + '@id': schema:Head + HealthAndBeautyBusiness: + '@id': schema:HealthAndBeautyBusiness + HealthAspectEnumeration: + '@id': schema:HealthAspectEnumeration + HealthCare: + '@id': schema:HealthCare + HealthClub: + '@id': schema:HealthClub + HealthInsurancePlan: + '@id': schema:HealthInsurancePlan + HealthPlanCostSharingSpecification: + '@id': schema:HealthPlanCostSharingSpecification + HealthPlanFormulary: + '@id': schema:HealthPlanFormulary + HealthPlanNetwork: + '@id': schema:HealthPlanNetwork + HealthTopicContent: + '@id': schema:HealthTopicContent + HearingImpairedSupported: + '@id': schema:HearingImpairedSupported + Hematologic: + '@id': schema:Hematologic + HighSchool: + '@id': schema:HighSchool + HinduDiet: + '@id': schema:HinduDiet + HinduTemple: + '@id': schema:HinduTemple + HobbyShop: + '@id': schema:HobbyShop + HomeAndConstructionBusiness: + '@id': schema:HomeAndConstructionBusiness + HomeGoodsStore: + '@id': schema:HomeGoodsStore + Homeopathic: + '@id': schema:Homeopathic + Hospital: + '@id': schema:Hospital + Hostel: + '@id': schema:Hostel + Hotel: + '@id': schema:Hotel + HotelRoom: + '@id': schema:HotelRoom + House: + '@id': schema:House + HousePainter: + '@id': schema:HousePainter + HowOrWhereHealthAspect: + '@id': schema:HowOrWhereHealthAspect + HowTo: + '@id': schema:HowTo + HowToDirection: + '@id': schema:HowToDirection + HowToItem: + '@id': schema:HowToItem + HowToSection: + '@id': schema:HowToSection + HowToStep: + '@id': schema:HowToStep + HowToSupply: + '@id': schema:HowToSupply + HowToTip: + '@id': schema:HowToTip + HowToTool: + '@id': schema:HowToTool + IceCreamShop: + '@id': schema:IceCreamShop + IgnoreAction: + '@id': schema:IgnoreAction + ImageGallery: + '@id': schema:ImageGallery + ImageObject: + '@id': schema:ImageObject + ImagingTest: + '@id': schema:ImagingTest + InForce: + '@id': schema:InForce + InStock: + '@id': schema:InStock + InStoreOnly: + '@id': schema:InStoreOnly + IndividualProduct: + '@id': schema:IndividualProduct + Infectious: + '@id': schema:Infectious + InfectiousAgentClass: + '@id': schema:InfectiousAgentClass + InfectiousDisease: + '@id': schema:InfectiousDisease + InformAction: + '@id': schema:InformAction + InsertAction: + '@id': schema:InsertAction + InstallAction: + '@id': schema:InstallAction + InsuranceAgency: + '@id': schema:InsuranceAgency + Intangible: + '@id': schema:Intangible + Integer: + '@id': schema:Integer + InteractAction: + '@id': schema:InteractAction + InteractionCounter: + '@id': schema:InteractionCounter + InternationalTrial: + '@id': schema:InternationalTrial + InternetCafe: + '@id': schema:InternetCafe + InvestmentFund: + '@id': schema:InvestmentFund + InvestmentOrDeposit: + '@id': schema:InvestmentOrDeposit + InviteAction: + '@id': schema:InviteAction + Invoice: + '@id': schema:Invoice + ItemAvailability: + '@id': schema:ItemAvailability + ItemList: + '@id': schema:ItemList + ItemListOrderAscending: + '@id': schema:ItemListOrderAscending + ItemListOrderDescending: + '@id': schema:ItemListOrderDescending + ItemListOrderType: + '@id': schema:ItemListOrderType + ItemListUnordered: + '@id': schema:ItemListUnordered + ItemPage: + '@id': schema:ItemPage + JewelryStore: + '@id': schema:JewelryStore + JobPosting: + '@id': schema:JobPosting + JoinAction: + '@id': schema:JoinAction + Joint: + '@id': schema:Joint + KosherDiet: + '@id': schema:KosherDiet + LaboratoryScience: + '@id': schema:LaboratoryScience + LakeBodyOfWater: + '@id': schema:LakeBodyOfWater + Landform: + '@id': schema:Landform + LandmarksOrHistoricalBuildings: + '@id': schema:LandmarksOrHistoricalBuildings + Language: + '@id': schema:Language + LaserDiscFormat: + '@id': schema:LaserDiscFormat + LearningResource: + '@id': schema:LearningResource + LeaveAction: + '@id': schema:LeaveAction + LeftHandDriving: + '@id': schema:LeftHandDriving + LegalForceStatus: + '@id': schema:LegalForceStatus + LegalService: + '@id': schema:LegalService + LegalValueLevel: + '@id': schema:LegalValueLevel + Legislation: + '@id': schema:Legislation + LegislationObject: + '@id': schema:LegislationObject + LegislativeBuilding: + '@id': schema:LegislativeBuilding + LeisureTimeActivity: + '@id': schema:LeisureTimeActivity + LendAction: + '@id': schema:LendAction + Library: + '@id': schema:Library + LibrarySystem: + '@id': schema:LibrarySystem + LifestyleModification: + '@id': schema:LifestyleModification + Ligament: + '@id': schema:Ligament + LikeAction: + '@id': schema:LikeAction + LimitedAvailability: + '@id': schema:LimitedAvailability + LimitedByGuaranteeCharity: + '@id': schema:LimitedByGuaranteeCharity + LinkRole: + '@id': schema:LinkRole + LiquorStore: + '@id': schema:LiquorStore + ListItem: + '@id': schema:ListItem + ListenAction: + '@id': schema:ListenAction + LiteraryEvent: + '@id': schema:LiteraryEvent + LiveAlbum: + '@id': schema:LiveAlbum + LiveBlogPosting: + '@id': schema:LiveBlogPosting + LivingWithHealthAspect: + '@id': schema:LivingWithHealthAspect + LoanOrCredit: + '@id': schema:LoanOrCredit + LocalBusiness: + '@id': schema:LocalBusiness + LocationFeatureSpecification: + '@id': schema:LocationFeatureSpecification + LockerDelivery: + '@id': schema:LockerDelivery + Locksmith: + '@id': schema:Locksmith + LodgingBusiness: + '@id': schema:LodgingBusiness + LodgingReservation: + '@id': schema:LodgingReservation + Longitudinal: + '@id': schema:Longitudinal + LoseAction: + '@id': schema:LoseAction + LowCalorieDiet: + '@id': schema:LowCalorieDiet + LowFatDiet: + '@id': schema:LowFatDiet + LowLactoseDiet: + '@id': schema:LowLactoseDiet + LowSaltDiet: + '@id': schema:LowSaltDiet + Lung: + '@id': schema:Lung + LymphaticVessel: + '@id': schema:LymphaticVessel + MRI: + '@id': schema:MRI + Male: + '@id': schema:Male + Manuscript: + '@id': schema:Manuscript + Map: + '@id': schema:Map + MapCategoryType: + '@id': schema:MapCategoryType + MarryAction: + '@id': schema:MarryAction + Mass: + '@id': schema:Mass + MaximumDoseSchedule: + '@id': schema:MaximumDoseSchedule + MayTreatHealthAspect: + '@id': schema:MayTreatHealthAspect + MediaGallery: + '@id': schema:MediaGallery + MediaManipulationRatingEnumeration: + '@id': schema:MediaManipulationRatingEnumeration + MediaObject: + '@id': schema:MediaObject + MediaReview: + '@id': schema:MediaReview + MediaSubscription: + '@id': schema:MediaSubscription + MedicalAudience: + '@id': schema:MedicalAudience + MedicalAudienceType: + '@id': schema:MedicalAudienceType + MedicalBusiness: + '@id': schema:MedicalBusiness + MedicalCause: + '@id': schema:MedicalCause + MedicalClinic: + '@id': schema:MedicalClinic + MedicalCode: + '@id': schema:MedicalCode + MedicalCondition: + '@id': schema:MedicalCondition + MedicalConditionStage: + '@id': schema:MedicalConditionStage + MedicalContraindication: + '@id': schema:MedicalContraindication + MedicalDevice: + '@id': schema:MedicalDevice + MedicalDevicePurpose: + '@id': schema:MedicalDevicePurpose + MedicalEntity: + '@id': schema:MedicalEntity + MedicalEnumeration: + '@id': schema:MedicalEnumeration + MedicalEvidenceLevel: + '@id': schema:MedicalEvidenceLevel + MedicalGuideline: + '@id': schema:MedicalGuideline + MedicalGuidelineContraindication: + '@id': schema:MedicalGuidelineContraindication + MedicalGuidelineRecommendation: + '@id': schema:MedicalGuidelineRecommendation + MedicalImagingTechnique: + '@id': schema:MedicalImagingTechnique + MedicalIndication: + '@id': schema:MedicalIndication + MedicalIntangible: + '@id': schema:MedicalIntangible + MedicalObservationalStudy: + '@id': schema:MedicalObservationalStudy + MedicalObservationalStudyDesign: + '@id': schema:MedicalObservationalStudyDesign + MedicalOrganization: + '@id': schema:MedicalOrganization + MedicalProcedure: + '@id': schema:MedicalProcedure + MedicalProcedureType: + '@id': schema:MedicalProcedureType + MedicalResearcher: + '@id': schema:MedicalResearcher + MedicalRiskCalculator: + '@id': schema:MedicalRiskCalculator + MedicalRiskEstimator: + '@id': schema:MedicalRiskEstimator + MedicalRiskFactor: + '@id': schema:MedicalRiskFactor + MedicalRiskScore: + '@id': schema:MedicalRiskScore + MedicalScholarlyArticle: + '@id': schema:MedicalScholarlyArticle + MedicalSign: + '@id': schema:MedicalSign + MedicalSignOrSymptom: + '@id': schema:MedicalSignOrSymptom + MedicalSpecialty: + '@id': schema:MedicalSpecialty + MedicalStudy: + '@id': schema:MedicalStudy + MedicalStudyStatus: + '@id': schema:MedicalStudyStatus + MedicalSymptom: + '@id': schema:MedicalSymptom + MedicalTest: + '@id': schema:MedicalTest + MedicalTestPanel: + '@id': schema:MedicalTestPanel + MedicalTherapy: + '@id': schema:MedicalTherapy + MedicalTrial: + '@id': schema:MedicalTrial + MedicalTrialDesign: + '@id': schema:MedicalTrialDesign + MedicalWebPage: + '@id': schema:MedicalWebPage + MedicineSystem: + '@id': schema:MedicineSystem + MeetingRoom: + '@id': schema:MeetingRoom + MensClothingStore: + '@id': schema:MensClothingStore + Menu: + '@id': schema:Menu + MenuItem: + '@id': schema:MenuItem + MenuSection: + '@id': schema:MenuSection + MerchantReturnEnumeration: + '@id': schema:MerchantReturnEnumeration + MerchantReturnFiniteReturnWindow: + '@id': schema:MerchantReturnFiniteReturnWindow + MerchantReturnNotPermitted: + '@id': schema:MerchantReturnNotPermitted + MerchantReturnPolicy: + '@id': schema:MerchantReturnPolicy + MerchantReturnUnlimitedWindow: + '@id': schema:MerchantReturnUnlimitedWindow + MerchantReturnUnspecified: + '@id': schema:MerchantReturnUnspecified + Message: + '@id': schema:Message + MiddleSchool: + '@id': schema:MiddleSchool + Midwifery: + '@id': schema:Midwifery + MisconceptionsHealthAspect: + '@id': schema:MisconceptionsHealthAspect + MissingContext: + '@id': schema:MissingContext + MixedEventAttendanceMode: + '@id': schema:MixedEventAttendanceMode + MixtapeAlbum: + '@id': schema:MixtapeAlbum + MobileApplication: + '@id': schema:MobileApplication + MobilePhoneStore: + '@id': schema:MobilePhoneStore + Monday: + '@id': schema:Monday + MonetaryAmount: + '@id': schema:MonetaryAmount + MonetaryAmountDistribution: + '@id': schema:MonetaryAmountDistribution + MonetaryGrant: + '@id': schema:MonetaryGrant + MoneyTransfer: + '@id': schema:MoneyTransfer + MortgageLoan: + '@id': schema:MortgageLoan + Mosque: + '@id': schema:Mosque + Motel: + '@id': schema:Motel + Motorcycle: + '@id': schema:Motorcycle + MotorcycleDealer: + '@id': schema:MotorcycleDealer + MotorcycleRepair: + '@id': schema:MotorcycleRepair + MotorizedBicycle: + '@id': schema:MotorizedBicycle + Mountain: + '@id': schema:Mountain + MoveAction: + '@id': schema:MoveAction + Movie: + '@id': schema:Movie + MovieClip: + '@id': schema:MovieClip + MovieRentalStore: + '@id': schema:MovieRentalStore + MovieSeries: + '@id': schema:MovieSeries + MovieTheater: + '@id': schema:MovieTheater + MovingCompany: + '@id': schema:MovingCompany + MultiCenterTrial: + '@id': schema:MultiCenterTrial + MultiPlayer: + '@id': schema:MultiPlayer + MulticellularParasite: + '@id': schema:MulticellularParasite + Muscle: + '@id': schema:Muscle + Musculoskeletal: + '@id': schema:Musculoskeletal + MusculoskeletalExam: + '@id': schema:MusculoskeletalExam + Museum: + '@id': schema:Museum + MusicAlbum: + '@id': schema:MusicAlbum + MusicAlbumProductionType: + '@id': schema:MusicAlbumProductionType + MusicAlbumReleaseType: + '@id': schema:MusicAlbumReleaseType + MusicComposition: + '@id': schema:MusicComposition + MusicEvent: + '@id': schema:MusicEvent + MusicGroup: + '@id': schema:MusicGroup + MusicPlaylist: + '@id': schema:MusicPlaylist + MusicRecording: + '@id': schema:MusicRecording + MusicRelease: + '@id': schema:MusicRelease + MusicReleaseFormatType: + '@id': schema:MusicReleaseFormatType + MusicStore: + '@id': schema:MusicStore + MusicVenue: + '@id': schema:MusicVenue + MusicVideoObject: + '@id': schema:MusicVideoObject + NGO: + '@id': schema:NGO + NLNonprofitType: + '@id': schema:NLNonprofitType + NailSalon: + '@id': schema:NailSalon + Neck: + '@id': schema:Neck + Nerve: + '@id': schema:Nerve + Neuro: + '@id': schema:Neuro + Neurologic: + '@id': schema:Neurologic + NewCondition: + '@id': schema:NewCondition + NewsArticle: + '@id': schema:NewsArticle + NewsMediaOrganization: + '@id': schema:NewsMediaOrganization + Newspaper: + '@id': schema:Newspaper + NightClub: + '@id': schema:NightClub + NoninvasiveProcedure: + '@id': schema:NoninvasiveProcedure + Nonprofit501a: + '@id': schema:Nonprofit501a + Nonprofit501c1: + '@id': schema:Nonprofit501c1 + Nonprofit501c10: + '@id': schema:Nonprofit501c10 + Nonprofit501c11: + '@id': schema:Nonprofit501c11 + Nonprofit501c12: + '@id': schema:Nonprofit501c12 + Nonprofit501c13: + '@id': schema:Nonprofit501c13 + Nonprofit501c14: + '@id': schema:Nonprofit501c14 + Nonprofit501c15: + '@id': schema:Nonprofit501c15 + Nonprofit501c16: + '@id': schema:Nonprofit501c16 + Nonprofit501c17: + '@id': schema:Nonprofit501c17 + Nonprofit501c18: + '@id': schema:Nonprofit501c18 + Nonprofit501c19: + '@id': schema:Nonprofit501c19 + Nonprofit501c2: + '@id': schema:Nonprofit501c2 + Nonprofit501c20: + '@id': schema:Nonprofit501c20 + Nonprofit501c21: + '@id': schema:Nonprofit501c21 + Nonprofit501c22: + '@id': schema:Nonprofit501c22 + Nonprofit501c23: + '@id': schema:Nonprofit501c23 + Nonprofit501c24: + '@id': schema:Nonprofit501c24 + Nonprofit501c25: + '@id': schema:Nonprofit501c25 + Nonprofit501c26: + '@id': schema:Nonprofit501c26 + Nonprofit501c27: + '@id': schema:Nonprofit501c27 + Nonprofit501c28: + '@id': schema:Nonprofit501c28 + Nonprofit501c3: + '@id': schema:Nonprofit501c3 + Nonprofit501c4: + '@id': schema:Nonprofit501c4 + Nonprofit501c5: + '@id': schema:Nonprofit501c5 + Nonprofit501c6: + '@id': schema:Nonprofit501c6 + Nonprofit501c7: + '@id': schema:Nonprofit501c7 + Nonprofit501c8: + '@id': schema:Nonprofit501c8 + Nonprofit501c9: + '@id': schema:Nonprofit501c9 + Nonprofit501d: + '@id': schema:Nonprofit501d + Nonprofit501e: + '@id': schema:Nonprofit501e + Nonprofit501f: + '@id': schema:Nonprofit501f + Nonprofit501k: + '@id': schema:Nonprofit501k + Nonprofit501n: + '@id': schema:Nonprofit501n + Nonprofit501q: + '@id': schema:Nonprofit501q + Nonprofit527: + '@id': schema:Nonprofit527 + NonprofitANBI: + '@id': schema:NonprofitANBI + NonprofitSBBI: + '@id': schema:NonprofitSBBI + NonprofitType: + '@id': schema:NonprofitType + Nose: + '@id': schema:Nose + NotInForce: + '@id': schema:NotInForce + NotYetRecruiting: + '@id': schema:NotYetRecruiting + Notary: + '@id': schema:Notary + NoteDigitalDocument: + '@id': schema:NoteDigitalDocument + Number: + '@id': schema:Number + Nursing: + '@id': schema:Nursing + NutritionInformation: + '@id': schema:NutritionInformation + OTC: + '@id': schema:OTC + Observation: + '@id': schema:Observation + Observational: + '@id': schema:Observational + Obstetric: + '@id': schema:Obstetric + Occupation: + '@id': schema:Occupation + OccupationalActivity: + '@id': schema:OccupationalActivity + OccupationalTherapy: + '@id': schema:OccupationalTherapy + OceanBodyOfWater: + '@id': schema:OceanBodyOfWater + Offer: + '@id': schema:Offer + OfferCatalog: + '@id': schema:OfferCatalog + OfferForLease: + '@id': schema:OfferForLease + OfferForPurchase: + '@id': schema:OfferForPurchase + OfferItemCondition: + '@id': schema:OfferItemCondition + OfferShippingDetails: + '@id': schema:OfferShippingDetails + OfficeEquipmentStore: + '@id': schema:OfficeEquipmentStore + OfficialLegalValue: + '@id': schema:OfficialLegalValue + OfflineEventAttendanceMode: + '@id': schema:OfflineEventAttendanceMode + OfflinePermanently: + '@id': schema:OfflinePermanently + OfflineTemporarily: + '@id': schema:OfflineTemporarily + OnDemandEvent: + '@id': schema:OnDemandEvent + OnSitePickup: + '@id': schema:OnSitePickup + Oncologic: + '@id': schema:Oncologic + OneTimePayments: + '@id': schema:OneTimePayments + Online: + '@id': schema:Online + OnlineEventAttendanceMode: + '@id': schema:OnlineEventAttendanceMode + OnlineFull: + '@id': schema:OnlineFull + OnlineOnly: + '@id': schema:OnlineOnly + OpenTrial: + '@id': schema:OpenTrial + OpeningHoursSpecification: + '@id': schema:OpeningHoursSpecification + OpinionNewsArticle: + '@id': schema:OpinionNewsArticle + Optician: + '@id': schema:Optician + Optometric: + '@id': schema:Optometric + Order: + '@id': schema:Order + OrderAction: + '@id': schema:OrderAction + OrderCancelled: + '@id': schema:OrderCancelled + OrderDelivered: + '@id': schema:OrderDelivered + OrderInTransit: + '@id': schema:OrderInTransit + OrderItem: + '@id': schema:OrderItem + OrderPaymentDue: + '@id': schema:OrderPaymentDue + OrderPickupAvailable: + '@id': schema:OrderPickupAvailable + OrderProblem: + '@id': schema:OrderProblem + OrderProcessing: + '@id': schema:OrderProcessing + OrderReturned: + '@id': schema:OrderReturned + OrderStatus: + '@id': schema:OrderStatus + Organization: + '@id': schema:Organization + OrganizationRole: + '@id': schema:OrganizationRole + OrganizeAction: + '@id': schema:OrganizeAction + OriginalShippingFees: + '@id': schema:OriginalShippingFees + Osteopathic: + '@id': schema:Osteopathic + Otolaryngologic: + '@id': schema:Otolaryngologic + OutOfStock: + '@id': schema:OutOfStock + OutletStore: + '@id': schema:OutletStore + OverviewHealthAspect: + '@id': schema:OverviewHealthAspect + OwnershipInfo: + '@id': schema:OwnershipInfo + PET: + '@id': schema:PET + PaidLeave: + '@id': schema:PaidLeave + PaintAction: + '@id': schema:PaintAction + Painting: + '@id': schema:Painting + PalliativeProcedure: + '@id': schema:PalliativeProcedure + Paperback: + '@id': schema:Paperback + ParcelDelivery: + '@id': schema:ParcelDelivery + ParcelService: + '@id': schema:ParcelService + ParentAudience: + '@id': schema:ParentAudience + ParentalSupport: + '@id': schema:ParentalSupport + Park: + '@id': schema:Park + ParkingFacility: + '@id': schema:ParkingFacility + ParkingMap: + '@id': schema:ParkingMap + PartiallyInForce: + '@id': schema:PartiallyInForce + Pathology: + '@id': schema:Pathology + PathologyTest: + '@id': schema:PathologyTest + Patient: + '@id': schema:Patient + PatientExperienceHealthAspect: + '@id': schema:PatientExperienceHealthAspect + PawnShop: + '@id': schema:PawnShop + PayAction: + '@id': schema:PayAction + PaymentAutomaticallyApplied: + '@id': schema:PaymentAutomaticallyApplied + PaymentCard: + '@id': schema:PaymentCard + PaymentChargeSpecification: + '@id': schema:PaymentChargeSpecification + PaymentComplete: + '@id': schema:PaymentComplete + PaymentDeclined: + '@id': schema:PaymentDeclined + PaymentDue: + '@id': schema:PaymentDue + PaymentMethod: + '@id': schema:PaymentMethod + PaymentPastDue: + '@id': schema:PaymentPastDue + PaymentService: + '@id': schema:PaymentService + PaymentStatusType: + '@id': schema:PaymentStatusType + Pediatric: + '@id': schema:Pediatric + PeopleAudience: + '@id': schema:PeopleAudience + PercutaneousProcedure: + '@id': schema:PercutaneousProcedure + PerformAction: + '@id': schema:PerformAction + PerformanceRole: + '@id': schema:PerformanceRole + PerformingArtsTheater: + '@id': schema:PerformingArtsTheater + PerformingGroup: + '@id': schema:PerformingGroup + Periodical: + '@id': schema:Periodical + Permit: + '@id': schema:Permit + Person: + '@id': schema:Person + PetStore: + '@id': schema:PetStore + Pharmacy: + '@id': schema:Pharmacy + PharmacySpecialty: + '@id': schema:PharmacySpecialty + Photograph: + '@id': schema:Photograph + PhotographAction: + '@id': schema:PhotographAction + PhysicalActivity: + '@id': schema:PhysicalActivity + PhysicalActivityCategory: + '@id': schema:PhysicalActivityCategory + PhysicalExam: + '@id': schema:PhysicalExam + PhysicalTherapy: + '@id': schema:PhysicalTherapy + Physician: + '@id': schema:Physician + Physiotherapy: + '@id': schema:Physiotherapy + Place: + '@id': schema:Place + PlaceOfWorship: + '@id': schema:PlaceOfWorship + PlaceboControlledTrial: + '@id': schema:PlaceboControlledTrial + PlanAction: + '@id': schema:PlanAction + PlasticSurgery: + '@id': schema:PlasticSurgery + Play: + '@id': schema:Play + PlayAction: + '@id': schema:PlayAction + Playground: + '@id': schema:Playground + Plumber: + '@id': schema:Plumber + PodcastEpisode: + '@id': schema:PodcastEpisode + PodcastSeason: + '@id': schema:PodcastSeason + PodcastSeries: + '@id': schema:PodcastSeries + Podiatric: + '@id': schema:Podiatric + PoliceStation: + '@id': schema:PoliceStation + Pond: + '@id': schema:Pond + PostOffice: + '@id': schema:PostOffice + PostalAddress: + '@id': schema:PostalAddress + PostalCodeRangeSpecification: + '@id': schema:PostalCodeRangeSpecification + Poster: + '@id': schema:Poster + PotentialActionStatus: + '@id': schema:PotentialActionStatus + PreOrder: + '@id': schema:PreOrder + PreOrderAction: + '@id': schema:PreOrderAction + PreSale: + '@id': schema:PreSale + PrependAction: + '@id': schema:PrependAction + Preschool: + '@id': schema:Preschool + PrescriptionOnly: + '@id': schema:PrescriptionOnly + PresentationDigitalDocument: + '@id': schema:PresentationDigitalDocument + PreventionHealthAspect: + '@id': schema:PreventionHealthAspect + PreventionIndication: + '@id': schema:PreventionIndication + PriceSpecification: + '@id': schema:PriceSpecification + PrimaryCare: + '@id': schema:PrimaryCare + Prion: + '@id': schema:Prion + Product: + '@id': schema:Product + ProductCollection: + '@id': schema:ProductCollection + ProductGroup: + '@id': schema:ProductGroup + ProductModel: + '@id': schema:ProductModel + ProductReturnEnumeration: + '@id': schema:ProductReturnEnumeration + ProductReturnFiniteReturnWindow: + '@id': schema:ProductReturnFiniteReturnWindow + ProductReturnNotPermitted: + '@id': schema:ProductReturnNotPermitted + ProductReturnPolicy: + '@id': schema:ProductReturnPolicy + ProductReturnUnlimitedWindow: + '@id': schema:ProductReturnUnlimitedWindow + ProductReturnUnspecified: + '@id': schema:ProductReturnUnspecified + ProfessionalService: + '@id': schema:ProfessionalService + ProfilePage: + '@id': schema:ProfilePage + PrognosisHealthAspect: + '@id': schema:PrognosisHealthAspect + ProgramMembership: + '@id': schema:ProgramMembership + Project: + '@id': schema:Project + PronounceableText: + '@id': schema:PronounceableText + Property: + '@id': schema:Property + PropertyValue: + '@id': schema:PropertyValue + PropertyValueSpecification: + '@id': schema:PropertyValueSpecification + Protozoa: + '@id': schema:Protozoa + Psychiatric: + '@id': schema:Psychiatric + PsychologicalTreatment: + '@id': schema:PsychologicalTreatment + PublicHealth: + '@id': schema:PublicHealth + PublicHolidays: + '@id': schema:PublicHolidays + PublicSwimmingPool: + '@id': schema:PublicSwimmingPool + PublicToilet: + '@id': schema:PublicToilet + PublicationEvent: + '@id': schema:PublicationEvent + PublicationIssue: + '@id': schema:PublicationIssue + PublicationVolume: + '@id': schema:PublicationVolume + Pulmonary: + '@id': schema:Pulmonary + QAPage: + '@id': schema:QAPage + QualitativeValue: + '@id': schema:QualitativeValue + QuantitativeValue: + '@id': schema:QuantitativeValue + QuantitativeValueDistribution: + '@id': schema:QuantitativeValueDistribution + Quantity: + '@id': schema:Quantity + Question: + '@id': schema:Question + Quiz: + '@id': schema:Quiz + Quotation: + '@id': schema:Quotation + QuoteAction: + '@id': schema:QuoteAction + RVPark: + '@id': schema:RVPark + RadiationTherapy: + '@id': schema:RadiationTherapy + RadioBroadcastService: + '@id': schema:RadioBroadcastService + RadioChannel: + '@id': schema:RadioChannel + RadioClip: + '@id': schema:RadioClip + RadioEpisode: + '@id': schema:RadioEpisode + RadioSeason: + '@id': schema:RadioSeason + RadioSeries: + '@id': schema:RadioSeries + RadioStation: + '@id': schema:RadioStation + Radiography: + '@id': schema:Radiography + RandomizedTrial: + '@id': schema:RandomizedTrial + Rating: + '@id': schema:Rating + ReactAction: + '@id': schema:ReactAction + ReadAction: + '@id': schema:ReadAction + ReadPermission: + '@id': schema:ReadPermission + RealEstateAgent: + '@id': schema:RealEstateAgent + RealEstateListing: + '@id': schema:RealEstateListing + RearWheelDriveConfiguration: + '@id': schema:RearWheelDriveConfiguration + ReceiveAction: + '@id': schema:ReceiveAction + Recipe: + '@id': schema:Recipe + Recommendation: + '@id': schema:Recommendation + RecommendedDoseSchedule: + '@id': schema:RecommendedDoseSchedule + Recruiting: + '@id': schema:Recruiting + RecyclingCenter: + '@id': schema:RecyclingCenter + RefundTypeEnumeration: + '@id': schema:RefundTypeEnumeration + RefurbishedCondition: + '@id': schema:RefurbishedCondition + RegisterAction: + '@id': schema:RegisterAction + Registry: + '@id': schema:Registry + ReimbursementCap: + '@id': schema:ReimbursementCap + RejectAction: + '@id': schema:RejectAction + RelatedTopicsHealthAspect: + '@id': schema:RelatedTopicsHealthAspect + RemixAlbum: + '@id': schema:RemixAlbum + Renal: + '@id': schema:Renal + RentAction: + '@id': schema:RentAction + RentalCarReservation: + '@id': schema:RentalCarReservation + RentalVehicleUsage: + '@id': schema:RentalVehicleUsage + RepaymentSpecification: + '@id': schema:RepaymentSpecification + ReplaceAction: + '@id': schema:ReplaceAction + ReplyAction: + '@id': schema:ReplyAction + Report: + '@id': schema:Report + ReportageNewsArticle: + '@id': schema:ReportageNewsArticle + ReportedDoseSchedule: + '@id': schema:ReportedDoseSchedule + ResearchProject: + '@id': schema:ResearchProject + Researcher: + '@id': schema:Researcher + Reservation: + '@id': schema:Reservation + ReservationCancelled: + '@id': schema:ReservationCancelled + ReservationConfirmed: + '@id': schema:ReservationConfirmed + ReservationHold: + '@id': schema:ReservationHold + ReservationPackage: + '@id': schema:ReservationPackage + ReservationPending: + '@id': schema:ReservationPending + ReservationStatusType: + '@id': schema:ReservationStatusType + ReserveAction: + '@id': schema:ReserveAction + Reservoir: + '@id': schema:Reservoir + Residence: + '@id': schema:Residence + Resort: + '@id': schema:Resort + RespiratoryTherapy: + '@id': schema:RespiratoryTherapy + Restaurant: + '@id': schema:Restaurant + RestockingFees: + '@id': schema:RestockingFees + RestrictedDiet: + '@id': schema:RestrictedDiet + ResultsAvailable: + '@id': schema:ResultsAvailable + ResultsNotAvailable: + '@id': schema:ResultsNotAvailable + ResumeAction: + '@id': schema:ResumeAction + Retail: + '@id': schema:Retail + ReturnAction: + '@id': schema:ReturnAction + ReturnFeesEnumeration: + '@id': schema:ReturnFeesEnumeration + ReturnShippingFees: + '@id': schema:ReturnShippingFees + Review: + '@id': schema:Review + ReviewAction: + '@id': schema:ReviewAction + ReviewNewsArticle: + '@id': schema:ReviewNewsArticle + Rheumatologic: + '@id': schema:Rheumatologic + RightHandDriving: + '@id': schema:RightHandDriving + RisksOrComplicationsHealthAspect: + '@id': schema:RisksOrComplicationsHealthAspect + RiverBodyOfWater: + '@id': schema:RiverBodyOfWater + Role: + '@id': schema:Role + RoofingContractor: + '@id': schema:RoofingContractor + Room: + '@id': schema:Room + RsvpAction: + '@id': schema:RsvpAction + RsvpResponseMaybe: + '@id': schema:RsvpResponseMaybe + RsvpResponseNo: + '@id': schema:RsvpResponseNo + RsvpResponseType: + '@id': schema:RsvpResponseType + RsvpResponseYes: + '@id': schema:RsvpResponseYes + SaleEvent: + '@id': schema:SaleEvent + SatiricalArticle: + '@id': schema:SatiricalArticle + Saturday: + '@id': schema:Saturday + Schedule: + '@id': schema:Schedule + ScheduleAction: + '@id': schema:ScheduleAction + ScholarlyArticle: + '@id': schema:ScholarlyArticle + School: + '@id': schema:School + SchoolDistrict: + '@id': schema:SchoolDistrict + ScreeningEvent: + '@id': schema:ScreeningEvent + ScreeningHealthAspect: + '@id': schema:ScreeningHealthAspect + Sculpture: + '@id': schema:Sculpture + SeaBodyOfWater: + '@id': schema:SeaBodyOfWater + SearchAction: + '@id': schema:SearchAction + SearchResultsPage: + '@id': schema:SearchResultsPage + Season: + '@id': schema:Season + Seat: + '@id': schema:Seat + SeatingMap: + '@id': schema:SeatingMap + SeeDoctorHealthAspect: + '@id': schema:SeeDoctorHealthAspect + SelfCareHealthAspect: + '@id': schema:SelfCareHealthAspect + SelfStorage: + '@id': schema:SelfStorage + SellAction: + '@id': schema:SellAction + SendAction: + '@id': schema:SendAction + Series: + '@id': schema:Series + Service: + '@id': schema:Service + ServiceChannel: + '@id': schema:ServiceChannel + ShareAction: + '@id': schema:ShareAction + SheetMusic: + '@id': schema:SheetMusic + ShippingDeliveryTime: + '@id': schema:ShippingDeliveryTime + ShippingRateSettings: + '@id': schema:ShippingRateSettings + ShoeStore: + '@id': schema:ShoeStore + ShoppingCenter: + '@id': schema:ShoppingCenter + ShortStory: + '@id': schema:ShortStory + SideEffectsHealthAspect: + '@id': schema:SideEffectsHealthAspect + SingleBlindedTrial: + '@id': schema:SingleBlindedTrial + SingleCenterTrial: + '@id': schema:SingleCenterTrial + SingleFamilyResidence: + '@id': schema:SingleFamilyResidence + SinglePlayer: + '@id': schema:SinglePlayer + SingleRelease: + '@id': schema:SingleRelease + SiteNavigationElement: + '@id': schema:SiteNavigationElement + SkiResort: + '@id': schema:SkiResort + Skin: + '@id': schema:Skin + SocialEvent: + '@id': schema:SocialEvent + SocialMediaPosting: + '@id': schema:SocialMediaPosting + SoftwareApplication: + '@id': schema:SoftwareApplication + SoftwareSourceCode: + '@id': schema:SoftwareSourceCode + SoldOut: + '@id': schema:SoldOut + SomeProducts: + '@id': schema:SomeProducts + SoundtrackAlbum: + '@id': schema:SoundtrackAlbum + SpeakableSpecification: + '@id': schema:SpeakableSpecification + SpecialAnnouncement: + '@id': schema:SpecialAnnouncement + Specialty: + '@id': schema:Specialty + SpeechPathology: + '@id': schema:SpeechPathology + SpokenWordAlbum: + '@id': schema:SpokenWordAlbum + SportingGoodsStore: + '@id': schema:SportingGoodsStore + SportsActivityLocation: + '@id': schema:SportsActivityLocation + SportsClub: + '@id': schema:SportsClub + SportsEvent: + '@id': schema:SportsEvent + SportsOrganization: + '@id': schema:SportsOrganization + SportsTeam: + '@id': schema:SportsTeam + SpreadsheetDigitalDocument: + '@id': schema:SpreadsheetDigitalDocument + StadiumOrArena: + '@id': schema:StadiumOrArena + StagesHealthAspect: + '@id': schema:StagesHealthAspect + State: + '@id': schema:State + StatisticalPopulation: + '@id': schema:StatisticalPopulation + StatusEnumeration: + '@id': schema:StatusEnumeration + SteeringPositionValue: + '@id': schema:SteeringPositionValue + Store: + '@id': schema:Store + StoreCreditRefund: + '@id': schema:StoreCreditRefund + StrengthTraining: + '@id': schema:StrengthTraining + StructuredValue: + '@id': schema:StructuredValue + StudioAlbum: + '@id': schema:StudioAlbum + StupidType: + '@id': schema:StupidType + SubscribeAction: + '@id': schema:SubscribeAction + Substance: + '@id': schema:Substance + SubwayStation: + '@id': schema:SubwayStation + Suite: + '@id': schema:Suite + Sunday: + '@id': schema:Sunday + SuperficialAnatomy: + '@id': schema:SuperficialAnatomy + Surgical: + '@id': schema:Surgical + SurgicalProcedure: + '@id': schema:SurgicalProcedure + SuspendAction: + '@id': schema:SuspendAction + Suspended: + '@id': schema:Suspended + SymptomsHealthAspect: + '@id': schema:SymptomsHealthAspect + Synagogue: + '@id': schema:Synagogue + TVClip: + '@id': schema:TVClip + TVEpisode: + '@id': schema:TVEpisode + TVSeason: + '@id': schema:TVSeason + TVSeries: + '@id': schema:TVSeries + Table: + '@id': schema:Table + TakeAction: + '@id': schema:TakeAction + TattooParlor: + '@id': schema:TattooParlor + Taxi: + '@id': schema:Taxi + TaxiReservation: + '@id': schema:TaxiReservation + TaxiService: + '@id': schema:TaxiService + TaxiStand: + '@id': schema:TaxiStand + TaxiVehicleUsage: + '@id': schema:TaxiVehicleUsage + TechArticle: + '@id': schema:TechArticle + TelevisionChannel: + '@id': schema:TelevisionChannel + TelevisionStation: + '@id': schema:TelevisionStation + TennisComplex: + '@id': schema:TennisComplex + Terminated: + '@id': schema:Terminated + Text: + '@id': schema:Text + TextDigitalDocument: + '@id': schema:TextDigitalDocument + TheaterEvent: + '@id': schema:TheaterEvent + TheaterGroup: + '@id': schema:TheaterGroup + Therapeutic: + '@id': schema:Therapeutic + TherapeuticProcedure: + '@id': schema:TherapeuticProcedure + Thesis: + '@id': schema:Thesis + Thing: + '@id': schema:Thing + Throat: + '@id': schema:Throat + Thursday: + '@id': schema:Thursday + Ticket: + '@id': schema:Ticket + TieAction: + '@id': schema:TieAction + Time: + '@id': schema:Time + TipAction: + '@id': schema:TipAction + TireShop: + '@id': schema:TireShop + TollFree: + '@id': schema:TollFree + TouristAttraction: + '@id': schema:TouristAttraction + TouristDestination: + '@id': schema:TouristDestination + TouristInformationCenter: + '@id': schema:TouristInformationCenter + TouristTrip: + '@id': schema:TouristTrip + Toxicologic: + '@id': schema:Toxicologic + ToyStore: + '@id': schema:ToyStore + TrackAction: + '@id': schema:TrackAction + TradeAction: + '@id': schema:TradeAction + TraditionalChinese: + '@id': schema:TraditionalChinese + TrainReservation: + '@id': schema:TrainReservation + TrainStation: + '@id': schema:TrainStation + TrainTrip: + '@id': schema:TrainTrip + TransferAction: + '@id': schema:TransferAction + TransitMap: + '@id': schema:TransitMap + TravelAction: + '@id': schema:TravelAction + TravelAgency: + '@id': schema:TravelAgency + TreatmentIndication: + '@id': schema:TreatmentIndication + TreatmentsHealthAspect: + '@id': schema:TreatmentsHealthAspect + Trip: + '@id': schema:Trip + TripleBlindedTrial: + '@id': schema:TripleBlindedTrial + 'True': + '@id': schema:True + Tuesday: + '@id': schema:Tuesday + TypeAndQuantityNode: + '@id': schema:TypeAndQuantityNode + TypesHealthAspect: + '@id': schema:TypesHealthAspect + UKNonprofitType: + '@id': schema:UKNonprofitType + UKTrust: + '@id': schema:UKTrust + URL: + '@id': schema:URL + USNonprofitType: + '@id': schema:USNonprofitType + Ultrasound: + '@id': schema:Ultrasound + UnRegisterAction: + '@id': schema:UnRegisterAction + UnemploymentSupport: + '@id': schema:UnemploymentSupport + UnincorporatedAssociationCharity: + '@id': schema:UnincorporatedAssociationCharity + UnitPriceSpecification: + '@id': schema:UnitPriceSpecification + UnofficialLegalValue: + '@id': schema:UnofficialLegalValue + UpdateAction: + '@id': schema:UpdateAction + Urologic: + '@id': schema:Urologic + UsageOrScheduleHealthAspect: + '@id': schema:UsageOrScheduleHealthAspect + UseAction: + '@id': schema:UseAction + UsedCondition: + '@id': schema:UsedCondition + UserBlocks: + '@id': schema:UserBlocks + UserCheckins: + '@id': schema:UserCheckins + UserComments: + '@id': schema:UserComments + UserDownloads: + '@id': schema:UserDownloads + UserInteraction: + '@id': schema:UserInteraction + UserLikes: + '@id': schema:UserLikes + UserPageVisits: + '@id': schema:UserPageVisits + UserPlays: + '@id': schema:UserPlays + UserPlusOnes: + '@id': schema:UserPlusOnes + UserReview: + '@id': schema:UserReview + UserTweets: + '@id': schema:UserTweets + VeganDiet: + '@id': schema:VeganDiet + VegetarianDiet: + '@id': schema:VegetarianDiet + Vehicle: + '@id': schema:Vehicle + Vein: + '@id': schema:Vein + VenueMap: + '@id': schema:VenueMap + Vessel: + '@id': schema:Vessel + VeterinaryCare: + '@id': schema:VeterinaryCare + VideoGallery: + '@id': schema:VideoGallery + VideoGame: + '@id': schema:VideoGame + VideoGameClip: + '@id': schema:VideoGameClip + VideoGameSeries: + '@id': schema:VideoGameSeries + VideoObject: + '@id': schema:VideoObject + ViewAction: + '@id': schema:ViewAction + VinylFormat: + '@id': schema:VinylFormat + VirtualLocation: + '@id': schema:VirtualLocation + Virus: + '@id': schema:Virus + VisualArtsEvent: + '@id': schema:VisualArtsEvent + VisualArtwork: + '@id': schema:VisualArtwork + VitalSign: + '@id': schema:VitalSign + Volcano: + '@id': schema:Volcano + VoteAction: + '@id': schema:VoteAction + WPAdBlock: + '@id': schema:WPAdBlock + WPFooter: + '@id': schema:WPFooter + WPHeader: + '@id': schema:WPHeader + WPSideBar: + '@id': schema:WPSideBar + WantAction: + '@id': schema:WantAction + WarrantyPromise: + '@id': schema:WarrantyPromise + WarrantyScope: + '@id': schema:WarrantyScope + WatchAction: + '@id': schema:WatchAction + Waterfall: + '@id': schema:Waterfall + WearAction: + '@id': schema:WearAction + WebAPI: + '@id': schema:WebAPI + WebApplication: + '@id': schema:WebApplication + WebContent: + '@id': schema:WebContent + WebPage: + '@id': schema:WebPage + WebPageElement: + '@id': schema:WebPageElement + WebSite: + '@id': schema:WebSite + Wednesday: + '@id': schema:Wednesday + WesternConventional: + '@id': schema:WesternConventional + Wholesale: + '@id': schema:Wholesale + WholesaleStore: + '@id': schema:WholesaleStore + WinAction: + '@id': schema:WinAction + Winery: + '@id': schema:Winery + Withdrawn: + '@id': schema:Withdrawn + WorkBasedProgram: + '@id': schema:WorkBasedProgram + WorkersUnion: + '@id': schema:WorkersUnion + WriteAction: + '@id': schema:WriteAction + WritePermission: + '@id': schema:WritePermission + XPathType: + '@id': schema:XPathType + XRay: + '@id': schema:XRay + ZoneBoardingPolicy: + '@id': schema:ZoneBoardingPolicy + Zoo: + '@id': schema:Zoo + about: + '@id': schema:about + abridged: + '@id': schema:abridged + abstract: + '@id': schema:abstract + accelerationTime: + '@id': schema:accelerationTime + acceptedAnswer: + '@id': schema:acceptedAnswer + acceptedOffer: + '@id': schema:acceptedOffer + acceptedPaymentMethod: + '@id': schema:acceptedPaymentMethod + acceptsReservations: + '@id': schema:acceptsReservations + accessCode: + '@id': schema:accessCode + accessMode: + '@id': schema:accessMode + accessModeSufficient: + '@id': schema:accessModeSufficient + accessibilityAPI: + '@id': schema:accessibilityAPI + accessibilityControl: + '@id': schema:accessibilityControl + accessibilityFeature: + '@id': schema:accessibilityFeature + accessibilityHazard: + '@id': schema:accessibilityHazard + accessibilitySummary: + '@id': schema:accessibilitySummary + accommodationCategory: + '@id': schema:accommodationCategory + accommodationFloorPlan: + '@id': schema:accommodationFloorPlan + accountId: + '@id': schema:accountId + accountMinimumInflow: + '@id': schema:accountMinimumInflow + accountOverdraftLimit: + '@id': schema:accountOverdraftLimit + accountablePerson: + '@id': schema:accountablePerson + acquireLicensePage: + '@id': schema:acquireLicensePage + '@type': '@id' + acquiredFrom: + '@id': schema:acquiredFrom + acrissCode: + '@id': schema:acrissCode + actionAccessibilityRequirement: + '@id': schema:actionAccessibilityRequirement + actionApplication: + '@id': schema:actionApplication + actionOption: + '@id': schema:actionOption + actionPlatform: + '@id': schema:actionPlatform + actionStatus: + '@id': schema:actionStatus + actionableFeedbackPolicy: + '@id': schema:actionableFeedbackPolicy + '@type': '@id' + activeIngredient: + '@id': schema:activeIngredient + activityDuration: + '@id': schema:activityDuration + activityFrequency: + '@id': schema:activityFrequency + actor: + '@id': schema:actor + actors: + '@id': schema:actors + addOn: + '@id': schema:addOn + additionalName: + '@id': schema:additionalName + additionalNumberOfGuests: + '@id': schema:additionalNumberOfGuests + additionalProperty: + '@id': schema:additionalProperty + additionalType: + '@id': schema:additionalType + '@type': '@id' + additionalVariable: + '@id': schema:additionalVariable + address: + '@id': schema:address + addressCountry: + '@id': schema:addressCountry + addressLocality: + '@id': schema:addressLocality + addressRegion: + '@id': schema:addressRegion + administrationRoute: + '@id': schema:administrationRoute + advanceBookingRequirement: + '@id': schema:advanceBookingRequirement + adverseOutcome: + '@id': schema:adverseOutcome + affectedBy: + '@id': schema:affectedBy + affiliation: + '@id': schema:affiliation + afterMedia: + '@id': schema:afterMedia + '@type': '@id' + agent: + '@id': schema:agent + aggregateRating: + '@id': schema:aggregateRating + aircraft: + '@id': schema:aircraft + album: + '@id': schema:album + albumProductionType: + '@id': schema:albumProductionType + albumRelease: + '@id': schema:albumRelease + albumReleaseType: + '@id': schema:albumReleaseType + albums: + '@id': schema:albums + alcoholWarning: + '@id': schema:alcoholWarning + algorithm: + '@id': schema:algorithm + alignmentType: + '@id': schema:alignmentType + alternateName: + '@id': schema:alternateName + alternativeHeadline: + '@id': schema:alternativeHeadline + alumni: + '@id': schema:alumni + alumniOf: + '@id': schema:alumniOf + amenityFeature: + '@id': schema:amenityFeature + amount: + '@id': schema:amount + amountOfThisGood: + '@id': schema:amountOfThisGood + announcementLocation: + '@id': schema:announcementLocation + annualPercentageRate: + '@id': schema:annualPercentageRate + answerCount: + '@id': schema:answerCount + answerExplanation: + '@id': schema:answerExplanation + antagonist: + '@id': schema:antagonist + appearance: + '@id': schema:appearance + applicableLocation: + '@id': schema:applicableLocation + applicantLocationRequirements: + '@id': schema:applicantLocationRequirements + application: + '@id': schema:application + applicationCategory: + '@id': schema:applicationCategory + applicationContact: + '@id': schema:applicationContact + applicationDeadline: + '@id': schema:applicationDeadline + '@type': Date + applicationStartDate: + '@id': schema:applicationStartDate + '@type': Date + applicationSubCategory: + '@id': schema:applicationSubCategory + applicationSuite: + '@id': schema:applicationSuite + appliesToDeliveryMethod: + '@id': schema:appliesToDeliveryMethod + appliesToPaymentMethod: + '@id': schema:appliesToPaymentMethod + archiveHeld: + '@id': schema:archiveHeld + area: + '@id': schema:area + areaServed: + '@id': schema:areaServed + arrivalAirport: + '@id': schema:arrivalAirport + arrivalBoatTerminal: + '@id': schema:arrivalBoatTerminal + arrivalBusStop: + '@id': schema:arrivalBusStop + arrivalGate: + '@id': schema:arrivalGate + arrivalPlatform: + '@id': schema:arrivalPlatform + arrivalStation: + '@id': schema:arrivalStation + arrivalTerminal: + '@id': schema:arrivalTerminal + arrivalTime: + '@id': schema:arrivalTime + '@type': DateTime + artEdition: + '@id': schema:artEdition + artMedium: + '@id': schema:artMedium + arterialBranch: + '@id': schema:arterialBranch + artform: + '@id': schema:artform + articleBody: + '@id': schema:articleBody + articleSection: + '@id': schema:articleSection + artist: + '@id': schema:artist + artworkSurface: + '@id': schema:artworkSurface + aspect: + '@id': schema:aspect + assembly: + '@id': schema:assembly + assemblyVersion: + '@id': schema:assemblyVersion + assesses: + '@id': schema:assesses + associatedAnatomy: + '@id': schema:associatedAnatomy + associatedArticle: + '@id': schema:associatedArticle + associatedMedia: + '@id': schema:associatedMedia + associatedPathophysiology: + '@id': schema:associatedPathophysiology + athlete: + '@id': schema:athlete + attendee: + '@id': schema:attendee + attendees: + '@id': schema:attendees + audience: + '@id': schema:audience + audienceType: + '@id': schema:audienceType + audio: + '@id': schema:audio + authenticator: + '@id': schema:authenticator + author: + '@id': schema:author + availability: + '@id': schema:availability + availabilityEnds: + '@id': schema:availabilityEnds + '@type': Date + availabilityStarts: + '@id': schema:availabilityStarts + '@type': Date + availableAtOrFrom: + '@id': schema:availableAtOrFrom + availableChannel: + '@id': schema:availableChannel + availableDeliveryMethod: + '@id': schema:availableDeliveryMethod + availableFrom: + '@id': schema:availableFrom + '@type': DateTime + availableIn: + '@id': schema:availableIn + availableLanguage: + '@id': schema:availableLanguage + availableOnDevice: + '@id': schema:availableOnDevice + availableService: + '@id': schema:availableService + availableStrength: + '@id': schema:availableStrength + availableTest: + '@id': schema:availableTest + availableThrough: + '@id': schema:availableThrough + '@type': DateTime + award: + '@id': schema:award + awards: + '@id': schema:awards + awayTeam: + '@id': schema:awayTeam + backstory: + '@id': schema:backstory + bankAccountType: + '@id': schema:bankAccountType + baseSalary: + '@id': schema:baseSalary + bccRecipient: + '@id': schema:bccRecipient + bed: + '@id': schema:bed + beforeMedia: + '@id': schema:beforeMedia + '@type': '@id' + beneficiaryBank: + '@id': schema:beneficiaryBank + benefits: + '@id': schema:benefits + benefitsSummaryUrl: + '@id': schema:benefitsSummaryUrl + '@type': '@id' + bestRating: + '@id': schema:bestRating + bibo: http://purl.org/ontology/bibo/ + billingAddress: + '@id': schema:billingAddress + billingIncrement: + '@id': schema:billingIncrement + billingPeriod: + '@id': schema:billingPeriod + biomechnicalClass: + '@id': schema:biomechnicalClass + birthDate: + '@id': schema:birthDate + '@type': Date + birthPlace: + '@id': schema:birthPlace + bitrate: + '@id': schema:bitrate + blogPost: + '@id': schema:blogPost + blogPosts: + '@id': schema:blogPosts + bloodSupply: + '@id': schema:bloodSupply + boardingGroup: + '@id': schema:boardingGroup + boardingPolicy: + '@id': schema:boardingPolicy + bodyLocation: + '@id': schema:bodyLocation + bodyType: + '@id': schema:bodyType + bookEdition: + '@id': schema:bookEdition + bookFormat: + '@id': schema:bookFormat + bookingAgent: + '@id': schema:bookingAgent + bookingTime: + '@id': schema:bookingTime + '@type': DateTime + borrower: + '@id': schema:borrower + box: + '@id': schema:box + branch: + '@id': schema:branch + branchCode: + '@id': schema:branchCode + branchOf: + '@id': schema:branchOf + brand: + '@id': schema:brand + breadcrumb: + '@id': schema:breadcrumb + breastfeedingWarning: + '@id': schema:breastfeedingWarning + broadcastAffiliateOf: + '@id': schema:broadcastAffiliateOf + broadcastChannelId: + '@id': schema:broadcastChannelId + broadcastDisplayName: + '@id': schema:broadcastDisplayName + broadcastFrequency: + '@id': schema:broadcastFrequency + broadcastFrequencyValue: + '@id': schema:broadcastFrequencyValue + broadcastOfEvent: + '@id': schema:broadcastOfEvent + broadcastServiceTier: + '@id': schema:broadcastServiceTier + broadcastSignalModulation: + '@id': schema:broadcastSignalModulation + broadcastSubChannel: + '@id': schema:broadcastSubChannel + broadcastTimezone: + '@id': schema:broadcastTimezone + broadcaster: + '@id': schema:broadcaster + broker: + '@id': schema:broker + browserRequirements: + '@id': schema:browserRequirements + busName: + '@id': schema:busName + busNumber: + '@id': schema:busNumber + businessDays: + '@id': schema:businessDays + businessFunction: + '@id': schema:businessFunction + buyer: + '@id': schema:buyer + byArtist: + '@id': schema:byArtist + byDay: + '@id': schema:byDay + byMonth: + '@id': schema:byMonth + byMonthDay: + '@id': schema:byMonthDay + byMonthWeek: + '@id': schema:byMonthWeek + callSign: + '@id': schema:callSign + calories: + '@id': schema:calories + candidate: + '@id': schema:candidate + caption: + '@id': schema:caption + carbohydrateContent: + '@id': schema:carbohydrateContent + cargoVolume: + '@id': schema:cargoVolume + carrier: + '@id': schema:carrier + carrierRequirements: + '@id': schema:carrierRequirements + cashBack: + '@id': schema:cashBack + catalog: + '@id': schema:catalog + catalogNumber: + '@id': schema:catalogNumber + category: + '@id': schema:category + causeOf: + '@id': schema:causeOf + ccRecipient: + '@id': schema:ccRecipient + character: + '@id': schema:character + characterAttribute: + '@id': schema:characterAttribute + characterName: + '@id': schema:characterName + cheatCode: + '@id': schema:cheatCode + checkinTime: + '@id': schema:checkinTime + '@type': DateTime + checkoutTime: + '@id': schema:checkoutTime + '@type': DateTime + childMaxAge: + '@id': schema:childMaxAge + childMinAge: + '@id': schema:childMinAge + children: + '@id': schema:children + cholesterolContent: + '@id': schema:cholesterolContent + circle: + '@id': schema:circle + citation: + '@id': schema:citation + claimReviewed: + '@id': schema:claimReviewed + clincalPharmacology: + '@id': schema:clincalPharmacology + clinicalPharmacology: + '@id': schema:clinicalPharmacology + clipNumber: + '@id': schema:clipNumber + closes: + '@id': schema:closes + coach: + '@id': schema:coach + code: + '@id': schema:code + codeRepository: + '@id': schema:codeRepository + '@type': '@id' + codeSampleType: + '@id': schema:codeSampleType + codeValue: + '@id': schema:codeValue + codingSystem: + '@id': schema:codingSystem + colleague: + '@id': schema:colleague + '@type': '@id' + colleagues: + '@id': schema:colleagues + collection: + '@id': schema:collection + collectionSize: + '@id': schema:collectionSize + color: + '@id': schema:color + colorist: + '@id': schema:colorist + comment: + '@id': schema:comment + commentCount: + '@id': schema:commentCount + commentText: + '@id': schema:commentText + commentTime: + '@id': schema:commentTime + '@type': Date + competencyRequired: + '@id': schema:competencyRequired + competitor: + '@id': schema:competitor + composer: + '@id': schema:composer + comprisedOf: + '@id': schema:comprisedOf + conditionsOfAccess: + '@id': schema:conditionsOfAccess + confirmationNumber: + '@id': schema:confirmationNumber + connectedTo: + '@id': schema:connectedTo + constrainingProperty: + '@id': schema:constrainingProperty + contactOption: + '@id': schema:contactOption + contactPoint: + '@id': schema:contactPoint + contactPoints: + '@id': schema:contactPoints + contactType: + '@id': schema:contactType + contactlessPayment: + '@id': schema:contactlessPayment + containedIn: + '@id': schema:containedIn + containedInPlace: + '@id': schema:containedInPlace + containsPlace: + '@id': schema:containsPlace + containsSeason: + '@id': schema:containsSeason + contentLocation: + '@id': schema:contentLocation + contentRating: + '@id': schema:contentRating + contentReferenceTime: + '@id': schema:contentReferenceTime + '@type': DateTime + contentSize: + '@id': schema:contentSize + contentType: + '@id': schema:contentType + contentUrl: + '@id': schema:contentUrl + '@type': '@id' + contraindication: + '@id': schema:contraindication + contributor: + '@id': schema:contributor + cookTime: + '@id': schema:cookTime + cookingMethod: + '@id': schema:cookingMethod + copyrightHolder: + '@id': schema:copyrightHolder + copyrightYear: + '@id': schema:copyrightYear + correction: + '@id': schema:correction + correctionsPolicy: + '@id': schema:correctionsPolicy + '@type': '@id' + costCategory: + '@id': schema:costCategory + costCurrency: + '@id': schema:costCurrency + costOrigin: + '@id': schema:costOrigin + costPerUnit: + '@id': schema:costPerUnit + countriesNotSupported: + '@id': schema:countriesNotSupported + countriesSupported: + '@id': schema:countriesSupported + countryOfOrigin: + '@id': schema:countryOfOrigin + course: + '@id': schema:course + courseCode: + '@id': schema:courseCode + courseMode: + '@id': schema:courseMode + coursePrerequisites: + '@id': schema:coursePrerequisites + courseWorkload: + '@id': schema:courseWorkload + coverageEndTime: + '@id': schema:coverageEndTime + '@type': DateTime + coverageStartTime: + '@id': schema:coverageStartTime + '@type': DateTime + creativeWorkStatus: + '@id': schema:creativeWorkStatus + creator: + '@id': schema:creator + credentialCategory: + '@id': schema:credentialCategory + creditedTo: + '@id': schema:creditedTo + cssSelector: + '@id': schema:cssSelector + currenciesAccepted: + '@id': schema:currenciesAccepted + currency: + '@id': schema:currency + currentExchangeRate: + '@id': schema:currentExchangeRate + customer: + '@id': schema:customer + cutoffTime: + '@id': schema:cutoffTime + cvdCollectionDate: + '@id': schema:cvdCollectionDate + cvdFacilityCounty: + '@id': schema:cvdFacilityCounty + cvdFacilityId: + '@id': schema:cvdFacilityId + cvdNumBeds: + '@id': schema:cvdNumBeds + cvdNumBedsOcc: + '@id': schema:cvdNumBedsOcc + cvdNumC19Died: + '@id': schema:cvdNumC19Died + cvdNumC19HOPats: + '@id': schema:cvdNumC19HOPats + cvdNumC19HospPats: + '@id': schema:cvdNumC19HospPats + cvdNumC19MechVentPats: + '@id': schema:cvdNumC19MechVentPats + cvdNumC19OFMechVentPats: + '@id': schema:cvdNumC19OFMechVentPats + cvdNumC19OverflowPats: + '@id': schema:cvdNumC19OverflowPats + cvdNumICUBeds: + '@id': schema:cvdNumICUBeds + cvdNumICUBedsOcc: + '@id': schema:cvdNumICUBedsOcc + cvdNumTotBeds: + '@id': schema:cvdNumTotBeds + cvdNumVent: + '@id': schema:cvdNumVent + cvdNumVentUse: + '@id': schema:cvdNumVentUse + dataFeedElement: + '@id': schema:dataFeedElement + dataset: + '@id': schema:dataset + datasetTimeInterval: + '@id': schema:datasetTimeInterval + '@type': DateTime + dateCreated: + '@id': schema:dateCreated + '@type': Date + dateDeleted: + '@id': schema:dateDeleted + '@type': Date + dateIssued: + '@id': schema:dateIssued + '@type': Date + dateModified: + '@id': schema:dateModified + '@type': Date + datePosted: + '@id': schema:datePosted + '@type': Date + datePublished: + '@id': schema:datePublished + '@type': Date + dateRead: + '@id': schema:dateRead + '@type': Date + dateReceived: + '@id': schema:dateReceived + '@type': DateTime + dateSent: + '@id': schema:dateSent + '@type': DateTime + dateVehicleFirstRegistered: + '@id': schema:dateVehicleFirstRegistered + '@type': Date + dateline: + '@id': schema:dateline + dayOfWeek: + '@id': schema:dayOfWeek + dc: http://purl.org/dc/elements/1.1/ + dcat: http://www.w3.org/ns/dcat# + dct: http://purl.org/dc/terms/ + dcterms: http://purl.org/dc/terms/ + dctype: http://purl.org/dc/dcmitype/ + deathDate: + '@id': schema:deathDate + '@type': Date + deathPlace: + '@id': schema:deathPlace + defaultValue: + '@id': schema:defaultValue + deliveryAddress: + '@id': schema:deliveryAddress + deliveryLeadTime: + '@id': schema:deliveryLeadTime + deliveryMethod: + '@id': schema:deliveryMethod + deliveryStatus: + '@id': schema:deliveryStatus + deliveryTime: + '@id': schema:deliveryTime + department: + '@id': schema:department + departureAirport: + '@id': schema:departureAirport + departureBoatTerminal: + '@id': schema:departureBoatTerminal + departureBusStop: + '@id': schema:departureBusStop + departureGate: + '@id': schema:departureGate + departurePlatform: + '@id': schema:departurePlatform + departureStation: + '@id': schema:departureStation + departureTerminal: + '@id': schema:departureTerminal + departureTime: + '@id': schema:departureTime + '@type': DateTime + dependencies: + '@id': schema:dependencies + depth: + '@id': schema:depth + description: + '@id': schema:description + device: + '@id': schema:device + diagnosis: + '@id': schema:diagnosis + diagram: + '@id': schema:diagram + diet: + '@id': schema:diet + dietFeatures: + '@id': schema:dietFeatures + differentialDiagnosis: + '@id': schema:differentialDiagnosis + director: + '@id': schema:director + directors: + '@id': schema:directors + disambiguatingDescription: + '@id': schema:disambiguatingDescription + discount: + '@id': schema:discount + discountCode: + '@id': schema:discountCode + discountCurrency: + '@id': schema:discountCurrency + discusses: + '@id': schema:discusses + discussionUrl: + '@id': schema:discussionUrl + '@type': '@id' + diseasePreventionInfo: + '@id': schema:diseasePreventionInfo + '@type': '@id' + diseaseSpreadStatistics: + '@id': schema:diseaseSpreadStatistics + '@type': '@id' + dissolutionDate: + '@id': schema:dissolutionDate + '@type': Date + distance: + '@id': schema:distance + distinguishingSign: + '@id': schema:distinguishingSign + distribution: + '@id': schema:distribution + diversityPolicy: + '@id': schema:diversityPolicy + '@type': '@id' + diversityStaffingReport: + '@id': schema:diversityStaffingReport + '@type': '@id' + documentation: + '@id': schema:documentation + '@type': '@id' + doesNotShip: + '@id': schema:doesNotShip + domainIncludes: + '@id': schema:domainIncludes + domiciledMortgage: + '@id': schema:domiciledMortgage + doorTime: + '@id': schema:doorTime + '@type': DateTime + dosageForm: + '@id': schema:dosageForm + doseSchedule: + '@id': schema:doseSchedule + doseUnit: + '@id': schema:doseUnit + doseValue: + '@id': schema:doseValue + downPayment: + '@id': schema:downPayment + downloadUrl: + '@id': schema:downloadUrl + '@type': '@id' + downvoteCount: + '@id': schema:downvoteCount + drainsTo: + '@id': schema:drainsTo + driveWheelConfiguration: + '@id': schema:driveWheelConfiguration + dropoffLocation: + '@id': schema:dropoffLocation + dropoffTime: + '@id': schema:dropoffTime + '@type': DateTime + drug: + '@id': schema:drug + drugClass: + '@id': schema:drugClass + drugUnit: + '@id': schema:drugUnit + duns: + '@id': schema:duns + duplicateTherapy: + '@id': schema:duplicateTherapy + duration: + '@id': schema:duration + durationOfWarranty: + '@id': schema:durationOfWarranty + duringMedia: + '@id': schema:duringMedia + '@type': '@id' + earlyPrepaymentPenalty: + '@id': schema:earlyPrepaymentPenalty + editEIDR: + '@id': schema:editEIDR + editor: + '@id': schema:editor + eduQuestionType: + '@id': schema:eduQuestionType + educationRequirements: + '@id': schema:educationRequirements + educationalAlignment: + '@id': schema:educationalAlignment + educationalCredentialAwarded: + '@id': schema:educationalCredentialAwarded + educationalFramework: + '@id': schema:educationalFramework + educationalLevel: + '@id': schema:educationalLevel + educationalProgramMode: + '@id': schema:educationalProgramMode + educationalRole: + '@id': schema:educationalRole + educationalUse: + '@id': schema:educationalUse + elevation: + '@id': schema:elevation + eli: http://data.europa.eu/eli/ontology# + eligibilityToWorkRequirement: + '@id': schema:eligibilityToWorkRequirement + eligibleCustomerType: + '@id': schema:eligibleCustomerType + eligibleDuration: + '@id': schema:eligibleDuration + eligibleQuantity: + '@id': schema:eligibleQuantity + eligibleRegion: + '@id': schema:eligibleRegion + eligibleTransactionVolume: + '@id': schema:eligibleTransactionVolume + email: + '@id': schema:email + embedUrl: + '@id': schema:embedUrl + '@type': '@id' + emissionsCO2: + '@id': schema:emissionsCO2 + employee: + '@id': schema:employee + employees: + '@id': schema:employees + employerOverview: + '@id': schema:employerOverview + employmentType: + '@id': schema:employmentType + employmentUnit: + '@id': schema:employmentUnit + encodesCreativeWork: + '@id': schema:encodesCreativeWork + encoding: + '@id': schema:encoding + encodingFormat: + '@id': schema:encodingFormat + encodingType: + '@id': schema:encodingType + encodings: + '@id': schema:encodings + endDate: + '@id': schema:endDate + '@type': Date + endOffset: + '@id': schema:endOffset + endTime: + '@id': schema:endTime + '@type': DateTime + endorsee: + '@id': schema:endorsee + endorsers: + '@id': schema:endorsers + energyEfficiencyScaleMax: + '@id': schema:energyEfficiencyScaleMax + energyEfficiencyScaleMin: + '@id': schema:energyEfficiencyScaleMin + engineDisplacement: + '@id': schema:engineDisplacement + enginePower: + '@id': schema:enginePower + engineType: + '@id': schema:engineType + entertainmentBusiness: + '@id': schema:entertainmentBusiness + epidemiology: + '@id': schema:epidemiology + episode: + '@id': schema:episode + episodeNumber: + '@id': schema:episodeNumber + episodes: + '@id': schema:episodes + equal: + '@id': schema:equal + error: + '@id': schema:error + estimatedCost: + '@id': schema:estimatedCost + estimatedFlightDuration: + '@id': schema:estimatedFlightDuration + estimatedSalary: + '@id': schema:estimatedSalary + estimatesRiskOf: + '@id': schema:estimatesRiskOf + ethicsPolicy: + '@id': schema:ethicsPolicy + '@type': '@id' + event: + '@id': schema:event + eventAttendanceMode: + '@id': schema:eventAttendanceMode + eventSchedule: + '@id': schema:eventSchedule + eventStatus: + '@id': schema:eventStatus + events: + '@id': schema:events + evidenceLevel: + '@id': schema:evidenceLevel + evidenceOrigin: + '@id': schema:evidenceOrigin + exampleOfWork: + '@id': schema:exampleOfWork + exceptDate: + '@id': schema:exceptDate + '@type': Date + exchangeRateSpread: + '@id': schema:exchangeRateSpread + executableLibraryName: + '@id': schema:executableLibraryName + exerciseCourse: + '@id': schema:exerciseCourse + exercisePlan: + '@id': schema:exercisePlan + exerciseRelatedDiet: + '@id': schema:exerciseRelatedDiet + exerciseType: + '@id': schema:exerciseType + exifData: + '@id': schema:exifData + expectedArrivalFrom: + '@id': schema:expectedArrivalFrom + '@type': Date + expectedArrivalUntil: + '@id': schema:expectedArrivalUntil + '@type': Date + expectedPrognosis: + '@id': schema:expectedPrognosis + expectsAcceptanceOf: + '@id': schema:expectsAcceptanceOf + experienceRequirements: + '@id': schema:experienceRequirements + expertConsiderations: + '@id': schema:expertConsiderations + expires: + '@id': schema:expires + '@type': Date + familyName: + '@id': schema:familyName + fatContent: + '@id': schema:fatContent + faxNumber: + '@id': schema:faxNumber + featureList: + '@id': schema:featureList + feesAndCommissionsSpecification: + '@id': schema:feesAndCommissionsSpecification + fiberContent: + '@id': schema:fiberContent + fileFormat: + '@id': schema:fileFormat + fileSize: + '@id': schema:fileSize + financialAidEligible: + '@id': schema:financialAidEligible + firstAppearance: + '@id': schema:firstAppearance + firstPerformance: + '@id': schema:firstPerformance + flightDistance: + '@id': schema:flightDistance + flightNumber: + '@id': schema:flightNumber + floorLevel: + '@id': schema:floorLevel + floorLimit: + '@id': schema:floorLimit + floorSize: + '@id': schema:floorSize + foaf: http://xmlns.com/foaf/0.1/ + followee: + '@id': schema:followee + follows: + '@id': schema:follows + followup: + '@id': schema:followup + foodEstablishment: + '@id': schema:foodEstablishment + foodEvent: + '@id': schema:foodEvent + foodWarning: + '@id': schema:foodWarning + founder: + '@id': schema:founder + founders: + '@id': schema:founders + foundingDate: + '@id': schema:foundingDate + '@type': Date + foundingLocation: + '@id': schema:foundingLocation + free: + '@id': schema:free + freeShippingThreshold: + '@id': schema:freeShippingThreshold + frequency: + '@id': schema:frequency + fromLocation: + '@id': schema:fromLocation + fuelCapacity: + '@id': schema:fuelCapacity + fuelConsumption: + '@id': schema:fuelConsumption + fuelEfficiency: + '@id': schema:fuelEfficiency + fuelType: + '@id': schema:fuelType + functionalClass: + '@id': schema:functionalClass + fundedItem: + '@id': schema:fundedItem + funder: + '@id': schema:funder + game: + '@id': schema:game + gameItem: + '@id': schema:gameItem + gameLocation: + '@id': schema:gameLocation + '@type': '@id' + gamePlatform: + '@id': schema:gamePlatform + gameServer: + '@id': schema:gameServer + gameTip: + '@id': schema:gameTip + gender: + '@id': schema:gender + genre: + '@id': schema:genre + geo: + '@id': schema:geo + geoContains: + '@id': schema:geoContains + geoCoveredBy: + '@id': schema:geoCoveredBy + geoCovers: + '@id': schema:geoCovers + geoCrosses: + '@id': schema:geoCrosses + geoDisjoint: + '@id': schema:geoDisjoint + geoEquals: + '@id': schema:geoEquals + geoIntersects: + '@id': schema:geoIntersects + geoMidpoint: + '@id': schema:geoMidpoint + geoOverlaps: + '@id': schema:geoOverlaps + geoRadius: + '@id': schema:geoRadius + geoTouches: + '@id': schema:geoTouches + geoWithin: + '@id': schema:geoWithin + geographicArea: + '@id': schema:geographicArea + gettingTestedInfo: + '@id': schema:gettingTestedInfo + '@type': '@id' + givenName: + '@id': schema:givenName + globalLocationNumber: + '@id': schema:globalLocationNumber + governmentBenefitsInfo: + '@id': schema:governmentBenefitsInfo + gracePeriod: + '@id': schema:gracePeriod + grantee: + '@id': schema:grantee + greater: + '@id': schema:greater + greaterOrEqual: + '@id': schema:greaterOrEqual + gtin: + '@id': schema:gtin + gtin12: + '@id': schema:gtin12 + gtin13: + '@id': schema:gtin13 + gtin14: + '@id': schema:gtin14 + gtin8: + '@id': schema:gtin8 + guideline: + '@id': schema:guideline + guidelineDate: + '@id': schema:guidelineDate + '@type': Date + guidelineSubject: + '@id': schema:guidelineSubject + handlingTime: + '@id': schema:handlingTime + hasBroadcastChannel: + '@id': schema:hasBroadcastChannel + hasCategoryCode: + '@id': schema:hasCategoryCode + hasCourse: + '@id': schema:hasCourse + hasCourseInstance: + '@id': schema:hasCourseInstance + hasCredential: + '@id': schema:hasCredential + hasDefinedTerm: + '@id': schema:hasDefinedTerm + hasDeliveryMethod: + '@id': schema:hasDeliveryMethod + hasDigitalDocumentPermission: + '@id': schema:hasDigitalDocumentPermission + hasDriveThroughService: + '@id': schema:hasDriveThroughService + hasEnergyConsumptionDetails: + '@id': schema:hasEnergyConsumptionDetails + hasEnergyEfficiencyCategory: + '@id': schema:hasEnergyEfficiencyCategory + hasHealthAspect: + '@id': schema:hasHealthAspect + hasMap: + '@id': schema:hasMap + '@type': '@id' + hasMenu: + '@id': schema:hasMenu + hasMenuItem: + '@id': schema:hasMenuItem + hasMenuSection: + '@id': schema:hasMenuSection + hasMerchantReturnPolicy: + '@id': schema:hasMerchantReturnPolicy + hasOccupation: + '@id': schema:hasOccupation + hasOfferCatalog: + '@id': schema:hasOfferCatalog + hasPOS: + '@id': schema:hasPOS + hasPart: + '@id': schema:hasPart + hasProductReturnPolicy: + '@id': schema:hasProductReturnPolicy + hasVariant: + '@id': schema:hasVariant + headline: + '@id': schema:headline + healthCondition: + '@id': schema:healthCondition + healthPlanCoinsuranceOption: + '@id': schema:healthPlanCoinsuranceOption + healthPlanCoinsuranceRate: + '@id': schema:healthPlanCoinsuranceRate + healthPlanCopay: + '@id': schema:healthPlanCopay + healthPlanCopayOption: + '@id': schema:healthPlanCopayOption + healthPlanCostSharing: + '@id': schema:healthPlanCostSharing + healthPlanDrugOption: + '@id': schema:healthPlanDrugOption + healthPlanDrugTier: + '@id': schema:healthPlanDrugTier + healthPlanId: + '@id': schema:healthPlanId + healthPlanMarketingUrl: + '@id': schema:healthPlanMarketingUrl + '@type': '@id' + healthPlanNetworkId: + '@id': schema:healthPlanNetworkId + healthPlanNetworkTier: + '@id': schema:healthPlanNetworkTier + healthPlanPharmacyCategory: + '@id': schema:healthPlanPharmacyCategory + healthcareReportingData: + '@id': schema:healthcareReportingData + height: + '@id': schema:height + highPrice: + '@id': schema:highPrice + hiringOrganization: + '@id': schema:hiringOrganization + holdingArchive: + '@id': schema:holdingArchive + homeLocation: + '@id': schema:homeLocation + homeTeam: + '@id': schema:homeTeam + honorificPrefix: + '@id': schema:honorificPrefix + honorificSuffix: + '@id': schema:honorificSuffix + hospitalAffiliation: + '@id': schema:hospitalAffiliation + hostingOrganization: + '@id': schema:hostingOrganization + hoursAvailable: + '@id': schema:hoursAvailable + howPerformed: + '@id': schema:howPerformed + http://publications.europa.eu/mdr/eli/index.html: + '@id': http://publications.europa.eu/mdr/eli/index.html + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#Automotive_Ontology_Working_Group: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#Automotive_Ontology_Working_Group + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#FIBO: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#FIBO + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#GLEIF: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#GLEIF + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#IIT-CNR.it: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#IIT-CNR.it + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#MBZ: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#MBZ + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#Tourism: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#Tourism + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_ActionCollabClass: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_ActionCollabClass + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_DatasetClass: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_DatasetClass + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_GoodRelationsClass: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_GoodRelationsClass + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_GoodRelationsTerms: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_GoodRelationsTerms + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_LRMIClass: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_LRMIClass + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_QAStackExchange: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_QAStackExchange + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_WikiDoc: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_WikiDoc + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_bibex: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_bibex + http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_rNews: + '@id': http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_rNews + httpMethod: + '@id': schema:httpMethod + https://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#STI_Accommodation_Ontology: + '@id': https://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#STI_Accommodation_Ontology + https://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#TP: + '@id': https://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#TP + https://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#TP-draws: + '@id': https://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#TP-draws + iataCode: + '@id': schema:iataCode + icaoCode: + '@id': schema:icaoCode + id: '@id' + identifier: + '@id': schema:identifier + identifyingExam: + '@id': schema:identifyingExam + identifyingTest: + '@id': schema:identifyingTest + illustrator: + '@id': schema:illustrator + image: + '@id': schema:image + '@type': '@id' + imagingTechnique: + '@id': schema:imagingTechnique + inAlbum: + '@id': schema:inAlbum + inBroadcastLineup: + '@id': schema:inBroadcastLineup + inCodeSet: + '@id': schema:inCodeSet + '@type': '@id' + inDefinedTermSet: + '@id': schema:inDefinedTermSet + '@type': '@id' + inLanguage: + '@id': schema:inLanguage + inPlaylist: + '@id': schema:inPlaylist + inProductGroupWithID: + '@id': schema:inProductGroupWithID + inStoreReturnsOffered: + '@id': schema:inStoreReturnsOffered + inSupportOf: + '@id': schema:inSupportOf + incentiveCompensation: + '@id': schema:incentiveCompensation + incentives: + '@id': schema:incentives + includedComposition: + '@id': schema:includedComposition + includedDataCatalog: + '@id': schema:includedDataCatalog + includedInDataCatalog: + '@id': schema:includedInDataCatalog + includedInHealthInsurancePlan: + '@id': schema:includedInHealthInsurancePlan + includedRiskFactor: + '@id': schema:includedRiskFactor + includesAttraction: + '@id': schema:includesAttraction + includesHealthPlanFormulary: + '@id': schema:includesHealthPlanFormulary + includesHealthPlanNetwork: + '@id': schema:includesHealthPlanNetwork + includesObject: + '@id': schema:includesObject + increasesRiskOf: + '@id': schema:increasesRiskOf + industry: + '@id': schema:industry + ineligibleRegion: + '@id': schema:ineligibleRegion + infectiousAgent: + '@id': schema:infectiousAgent + infectiousAgentClass: + '@id': schema:infectiousAgentClass + ingredients: + '@id': schema:ingredients + inker: + '@id': schema:inker + insertion: + '@id': schema:insertion + installUrl: + '@id': schema:installUrl + '@type': '@id' + instructor: + '@id': schema:instructor + instrument: + '@id': schema:instrument + intensity: + '@id': schema:intensity + interactingDrug: + '@id': schema:interactingDrug + interactionCount: + '@id': schema:interactionCount + interactionService: + '@id': schema:interactionService + interactionStatistic: + '@id': schema:interactionStatistic + interactionType: + '@id': schema:interactionType + interactivityType: + '@id': schema:interactivityType + interestRate: + '@id': schema:interestRate + inventoryLevel: + '@id': schema:inventoryLevel + inverseOf: + '@id': schema:inverseOf + isAcceptingNewPatients: + '@id': schema:isAcceptingNewPatients + isAccessibleForFree: + '@id': schema:isAccessibleForFree + isAccessoryOrSparePartFor: + '@id': schema:isAccessoryOrSparePartFor + isAvailableGenerically: + '@id': schema:isAvailableGenerically + isBasedOn: + '@id': schema:isBasedOn + '@type': '@id' + isBasedOnUrl: + '@id': schema:isBasedOnUrl + '@type': '@id' + isConsumableFor: + '@id': schema:isConsumableFor + isFamilyFriendly: + '@id': schema:isFamilyFriendly + isGift: + '@id': schema:isGift + isLiveBroadcast: + '@id': schema:isLiveBroadcast + isPartOf: + '@id': schema:isPartOf + '@type': '@id' + isPlanForApartment: + '@id': schema:isPlanForApartment + isProprietary: + '@id': schema:isProprietary + isRelatedTo: + '@id': schema:isRelatedTo + isResizable: + '@id': schema:isResizable + isSimilarTo: + '@id': schema:isSimilarTo + isUnlabelledFallback: + '@id': schema:isUnlabelledFallback + isVariantOf: + '@id': schema:isVariantOf + isbn: + '@id': schema:isbn + isicV4: + '@id': schema:isicV4 + isrcCode: + '@id': schema:isrcCode + issn: + '@id': schema:issn + issueNumber: + '@id': schema:issueNumber + issuedBy: + '@id': schema:issuedBy + issuedThrough: + '@id': schema:issuedThrough + iswcCode: + '@id': schema:iswcCode + item: + '@id': schema:item + itemCondition: + '@id': schema:itemCondition + itemListElement: + '@id': schema:itemListElement + itemListOrder: + '@id': schema:itemListOrder + itemLocation: + '@id': schema:itemLocation + itemOffered: + '@id': schema:itemOffered + itemReviewed: + '@id': schema:itemReviewed + itemShipped: + '@id': schema:itemShipped + itinerary: + '@id': schema:itinerary + jobBenefits: + '@id': schema:jobBenefits + jobImmediateStart: + '@id': schema:jobImmediateStart + jobLocation: + '@id': schema:jobLocation + jobLocationType: + '@id': schema:jobLocationType + jobStartDate: + '@id': schema:jobStartDate + jobTitle: + '@id': schema:jobTitle + jurisdiction: + '@id': schema:jurisdiction + keywords: + '@id': schema:keywords + knownVehicleDamages: + '@id': schema:knownVehicleDamages + knows: + '@id': schema:knows + knowsAbout: + '@id': schema:knowsAbout + knowsLanguage: + '@id': schema:knowsLanguage + labelDetails: + '@id': schema:labelDetails + '@type': '@id' + landlord: + '@id': schema:landlord + language: + '@id': schema:language + lastReviewed: + '@id': schema:lastReviewed + '@type': Date + latitude: + '@id': schema:latitude + layoutImage: + '@id': schema:layoutImage + '@type': '@id' + learningResourceType: + '@id': schema:learningResourceType + leaseLength: + '@id': schema:leaseLength + legalName: + '@id': schema:legalName + legalStatus: + '@id': schema:legalStatus + legislationApplies: + '@id': schema:legislationApplies + legislationChanges: + '@id': schema:legislationChanges + legislationConsolidates: + '@id': schema:legislationConsolidates + legislationDate: + '@id': schema:legislationDate + '@type': Date + legislationDateVersion: + '@id': schema:legislationDateVersion + '@type': Date + legislationIdentifier: + '@id': schema:legislationIdentifier + legislationJurisdiction: + '@id': schema:legislationJurisdiction + legislationLegalForce: + '@id': schema:legislationLegalForce + legislationLegalValue: + '@id': schema:legislationLegalValue + legislationPassedBy: + '@id': schema:legislationPassedBy + legislationResponsible: + '@id': schema:legislationResponsible + legislationTransposes: + '@id': schema:legislationTransposes + legislationType: + '@id': schema:legislationType + leiCode: + '@id': schema:leiCode + lender: + '@id': schema:lender + lesser: + '@id': schema:lesser + lesserOrEqual: + '@id': schema:lesserOrEqual + letterer: + '@id': schema:letterer + license: + '@id': schema:license + '@type': '@id' + line: + '@id': schema:line + linkRelationship: + '@id': schema:linkRelationship + liveBlogUpdate: + '@id': schema:liveBlogUpdate + loanMortgageMandateAmount: + '@id': schema:loanMortgageMandateAmount + loanPaymentAmount: + '@id': schema:loanPaymentAmount + loanPaymentFrequency: + '@id': schema:loanPaymentFrequency + loanRepaymentForm: + '@id': schema:loanRepaymentForm + loanTerm: + '@id': schema:loanTerm + loanType: + '@id': schema:loanType + location: + '@id': schema:location + locationCreated: + '@id': schema:locationCreated + lodgingUnitDescription: + '@id': schema:lodgingUnitDescription + lodgingUnitType: + '@id': schema:lodgingUnitType + logo: + '@id': schema:logo + '@type': '@id' + longitude: + '@id': schema:longitude + loser: + '@id': schema:loser + lowPrice: + '@id': schema:lowPrice + lyricist: + '@id': schema:lyricist + lyrics: + '@id': schema:lyrics + mainContentOfPage: + '@id': schema:mainContentOfPage + mainEntity: + '@id': schema:mainEntity + mainEntityOfPage: + '@id': schema:mainEntityOfPage + '@type': '@id' + maintainer: + '@id': schema:maintainer + makesOffer: + '@id': schema:makesOffer + manufacturer: + '@id': schema:manufacturer + map: + '@id': schema:map + '@type': '@id' + mapType: + '@id': schema:mapType + maps: + '@id': schema:maps + '@type': '@id' + marginOfError: + '@id': schema:marginOfError + '@type': DateTime + masthead: + '@id': schema:masthead + '@type': '@id' + material: + '@id': schema:material + materialExtent: + '@id': schema:materialExtent + maxPrice: + '@id': schema:maxPrice + maxValue: + '@id': schema:maxValue + maximumAttendeeCapacity: + '@id': schema:maximumAttendeeCapacity + maximumEnrollment: + '@id': schema:maximumEnrollment + maximumIntake: + '@id': schema:maximumIntake + maximumPhysicalAttendeeCapacity: + '@id': schema:maximumPhysicalAttendeeCapacity + maximumVirtualAttendeeCapacity: + '@id': schema:maximumVirtualAttendeeCapacity + mealService: + '@id': schema:mealService + measuredProperty: + '@id': schema:measuredProperty + measuredValue: + '@id': schema:measuredValue + measurementTechnique: + '@id': schema:measurementTechnique + mechanismOfAction: + '@id': schema:mechanismOfAction + mediaAuthenticityCategory: + '@id': schema:mediaAuthenticityCategory + median: + '@id': schema:median + medicalAudience: + '@id': schema:medicalAudience + medicalSpecialty: + '@id': schema:medicalSpecialty + medicineSystem: + '@id': schema:medicineSystem + meetsEmissionStandard: + '@id': schema:meetsEmissionStandard + member: + '@id': schema:member + memberOf: + '@id': schema:memberOf + members: + '@id': schema:members + membershipNumber: + '@id': schema:membershipNumber + membershipPointsEarned: + '@id': schema:membershipPointsEarned + memoryRequirements: + '@id': schema:memoryRequirements + mentions: + '@id': schema:mentions + menu: + '@id': schema:menu + menuAddOn: + '@id': schema:menuAddOn + merchant: + '@id': schema:merchant + merchantReturnDays: + '@id': schema:merchantReturnDays + merchantReturnLink: + '@id': schema:merchantReturnLink + '@type': '@id' + messageAttachment: + '@id': schema:messageAttachment + mileageFromOdometer: + '@id': schema:mileageFromOdometer + minPrice: + '@id': schema:minPrice + minValue: + '@id': schema:minValue + minimumPaymentDue: + '@id': schema:minimumPaymentDue + missionCoveragePrioritiesPolicy: + '@id': schema:missionCoveragePrioritiesPolicy + '@type': '@id' + model: + '@id': schema:model + modelDate: + '@id': schema:modelDate + '@type': Date + modifiedTime: + '@id': schema:modifiedTime + '@type': DateTime + monthlyMinimumRepaymentAmount: + '@id': schema:monthlyMinimumRepaymentAmount + mpn: + '@id': schema:mpn + multipleValues: + '@id': schema:multipleValues + muscleAction: + '@id': schema:muscleAction + musicArrangement: + '@id': schema:musicArrangement + musicBy: + '@id': schema:musicBy + musicCompositionForm: + '@id': schema:musicCompositionForm + musicGroupMember: + '@id': schema:musicGroupMember + musicReleaseFormat: + '@id': schema:musicReleaseFormat + musicalKey: + '@id': schema:musicalKey + naics: + '@id': schema:naics + name: + '@id': schema:name + namedPosition: + '@id': schema:namedPosition + nationality: + '@id': schema:nationality + naturalProgression: + '@id': schema:naturalProgression + nerve: + '@id': schema:nerve + nerveMotor: + '@id': schema:nerveMotor + netWorth: + '@id': schema:netWorth + newsUpdatesAndGuidelines: + '@id': schema:newsUpdatesAndGuidelines + '@type': '@id' + nextItem: + '@id': schema:nextItem + noBylinesPolicy: + '@id': schema:noBylinesPolicy + '@type': '@id' + nonEqual: + '@id': schema:nonEqual + nonProprietaryName: + '@id': schema:nonProprietaryName + nonprofitStatus: + '@id': schema:nonprofitStatus + normalRange: + '@id': schema:normalRange + nsn: + '@id': schema:nsn + numAdults: + '@id': schema:numAdults + numChildren: + '@id': schema:numChildren + numConstraints: + '@id': schema:numConstraints + numTracks: + '@id': schema:numTracks + numberOfAccommodationUnits: + '@id': schema:numberOfAccommodationUnits + numberOfAirbags: + '@id': schema:numberOfAirbags + numberOfAvailableAccommodationUnits: + '@id': schema:numberOfAvailableAccommodationUnits + numberOfAxles: + '@id': schema:numberOfAxles + numberOfBathroomsTotal: + '@id': schema:numberOfBathroomsTotal + numberOfBedrooms: + '@id': schema:numberOfBedrooms + numberOfBeds: + '@id': schema:numberOfBeds + numberOfCredits: + '@id': schema:numberOfCredits + numberOfDoors: + '@id': schema:numberOfDoors + numberOfEmployees: + '@id': schema:numberOfEmployees + numberOfEpisodes: + '@id': schema:numberOfEpisodes + numberOfForwardGears: + '@id': schema:numberOfForwardGears + numberOfFullBathrooms: + '@id': schema:numberOfFullBathrooms + numberOfItems: + '@id': schema:numberOfItems + numberOfLoanPayments: + '@id': schema:numberOfLoanPayments + numberOfPages: + '@id': schema:numberOfPages + numberOfPartialBathrooms: + '@id': schema:numberOfPartialBathrooms + numberOfPlayers: + '@id': schema:numberOfPlayers + numberOfPreviousOwners: + '@id': schema:numberOfPreviousOwners + numberOfRooms: + '@id': schema:numberOfRooms + numberOfSeasons: + '@id': schema:numberOfSeasons + numberedPosition: + '@id': schema:numberedPosition + nutrition: + '@id': schema:nutrition + object: + '@id': schema:object + observationDate: + '@id': schema:observationDate + '@type': DateTime + observedNode: + '@id': schema:observedNode + occupancy: + '@id': schema:occupancy + occupationLocation: + '@id': schema:occupationLocation + occupationalCategory: + '@id': schema:occupationalCategory + occupationalCredentialAwarded: + '@id': schema:occupationalCredentialAwarded + offerCount: + '@id': schema:offerCount + offeredBy: + '@id': schema:offeredBy + offers: + '@id': schema:offers + offersPrescriptionByMail: + '@id': schema:offersPrescriptionByMail + openingHours: + '@id': schema:openingHours + openingHoursSpecification: + '@id': schema:openingHoursSpecification + opens: + '@id': schema:opens + operatingSystem: + '@id': schema:operatingSystem + opponent: + '@id': schema:opponent + option: + '@id': schema:option + orderDate: + '@id': schema:orderDate + '@type': Date + orderDelivery: + '@id': schema:orderDelivery + orderItemNumber: + '@id': schema:orderItemNumber + orderItemStatus: + '@id': schema:orderItemStatus + orderNumber: + '@id': schema:orderNumber + orderQuantity: + '@id': schema:orderQuantity + orderStatus: + '@id': schema:orderStatus + orderedItem: + '@id': schema:orderedItem + organizer: + '@id': schema:organizer + originAddress: + '@id': schema:originAddress + originatesFrom: + '@id': schema:originatesFrom + overdosage: + '@id': schema:overdosage + owl: http://www.w3.org/2002/07/owl# + ownedFrom: + '@id': schema:ownedFrom + '@type': DateTime + ownedThrough: + '@id': schema:ownedThrough + '@type': DateTime + ownershipFundingInfo: + '@id': schema:ownershipFundingInfo + owns: + '@id': schema:owns + pageEnd: + '@id': schema:pageEnd + pageStart: + '@id': schema:pageStart + pagination: + '@id': schema:pagination + parent: + '@id': schema:parent + parentItem: + '@id': schema:parentItem + parentOrganization: + '@id': schema:parentOrganization + parentService: + '@id': schema:parentService + parents: + '@id': schema:parents + partOfEpisode: + '@id': schema:partOfEpisode + partOfInvoice: + '@id': schema:partOfInvoice + partOfOrder: + '@id': schema:partOfOrder + partOfSeason: + '@id': schema:partOfSeason + partOfSeries: + '@id': schema:partOfSeries + partOfSystem: + '@id': schema:partOfSystem + partOfTVSeries: + '@id': schema:partOfTVSeries + partOfTrip: + '@id': schema:partOfTrip + participant: + '@id': schema:participant + partySize: + '@id': schema:partySize + passengerPriorityStatus: + '@id': schema:passengerPriorityStatus + passengerSequenceNumber: + '@id': schema:passengerSequenceNumber + pathophysiology: + '@id': schema:pathophysiology + pattern: + '@id': schema:pattern + payload: + '@id': schema:payload + paymentAccepted: + '@id': schema:paymentAccepted + paymentDue: + '@id': schema:paymentDue + '@type': DateTime + paymentDueDate: + '@id': schema:paymentDueDate + '@type': Date + paymentMethod: + '@id': schema:paymentMethod + paymentMethodId: + '@id': schema:paymentMethodId + paymentStatus: + '@id': schema:paymentStatus + paymentUrl: + '@id': schema:paymentUrl + '@type': '@id' + penciler: + '@id': schema:penciler + percentile10: + '@id': schema:percentile10 + percentile25: + '@id': schema:percentile25 + percentile75: + '@id': schema:percentile75 + percentile90: + '@id': schema:percentile90 + performTime: + '@id': schema:performTime + performer: + '@id': schema:performer + performerIn: + '@id': schema:performerIn + performers: + '@id': schema:performers + permissionType: + '@id': schema:permissionType + permissions: + '@id': schema:permissions + permitAudience: + '@id': schema:permitAudience + permittedUsage: + '@id': schema:permittedUsage + petsAllowed: + '@id': schema:petsAllowed + phoneticText: + '@id': schema:phoneticText + photo: + '@id': schema:photo + photos: + '@id': schema:photos + physicalRequirement: + '@id': schema:physicalRequirement + physiologicalBenefits: + '@id': schema:physiologicalBenefits + pickupLocation: + '@id': schema:pickupLocation + pickupTime: + '@id': schema:pickupTime + '@type': DateTime + playMode: + '@id': schema:playMode + playerType: + '@id': schema:playerType + playersOnline: + '@id': schema:playersOnline + polygon: + '@id': schema:polygon + populationType: + '@id': schema:populationType + position: + '@id': schema:position + possibleComplication: + '@id': schema:possibleComplication + possibleTreatment: + '@id': schema:possibleTreatment + postOfficeBoxNumber: + '@id': schema:postOfficeBoxNumber + postOp: + '@id': schema:postOp + postalCode: + '@id': schema:postalCode + postalCodeBegin: + '@id': schema:postalCodeBegin + postalCodeEnd: + '@id': schema:postalCodeEnd + postalCodePrefix: + '@id': schema:postalCodePrefix + postalCodeRange: + '@id': schema:postalCodeRange + potentialAction: + '@id': schema:potentialAction + preOp: + '@id': schema:preOp + predecessorOf: + '@id': schema:predecessorOf + pregnancyCategory: + '@id': schema:pregnancyCategory + pregnancyWarning: + '@id': schema:pregnancyWarning + prepTime: + '@id': schema:prepTime + preparation: + '@id': schema:preparation + prescribingInfo: + '@id': schema:prescribingInfo + '@type': '@id' + prescriptionStatus: + '@id': schema:prescriptionStatus + previousItem: + '@id': schema:previousItem + previousStartDate: + '@id': schema:previousStartDate + '@type': Date + price: + '@id': schema:price + priceComponent: + '@id': schema:priceComponent + priceCurrency: + '@id': schema:priceCurrency + priceRange: + '@id': schema:priceRange + priceSpecification: + '@id': schema:priceSpecification + priceType: + '@id': schema:priceType + priceValidUntil: + '@id': schema:priceValidUntil + '@type': Date + primaryImageOfPage: + '@id': schema:primaryImageOfPage + primaryPrevention: + '@id': schema:primaryPrevention + printColumn: + '@id': schema:printColumn + printEdition: + '@id': schema:printEdition + printPage: + '@id': schema:printPage + printSection: + '@id': schema:printSection + procedure: + '@id': schema:procedure + procedureType: + '@id': schema:procedureType + processingTime: + '@id': schema:processingTime + processorRequirements: + '@id': schema:processorRequirements + producer: + '@id': schema:producer + produces: + '@id': schema:produces + productGroupID: + '@id': schema:productGroupID + productID: + '@id': schema:productID + productReturnDays: + '@id': schema:productReturnDays + productReturnLink: + '@id': schema:productReturnLink + '@type': '@id' + productSupported: + '@id': schema:productSupported + productionCompany: + '@id': schema:productionCompany + productionDate: + '@id': schema:productionDate + '@type': Date + proficiencyLevel: + '@id': schema:proficiencyLevel + programMembershipUsed: + '@id': schema:programMembershipUsed + programName: + '@id': schema:programName + programPrerequisites: + '@id': schema:programPrerequisites + programType: + '@id': schema:programType + programmingLanguage: + '@id': schema:programmingLanguage + programmingModel: + '@id': schema:programmingModel + propertyID: + '@id': schema:propertyID + proprietaryName: + '@id': schema:proprietaryName + proteinContent: + '@id': schema:proteinContent + provider: + '@id': schema:provider + providerMobility: + '@id': schema:providerMobility + providesBroadcastService: + '@id': schema:providesBroadcastService + providesService: + '@id': schema:providesService + publicAccess: + '@id': schema:publicAccess + publicTransportClosuresInfo: + '@id': schema:publicTransportClosuresInfo + '@type': '@id' + publication: + '@id': schema:publication + publicationType: + '@id': schema:publicationType + publishedBy: + '@id': schema:publishedBy + publishedOn: + '@id': schema:publishedOn + publisher: + '@id': schema:publisher + publisherImprint: + '@id': schema:publisherImprint + publishingPrinciples: + '@id': schema:publishingPrinciples + '@type': '@id' + purchaseDate: + '@id': schema:purchaseDate + '@type': Date + qualifications: + '@id': schema:qualifications + quarantineGuidelines: + '@id': schema:quarantineGuidelines + '@type': '@id' + query: + '@id': schema:query + quest: + '@id': schema:quest + question: + '@id': schema:question + rangeIncludes: + '@id': schema:rangeIncludes + ratingCount: + '@id': schema:ratingCount + ratingExplanation: + '@id': schema:ratingExplanation + ratingValue: + '@id': schema:ratingValue + rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# + rdfa: http://www.w3.org/ns/rdfa# + rdfs: http://www.w3.org/2000/01/rdf-schema# + readBy: + '@id': schema:readBy + readonlyValue: + '@id': schema:readonlyValue + realEstateAgent: + '@id': schema:realEstateAgent + recipe: + '@id': schema:recipe + recipeCategory: + '@id': schema:recipeCategory + recipeCuisine: + '@id': schema:recipeCuisine + recipeIngredient: + '@id': schema:recipeIngredient + recipeInstructions: + '@id': schema:recipeInstructions + recipeYield: + '@id': schema:recipeYield + recipient: + '@id': schema:recipient + recognizedBy: + '@id': schema:recognizedBy + recognizingAuthority: + '@id': schema:recognizingAuthority + recommendationStrength: + '@id': schema:recommendationStrength + recommendedIntake: + '@id': schema:recommendedIntake + recordLabel: + '@id': schema:recordLabel + recordedAs: + '@id': schema:recordedAs + recordedAt: + '@id': schema:recordedAt + recordedIn: + '@id': schema:recordedIn + recordingOf: + '@id': schema:recordingOf + recourseLoan: + '@id': schema:recourseLoan + referenceQuantity: + '@id': schema:referenceQuantity + referencesOrder: + '@id': schema:referencesOrder + refundType: + '@id': schema:refundType + regionDrained: + '@id': schema:regionDrained + regionsAllowed: + '@id': schema:regionsAllowed + relatedAnatomy: + '@id': schema:relatedAnatomy + relatedCondition: + '@id': schema:relatedCondition + relatedDrug: + '@id': schema:relatedDrug + relatedLink: + '@id': schema:relatedLink + '@type': '@id' + relatedStructure: + '@id': schema:relatedStructure + relatedTherapy: + '@id': schema:relatedTherapy + relatedTo: + '@id': schema:relatedTo + releaseDate: + '@id': schema:releaseDate + '@type': Date + releaseNotes: + '@id': schema:releaseNotes + releaseOf: + '@id': schema:releaseOf + releasedEvent: + '@id': schema:releasedEvent + relevantOccupation: + '@id': schema:relevantOccupation + relevantSpecialty: + '@id': schema:relevantSpecialty + remainingAttendeeCapacity: + '@id': schema:remainingAttendeeCapacity + renegotiableLoan: + '@id': schema:renegotiableLoan + repeatCount: + '@id': schema:repeatCount + repeatFrequency: + '@id': schema:repeatFrequency + repetitions: + '@id': schema:repetitions + replacee: + '@id': schema:replacee + replacer: + '@id': schema:replacer + replyToUrl: + '@id': schema:replyToUrl + '@type': '@id' + reportNumber: + '@id': schema:reportNumber + representativeOfPage: + '@id': schema:representativeOfPage + requiredCollateral: + '@id': schema:requiredCollateral + requiredGender: + '@id': schema:requiredGender + requiredMaxAge: + '@id': schema:requiredMaxAge + requiredMinAge: + '@id': schema:requiredMinAge + requiredQuantity: + '@id': schema:requiredQuantity + requirements: + '@id': schema:requirements + requiresSubscription: + '@id': schema:requiresSubscription + reservationFor: + '@id': schema:reservationFor + reservationId: + '@id': schema:reservationId + reservationStatus: + '@id': schema:reservationStatus + reservedTicket: + '@id': schema:reservedTicket + responsibilities: + '@id': schema:responsibilities + restPeriods: + '@id': schema:restPeriods + result: + '@id': 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servicePostalAddress: + '@id': schema:servicePostalAddress + serviceSmsNumber: + '@id': schema:serviceSmsNumber + serviceType: + '@id': schema:serviceType + serviceUrl: + '@id': schema:serviceUrl + '@type': '@id' + servingSize: + '@id': schema:servingSize + sharedContent: + '@id': schema:sharedContent + shippingDestination: + '@id': schema:shippingDestination + shippingDetails: + '@id': schema:shippingDetails + shippingLabel: + '@id': schema:shippingLabel + shippingRate: + '@id': schema:shippingRate + shippingSettingsLink: + '@id': schema:shippingSettingsLink + '@type': '@id' + sibling: + '@id': schema:sibling + siblings: + '@id': schema:siblings + signDetected: + '@id': schema:signDetected + signOrSymptom: + '@id': schema:signOrSymptom + significance: + '@id': schema:significance + significantLink: + '@id': schema:significantLink + '@type': '@id' + significantLinks: + '@id': schema:significantLinks + '@type': '@id' + size: + '@id': schema:size + skills: + '@id': schema:skills + skos: 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schema:superEvent + supersededBy: + '@id': schema:supersededBy + supply: + '@id': schema:supply + supplyTo: + '@id': schema:supplyTo + supportingData: + '@id': schema:supportingData + surface: + '@id': schema:surface + target: + '@id': schema:target + targetCollection: + '@id': schema:targetCollection + targetDescription: + '@id': schema:targetDescription + targetName: + '@id': schema:targetName + targetPlatform: + '@id': schema:targetPlatform + targetPopulation: + '@id': schema:targetPopulation + targetProduct: + '@id': schema:targetProduct + targetUrl: + '@id': schema:targetUrl + '@type': '@id' + taxID: + '@id': schema:taxID + teaches: + '@id': schema:teaches + telephone: + '@id': schema:telephone + temporal: + '@id': schema:temporal + temporalCoverage: + '@id': schema:temporalCoverage + termCode: + '@id': schema:termCode + termDuration: + '@id': schema:termDuration + termsOfService: + '@id': schema:termsOfService + termsPerYear: + '@id': schema:termsPerYear + text: + '@id': schema:text + textValue: + '@id': schema:textValue + thumbnail: + '@id': schema:thumbnail + thumbnailUrl: + '@id': schema:thumbnailUrl + '@type': '@id' + tickerSymbol: + '@id': schema:tickerSymbol + ticketNumber: + '@id': schema:ticketNumber + ticketToken: + '@id': schema:ticketToken + ticketedSeat: + '@id': schema:ticketedSeat + timeOfDay: + '@id': schema:timeOfDay + timeRequired: + '@id': schema:timeRequired + timeToComplete: + '@id': schema:timeToComplete + tissueSample: + '@id': schema:tissueSample + title: + '@id': schema:title + titleEIDR: + '@id': schema:titleEIDR + toLocation: + '@id': schema:toLocation + toRecipient: + '@id': schema:toRecipient + tongueWeight: + '@id': schema:tongueWeight + tool: + '@id': schema:tool + torque: + '@id': schema:torque + totalJobOpenings: + '@id': schema:totalJobOpenings + totalPaymentDue: + '@id': schema:totalPaymentDue + totalPrice: + '@id': schema:totalPrice + totalTime: + '@id': schema:totalTime + tourBookingPage: + '@id': 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schema:typeOfBed + typeOfGood: + '@id': schema:typeOfGood + typicalAgeRange: + '@id': schema:typicalAgeRange + typicalCreditsPerTerm: + '@id': schema:typicalCreditsPerTerm + typicalTest: + '@id': schema:typicalTest + underName: + '@id': schema:underName + unitCode: + '@id': schema:unitCode + unitText: + '@id': schema:unitText + unnamedSourcesPolicy: + '@id': schema:unnamedSourcesPolicy + '@type': '@id' + unsaturatedFatContent: + '@id': schema:unsaturatedFatContent + uploadDate: + '@id': schema:uploadDate + '@type': Date + upvoteCount: + '@id': schema:upvoteCount + url: + '@id': schema:url + '@type': '@id' + urlTemplate: + '@id': schema:urlTemplate + usageInfo: + '@id': schema:usageInfo + '@type': '@id' + usedToDiagnose: + '@id': schema:usedToDiagnose + userInteractionCount: + '@id': schema:userInteractionCount + usesDevice: + '@id': schema:usesDevice + usesHealthPlanIdStandard: + '@id': schema:usesHealthPlanIdStandard + validFor: + '@id': schema:validFor + validFrom: + '@id': schema:validFrom + '@type': Date + validIn: + '@id': schema:validIn + validThrough: + '@id': schema:validThrough + '@type': Date + validUntil: + '@id': schema:validUntil + '@type': Date + value: + '@id': schema:value + valueAddedTaxIncluded: + '@id': schema:valueAddedTaxIncluded + valueMaxLength: + '@id': schema:valueMaxLength + valueMinLength: + '@id': schema:valueMinLength + valueName: + '@id': schema:valueName + valuePattern: + '@id': schema:valuePattern + valueReference: + '@id': schema:valueReference + valueRequired: + '@id': schema:valueRequired + variableMeasured: + '@id': schema:variableMeasured + variablesMeasured: + '@id': schema:variablesMeasured + variantCover: + '@id': schema:variantCover + variesBy: + '@id': schema:variesBy + vatID: + '@id': schema:vatID + vehicleConfiguration: + '@id': schema:vehicleConfiguration + vehicleEngine: + '@id': schema:vehicleEngine + vehicleIdentificationNumber: + '@id': schema:vehicleIdentificationNumber + vehicleInteriorColor: + '@id': schema:vehicleInteriorColor + vehicleInteriorType: + '@id': schema:vehicleInteriorType + vehicleModelDate: + '@id': schema:vehicleModelDate + '@type': Date + vehicleSeatingCapacity: + '@id': schema:vehicleSeatingCapacity + vehicleSpecialUsage: + '@id': schema:vehicleSpecialUsage + vehicleTransmission: + '@id': schema:vehicleTransmission + vendor: + '@id': schema:vendor + verificationFactCheckingPolicy: + '@id': schema:verificationFactCheckingPolicy + '@type': '@id' + version: + '@id': schema:version + video: + '@id': schema:video + videoFormat: + '@id': schema:videoFormat + videoFrameSize: + '@id': schema:videoFrameSize + videoQuality: + '@id': schema:videoQuality + void: http://rdfs.org/ns/void# + volumeNumber: + '@id': schema:volumeNumber + warning: + '@id': schema:warning + warranty: + '@id': schema:warranty + warrantyPromise: + '@id': schema:warrantyPromise + warrantyScope: + '@id': schema:warrantyScope + webCheckinTime: + '@id': schema:webCheckinTime + '@type': DateTime + webFeed: + '@id': schema:webFeed + '@type': '@id' + weight: + '@id': schema:weight + weightTotal: + '@id': schema:weightTotal + wheelbase: + '@id': schema:wheelbase + width: + '@id': schema:width + winner: + '@id': schema:winner + wordCount: + '@id': schema:wordCount + workExample: + '@id': schema:workExample + workFeatured: + '@id': schema:workFeatured + workHours: + '@id': schema:workHours + workLocation: + '@id': schema:workLocation + workPerformed: + '@id': schema:workPerformed + workPresented: + '@id': schema:workPresented + workTranslation: + '@id': schema:workTranslation + workload: + '@id': schema:workload + worksFor: + '@id': schema:worksFor + worstRating: + '@id': schema:worstRating + xml: http://www.w3.org/XML/1998/namespace + xpath: + '@id': schema:xpath + xsd: http://www.w3.org/2001/XMLSchema# + yearBuilt: + '@id': schema:yearBuilt + yearlyRevenue: + '@id': schema:yearlyRevenue + yearsInOperation: + '@id': schema:yearsInOperation + yield: + '@id': schema:yield diff --git 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"http://contsem.unizar.es/def/sector-publico/pproc#", - "prefix": "pproc", - "title": "PPROC ontology", - "uri": "http://contsem.unizar.es/def/sector-publico/pproc" - }, - { - "namespace": "http://purl.org/ontology/prv/core#", - "prefix": "pr", - "title": "Property Reification Vocabulary", - "uri": "http://purl.org/ontology/prv/core#" - }, - { - "namespace": "http://www.loc.gov/premis/rdf/v1#", - "prefix": "premis", - "title": "PREMIS Ontology", - "uri": "http://www.loc.gov/premis/rdf/v1" - }, - { - "namespace": "http://ns.inria.fr/prissma/v2#", - "prefix": "prissma", - "title": "Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability", - "uri": "http://ns.inria.fr/prissma/v2#" - }, - { - "namespace": "http://purl.org/spar/pro/", - "prefix": "pro", - "title": "The Publishing Roles Ontology", - "uri": "http://purl.org/spar/pro" - }, - { - "namespace": "http://www.w3.org/ns/dx/prof/", - "prefix": "prof", - "title": "Profiles Vocabulary", - "uri": "http://www.w3.org/ns/dx/prof" - }, - { - "namespace": "http://www.w3.org/ns/prov#", - "prefix": "prov", - "title": "W3C PROVenance Interchange", - "uri": "http://www.w3.org/ns/prov#" - }, - { - "namespace": "http://ns.inria.fr/provoc#", - "prefix": "provoc", - "title": "Product Vocabulary", - "uri": "http://ns.inria.fr/provoc" - }, - { - "namespace": "http://purl.org/net/provenance/ns#", - "prefix": "prv", - "title": "Provenance Vocabulary Core Ontology", - "uri": "http://purl.org/net/provenance/ns#" - }, - { - "namespace": "http://purl.org/net/provenance/types#", - "prefix": "prvt", - "title": "Provenance Vocabulary types", - "uri": "http://purl.org/net/provenance/types#" - }, - { - "namespace": "http://purl.org/spar/pso/", - "prefix": "pso", - "title": "The Publishing Status Ontology", - "uri": "http://purl.org/spar/pso" - }, - { - "namespace": "http://www.ontotext.com/proton/protontop#", - "prefix": "ptop", - "title": "PROTON (Proto Ontology), Top Module", - "uri": "http://www.ontotext.com/proton/protontop" - }, - { - "namespace": "https://vocab.eccenca.com/pubsub/", - "prefix": "pubsub", - "title": "Eccenca Publish-Subscribe Vocabulary", - "uri": "https://vocab.eccenca.com/pubsub/" - }, - { - "namespace": "http://purl.org/spar/pwo/", - "prefix": "pwo", - "title": "The Publishing Workflow Ontology", - "uri": "http://purl.org/spar/pwo" - }, - { - "namespace": "http://purl.org/linked-data/cube#", - "prefix": "qb", - "title": "The data cube vocabulary", - "uri": "http://purl.org/linked-data/cube" - }, - { - "namespace": "http://purl.org/qb4olap/cubes#", - "prefix": "qb4o", - "title": "Vocabulary for publishing OLAP data cubes", - "uri": "http://purl.org/qb4olap/cubes" - }, - { - "namespace": "http://purl.oclc.org/NET/ssnx/qu/qu#", - "prefix": "qu", - "title": "Quantity Kinds and Units", - "uri": "http://purl.oclc.org/NET/ssnx/qu/qu" - }, - { - "namespace": "http://qudt.org/schema/qudt/", - "prefix": "qudt", - "title": "Quantities, Units, Dimensions and Types", - "uri": "http://qudt.org/schema/qudt" - }, - { - "namespace": "https://w3id.org/arco/ontology/arco/", - "prefix": "r-arco", - "title": "ArCo Ontology (ArCo network)", - "uri": "https://w3id.org/arco/ontology/arco" - }, - { - "namespace": "http://guava.iis.sinica.edu.tw/r4r/", - "prefix": "r4r", - "title": "Relations for Reusing (R4R) Ontology", - "uri": "http://guava.iis.sinica.edu.tw/r4r" - }, - { - "namespace": "http://www.w3.org/ns/radion#", - "prefix": "radion", - "title": "Repository Asset Distribution", - "uri": "http://www.w3.org/ns/radion#" - }, - { - "namespace": "http://iais.fraunhofer.de/vocabs/rami#", - "prefix": "rami", - "title": "rami - Reference Architecture Model", - "uri": "https://w3id.org/i40/rami/" - }, - { - "namespace": "http://purl.org/NET/raul#", - "prefix": "raul", - "title": "RAUL Vocabulary", - "uri": "http://vocab.deri.ie/raul" - }, - { - "namespace": "http://rdvocab.info/uri/schema/FRBRentitiesRDA/", - "prefix": "rdafrbr", - "title": "FRBR Entities for RDA", - "uri": "http://rdvocab.info/uri/schema/FRBRentitiesRDA" - }, - { - "namespace": "http://rdvocab.info/Elements/", - "prefix": "rdag1", - "title": "RDA Group 1 Elements", - "uri": "http://rdvocab.info/Elements" - }, - { - "namespace": "http://rdvocab.info/ElementsGr2/", - "prefix": "rdag2", - "title": "RDA Group 2 Elements", - "uri": "http://rdvocab.info/ElementsGr2" - }, - { - "namespace": "http://rdvocab.info/ElementsGr3/", - "prefix": "rdag3", - "title": "RDA Group 3 Elements", - "uri": "http://rdvocab.info/ElementsGr3" - }, - { - "namespace": "http://rdvocab.info/RDARelationshipsWEMI/", - "prefix": "rdarel", - "title": "RDA Relationships for Works, Expressions, Manifestations, Items", - "uri": "http://rdvocab.info/RDARelationshipsWEMI" - }, - { - "namespace": "http://metadataregistry.org/uri/schema/RDARelationshipsGR2/", - "prefix": "rdarel2", - "title": "RDA Relationships GR2", - "uri": "http://metadataregistry.org/uri/schema/RDARelationshipsGR2" - }, - { - "namespace": "http://rdvocab.info/roles/", - "prefix": "rdarole", - "title": "RDA Roles", - "uri": "http://rdvocab.info/roles" - }, - { - "namespace": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "prefix": "rdf", - "title": "The RDF Concepts Vocabulary", - "uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" - }, - { - "namespace": "http://www.w3.org/ns/rdfa#", - "prefix": "rdfa", - "title": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting", - "uri": "http://www.w3.org/ns/rdfa#" - }, - { - "namespace": "http://www.w3.org/2004/03/trix/rdfg-1/", - "prefix": "rdfg", - "title": "Graph", - "uri": "http://www.w3.org/2004/03/trix/rdfg-1/" - }, - { - "namespace": "https://w3id.org/rdfp/", - "prefix": "rdfp", - "title": "The RDF Presentation ontology", - "uri": "https://w3id.org/rdfp/" - }, - { - "namespace": "http://www.w3.org/2000/01/rdf-schema#", - "prefix": "rdfs", - "title": "The RDF Schema vocabulary", - "uri": "http://www.w3.org/2000/01/rdf-schema#" - }, - { - "namespace": "http://purl.org/ontology/rec/core#", - "prefix": "rec", - "title": "Recommendation Ontology", - "uri": "http://purl.org/ontology/rec/core#" - }, - { - "namespace": "http://www.w3.org/2001/02pd/rec54#", - "prefix": "rec54", - "title": "Model of the W3C Process", - "uri": "http://www.w3.org/2001/02pd/rec54#" - }, - { - "namespace": "http://purl.org/reco#", - "prefix": "reco", - "title": "RECommendations Ontology", - "uri": "http://purl.org/reco#" - }, - { - "namespace": "http://reegle.info/schema#", - "prefix": "reegle", - "title": "Renewable Energy and Energy Efficiency", - "uri": "http://reegle.info/schema" - }, - { - "namespace": "http://purl.org/vocab/relationship/", - "prefix": "rel", - "title": "Relationship", - "uri": "http://purl.org/vocab/relationship/" - }, - { - "namespace": "http://www.purl.org/net/remetca#", - "prefix": "remetca", - "title": "ReMetCa Ontology", - "uri": "http://www.purl.org/net/remetca#" - }, - { - "namespace": "http://purl.org/stuff/rev#", - "prefix": "rev", - "title": "Review Vocabulary", - "uri": "http://purl.org/stuff/rev#" - }, - { - "namespace": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#", - "prefix": "rlog", - "title": "RDF Logging Ontology", - "uri": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#" - }, - { - "namespace": "http://purl.org/wf4ever/ro#", - "prefix": "ro", - "title": "The Research Object Ontology", - "uri": "http://purl.org/wf4ever/ro" - }, - { - "namespace": "http://vocab.deri.ie/rooms#", - "prefix": "rooms", - "title": "Buildings and Rooms Vocabulary", - "uri": "http://vocab.deri.ie/rooms" - }, - { - "namespace": "http://www.w3.org/ns/regorg#", - "prefix": "rov", - "title": "Registered Organization Vocabulary", - "uri": "http://www.w3.org/ns/regorg" - }, - { - "namespace": "http://www.w3.org/ns/r2rml#", - "prefix": "rr", - "title": "RDB to RDF Mapping Language Schema", - "uri": "http://www.w3.org/ns/r2rml#" - }, - { - "namespace": "http://softeng.polito.it/rsctx#", - "prefix": "rsctx", - "title": "Recommender System Context", - "uri": "http://softeng.polito.it/rsctx" - }, - { - "namespace": "http://purl.org/rss/1.0/", - "prefix": "rss", - "title": "Vocabulary for Rich Site Summary (RSS) 1.0", - "uri": "http://purl.org/rss/1.0" - }, - { - "namespace": "http://purl.org/imbi/ru-meta.owl#", - "prefix": "ru", - "title": "Representational Units Metadata Ontology", - "uri": "http://purl.org/imbi/ru-meta.owl" - }, - { - "namespace": "http://rdfunit.aksw.org/ns/core#", - "prefix": "ruto", - "title": "Test-Driven Data Debugging Ontology", - "uri": "http://rdfunit.aksw.org/ns/core#" - }, - { - "namespace": "http://ns.inria.fr/s4ac/v2#", - "prefix": "s4ac", - "title": "Social Semantic SPARQL Security For Access Control Ontology", - "uri": "http://ns.inria.fr/s4ac/v2" - }, - { - "namespace": "https://w3id.org/def/saref4bldg#", - "prefix": "s4bldg", - "title": "SAREF extension for building devices", - "uri": "https://w3id.org/def/saref4bldg" - }, - { - "namespace": "https://w3id.org/saref4ee#", - "prefix": "s4ee", - "title": "SAREF4EE: the EEbus/Energy@home extension of SAREF", - "uri": "https://w3id.org/saref4ee" - }, - { - "namespace": "http://dati.san.beniculturali.it/SAN/", - "prefix": "san-lod", - "title": "SAN Ontologia", - "uri": "http://dati.san.beniculturali.it/SAN/" - }, - { - "namespace": "https://w3id.org/saref#", - "prefix": "saref", - "title": "SAREF: the Smart Appliances REFerence ontology", - "uri": "https://w3id.org/saref" - }, - { - "namespace": "https://w3id.org/def/saref4agri#", - "prefix": "saref4agri", - "title": "SAREF extension for Agriculture", - "uri": "https://w3id.org/def/saref4agri" - }, - { - "namespace": "http://purl.org/saws/ontology#", - "prefix": "saws", - "title": "Sharing Ancient Wisdoms Ontology", - "uri": "http://purl.org/saws/ontology" - }, - { - "namespace": "http://schema.org/", - "prefix": "schema", - "title": "Schema.org vocabulary", - "uri": "http://schema.org/" - }, - { - "namespace": "http://lod.taxonconcept.org/ontology/sci_people.owl#", - "prefix": "scip", - "title": "Scientific People Ontology", - "uri": "http://lod.taxonconcept.org/ontology/sci_people.owl" - }, - { - "namespace": "http://purl.org/spar/scoro/", - "prefix": "scoro", - "title": "Scholarly Contributions and Roles Ontology", - "uri": "http://purl.org/spar/scoro/" - }, - { - "namespace": "http://rdfs.org/scot/ns#", - "prefix": "scot", - "title": "Social Semantic Cloud of Tags", - "uri": "http://rdfs.org/scot/ns#" - }, - { - "namespace": "http://purl.org/NET/scovo#", - "prefix": "scovo", - "title": "The Statistical Core Vocabulary", - "uri": "http://vocab.deri.ie/scovo" - }, - { - "namespace": "http://purl.org/NET/schema-org-csv#", - "prefix": "scsv", - "title": "Schema.org CSV", - "uri": "http://vocab.deri.ie/scsv" - }, - { - "namespace": "http://www.w3.org/ns/sparql-service-description#", - "prefix": "sd", - "title": "SPARQL 1.1 Service Description", - "uri": "http://www.w3.org/ns/sparql-service-description" - }, - { - "namespace": "https://w3id.org/vocab/sdm#", - "prefix": "sdm", - "title": "SPARQL endpoint metadata", - "uri": "https://w3id.org/vocab/sdm" - }, - { - "namespace": "http://purl.org/linked-data/sdmx#", - "prefix": "sdmx", - "title": "SDMX-RDF vocabulary", - "uri": "http://purl.org/linked-data/sdmx" - }, - { - "namespace": "http://purl.org/linked-data/sdmx/2009/code#", - "prefix": "sdmx-code", - "title": "SDMX Code", - "uri": "http://purl.org/linked-data/sdmx/2009/code" - }, - { - "namespace": "http://purl.org/linked-data/sdmx/2009/dimension#", - "prefix": "sdmx-dimension", - "title": "SDMX Dimension", - "uri": "http://purl.org/linked-data/sdmx/2009/dimension" - }, - { - "namespace": "http://sindice.com/vocab/search#", - "prefix": "search", - "title": "Sindice Search Vocabulary", - "uri": "http://vocab.deri.ie/search" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seas", - "title": "SEAS ontology", - "uri": "https://w3id.org/seas/" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seas-eval", - "title": "The SEAS Evaluation ontology", - "uri": "https://w3id.org/seas/EvaluationOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seas-op", - "title": "The SEAS Failable System ontology", - "uri": "https://w3id.org/seas/OperatingOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seas-qudt", - "title": "QUDT Alignment.", - "uri": "https://w3id.org/seas/QUDTAlignment" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seas-stats", - "title": "The SEAS Statistics ontology.", - "uri": "https://w3id.org/seas/StatisticsOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seas-sys", - "title": "The SEAS System ontology", - "uri": "https://w3id.org/seas/SystemOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seasb", - "title": "The SEAS Battery ontology.", - "uri": "https://w3id.org/seas/BatteryOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seasbo", - "title": "The SEAS Building Ontology", - "uri": "https://w3id.org/seas/BuildingOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seasd", - "title": "The SEAS Device ontology", - "uri": "https://w3id.org/seas/DeviceOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seasfo", - "title": "The SEAS Forecasting ontology", - "uri": "https://w3id.org/seas/ForecastingOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seast", - "title": "The SEAS Time Ontology.", - "uri": "https://w3id.org/seas/TimeOntology" - }, - { - "namespace": "https://w3id.org/seas/", - "prefix": "seasto", - "title": "The SEAS Trading ontology", - "uri": "https://w3id.org/seas/TradingOntology" - }, - { - "namespace": "http://securitytoolbox.appspot.com/securityMain#", - "prefix": "security", - "title": "Security Ontology", - "uri": "http://securitytoolbox.appspot.com/securityMain" - }, - { - "namespace": "http://semanticweb.cs.vu.nl/2009/11/sem/", - "prefix": "sem", - "title": "The SEM Ontology", - "uri": "http://semanticweb.cs.vu.nl/2009/11/sem/" - }, - { - "namespace": "http://purl.org/SemSur/", - "prefix": "semsur", - "title": "The Semantic Survey Ontology (semsur)", - "uri": "http://purl.org/SemSur/" - }, - { - "namespace": "http://purl.org/seo/", - "prefix": "seo", - "title": "The Scientific Events Ontology", - "uri": "http://purl.org/seo/" - }, - { - "namespace": "http://www.ontologydesignpatterns.org/cp/owl/sequence.owl#", - "prefix": "seq", - "title": "Sequence Pattern", - "uri": "http://www.ontologydesignpatterns.org/cp/owl/sequence.owl" - }, - { - "namespace": "http://purl.org/ontology/service#", - "prefix": "service", - "title": "The Service Ontology", - "uri": "http://purl.org/ontology/service" - }, - { - "namespace": "http://www.opengis.net/ont/sf#", - "prefix": "sf", - "title": "Simplified Features Geometry", - "uri": "http://www.opengis.net/ont/sf" - }, - { - "namespace": "http://www.w3.org/ns/shacl#", - "prefix": "sh", - "title": "W3C Shapes Constraint Language (SHACL) Vocabulary", - "uri": "http://www.w3.org/ns/shacl#" - }, - { - "namespace": "http://dati.cdec.it/lod/shoah/", - "prefix": "shoah", - "title": "Shoah Vocabulary Specification", - "uri": "http://dati.cdec.it/lod/shoah/" - }, - { - "namespace": "http://paul.staroch.name/thesis/SmartHomeWeather.owl#", - "prefix": "shw", - "title": "Smart Home Weather", - "uri": "http://paul.staroch.name/thesis/SmartHomeWeather.owl#" - }, - { - "namespace": "http://purl.org/ontology/similarity/", - "prefix": "sim", - "title": "The Similarity Ontology", - "uri": "http://purl.org/ontology/similarity/" - }, - { - "namespace": "http://semanticscience.org/resource/", - "prefix": "sio", - "title": "Semanticscience Integrated Ontology", - "uri": "http://semanticscience.org/ontology/sio.owl" - }, - { - "namespace": "http://rdfs.org/sioc/ns#", - "prefix": "sioc", - "title": "Semantically-Interlinked Online Communities", - "uri": "http://rdfs.org/sioc/ns#" - }, - { - "namespace": "http://www.ontologydesignpatterns.org/cp/owl/situation.owl#", - "prefix": "situ", - "title": "Situation Pattern", - "uri": "http://www.ontologydesignpatterns.org/cp/owl/situation.owl" - }, - { - "namespace": "http://www.w3.org/2004/02/skos/core#", - "prefix": "skos", - "title": "Simple Knowledge Organization System", - "uri": "http://www.w3.org/2004/02/skos/core" - }, - { - "namespace": "http://www.w3.org/2008/05/skos-xl#", - "prefix": "skosxl", - "title": "SKOS eXtension for Labels", - "uri": "http://www.w3.org/2008/05/skos-xl" - }, - { - "namespace": "http://www.w3.org/ns/solid/terms#", - "prefix": "solid", - "title": "Solid terms", - "uri": "http://www.w3.org/ns/solid/terms" - }, - { - "namespace": "http://purl.org/net/soron/", - "prefix": "sor", - "title": "SORON: Social Relationships ONtology", - "uri": "http://purl.org/net/soron" - }, - { - 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Deprivation Score 2010", - "uri": "http://opendatacommunities.org/datasets/imd-score-2010" - }, - { - "namespace": "http://linked.opendata.cz/resource/domain/cenia.cz/", - "prefix": "cz-cenia-pollution", - "title": "Integrated pollution registry", - "uri": "http://linked.opendata.cz/resource/dataset/cenia.cz/irz" - }, - { - "namespace": "http://iserve.kmi.open.ac.uk/iserve/", - "prefix": "iserve", - "title": "iServe: Linked Services Registry", - "uri": "http://iserve.kmi.open.ac.uk/" - }, - { - "namespace": "http://www4.wiwiss.fu-berlin.de/euraxess/resource/", - "prefix": "fu-berlin-euraxess", - "title": "EURAXESS - Researchers in Motion", - "uri": "http://www4.wiwiss.fu-berlin.de/euraxess/" - }, - { - "namespace": "http://tuskegee.eagle-i.net/i/", - "prefix": "eagle-i-tuskegee", - "title": "eagle-i @ Tuskegee University", - "uri": "http://tuskegee.eagle-i.net" - }, - { - "namespace": "http://eudbpedia.deusto.es/resource/", - "prefix": "dbpedia-eu", - "title": "DBpedia in Basque", - "uri": "http://eudbpedia.deusto.es" - }, - { - "namespace": "https://w3id.org/foodie/open/cz/pLPIS_180616_WGS/", - "prefix": "LPIS Czech Republic", - "title": "Land parcel dataset (LPIS) from Czech Republic", - "uri": "https://www.foodie-cloud.org/fct/" - } -] diff --git a/fuji_server/data/linked_vocab.yaml b/fuji_server/data/linked_vocab.yaml new file mode 100644 index 00000000..22702cb2 --- /dev/null +++ b/fuji_server/data/linked_vocab.yaml @@ -0,0 +1,4190 @@ +- namespace: http://www.irit.fr/recherches/MELODI/ontologies/SAN# + prefix: SAN + title: SAN (Semantic Actuator Network) + uri: http://www.irit.fr/recherches/MELODI/ontologies/SAN +- namespace: https://w3id.org/arco/ontology/location/ + prefix: a-loc + title: Location Ontology (ArCo network) + uri: https://w3id.org/arco/ontology/location +- namespace: http://purl.org/acco/ns# + prefix: acco + title: Accomodation Ontology + uri: http://purl.org/acco/ns +- namespace: http://www.w3.org/ns/auth/acl# + prefix: acl + title: Basic Access Control ontology + uri: http://www.w3.org/ns/auth/acl +- namespace: http://acm.rkbexplorer.com/ontologies/acm# + prefix: acm + title: ACM Classification Ontology + uri: http://www.rkbexplorer.com/ontologies/acm +- namespace: http://privatealpha.com/ontology/certification/1# + prefix: acrt + title: Agent Certification Ontology + uri: http://privatealpha.com/ontology/certification/1# +- namespace: http://www.w3.org/ns/adms# + prefix: adms + title: Asset Description Metadata Schema + uri: http://www.w3.org/ns/adms +- namespace: http://purl.org/ontology/af/ + prefix: af + title: Audio Features Ontology + uri: http://purl.org/ontology/af/ +- namespace: http://www.agls.gov.au/agls/terms/ + prefix: agls + title: AGLS Metadata Terms + uri: http://www.agls.gov.au/agls/terms +- namespace: http://promsns.org/def/agr# + prefix: agr + title: Agreements ontology + uri: http://promsns.org/def/agr +- namespace: http://d-nb.info/standards/elementset/agrelon# + prefix: agrelon + title: Agent Relationship Ontology + uri: http://d-nb.info/standards/elementset/agrelon +- namespace: http://purl.org/vocab/aiiso/schema# + prefix: aiiso + title: Academic Institution Internal Structure Ontology + uri: http://purl.org/vocab/aiiso/schema +- namespace: https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl# + prefix: airs + title: Alliance of Information and Referral Services (AIRS) Vocabulary + uri: https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl# +- namespace: http://securitytoolbox.appspot.com/securityAlgorithms# + prefix: algo + title: Algorithms Ontology + uri: http://securitytoolbox.appspot.com/securityAlgorithms# +- namespace: http://open-services.net/ns/asset# + prefix: am + title: OSLC Asset Management Vocabulary + uri: http://open-services.net/ns/asset# +- namespace: https://w3id.org/i40/aml# + prefix: aml + title: AutomationML Ontology + uri: https://w3id.org/i40/aml +- namespace: http://w3id.org/amlo/core# + prefix: amlo-core + title: AMLO-core vocabulary + uri: http://w3id.org/amlo/core +- namespace: http://purl.org/ontology/ao/core# + prefix: ao + title: Association Ontology + uri: http://purl.org/ontology/ao/core# +- namespace: http://purl.org/linked-data/api/vocab# + prefix: api + title: Linked Data API Vocabulary + uri: http://purl.org/linked-data/api/vocab# +- namespace: http://semweb.mmlab.be/ns/apps4X# + prefix: apps4X + title: The vocabulary for Co-creation Events based on Open Data + uri: http://semweb.mmlab.be/ns/apps4X +- namespace: http://purl.org/archival/vocab/arch# + prefix: arch + title: Archival collections ontology + uri: http://purl.org/archival/vocab/arch +- namespace: https://w3id.org/arco/ontology/core/ + prefix: arco + title: Core Ontology (ArCo network) + uri: https://w3id.org/arco/ontology/core +- namespace: http://www.arpenteur.org/ontology/Arpenteur.owl# + prefix: arp + title: Arpenteur Ontology + uri: http://www.arpenteur.org/ontology/Arpenteur.owl +- namespace: http://bblfish.net/work/atom-owl/2006-06-06/# + prefix: awol + title: Atom Syndication Ontology + uri: http://bblfish.net/work/atom-owl/2006-06-06/ +- namespace: http://purl.oclc.org/NET/ssnx/meteo/aws# + prefix: aws + title: Ontology for Meteorological sensors + uri: http://purl.oclc.org/NET/ssnx/meteo/aws +- namespace: http://bag.basisregistraties.overheid.nl/def/bag# + prefix: bag + title: Vocabulary for the Dutch base registration of buildings and addresses (BAG) + uri: http://bag.basisregistraties.overheid.nl/def/bag +- namespace: http://www.bbc.co.uk/ontologies/bbc/ + prefix: bbc + title: BBC Ontology + uri: http://www.bbc.co.uk/ontologies/bbc +- namespace: http://www.bbc.co.uk/ontologies/cms/ + prefix: bbccms + title: BBC CMS Ontology + uri: http://www.bbc.co.uk/ontologies/cms +- namespace: http://www.bbc.co.uk/ontologies/coreconcepts/ + prefix: bbccore + title: BBC Core Concepts + uri: http://www.bbc.co.uk/ontologies/coreconcepts +- namespace: http://www.bbc.co.uk/ontologies/provenance/ + prefix: bbcprov + title: BBC Provenance Ontology + uri: http://www.bbc.co.uk/ontologies/provenance +- namespace: https://w3id.org/BCI-ontology# + prefix: bci + title: Brain Computing Interface (BCI) Ontology + uri: https://w3id.org/BCI-ontology +- namespace: http://rdfs.co/bevon/ + prefix: bevon + title: 'BEVON: Beverage Ontology' + uri: http://rdfs.co/bevon/ +- namespace: http://id.loc.gov/ontologies/bibframe/ + prefix: bf + title: BIBFRAME Vocabulary + uri: http://id.loc.gov/ontologies/bibframe/ +- namespace: http://purl.org/ontology/bibo/ + prefix: bibo + title: The Bibliographic Ontology + uri: http://purl.org/ontology/bibo/ +- namespace: http://purl.org/net/nknouf/ns/bibtex# + prefix: bibtex + title: BibTeX ontology + uri: http://purl.org/net/nknouf/ns/bibtex +- namespace: http://bimerr.iot.linkeddata.es/def/occupancy-profile# + prefix: bimerr-op + title: Occupancy Profile ontology + uri: http://bimerr.iot.linkeddata.es/def/occupancy-profile# +- namespace: http://purl.org/vocab/bio/0.1/ + prefix: bio + title: 'BIO: A vocabulary for biographical information' + uri: http://purl.org/vocab/bio/0.1/ +- namespace: http://purl.org/NET/biol/ns# + prefix: biol + title: Biological Taxonomy Vocabulary 0.2 (Core) + uri: http://purl.org/NET/biol/ns# +- namespace: http://www.biopax.org/release/biopax-level3.owl# + prefix: biopax + title: BioPAX Level 3 ontology + uri: http://www.biopax.org/release/biopax-level3.owl +- namespace: http://purl.org/biotop/biotop.owl# + prefix: biotop + title: BioTop + uri: http://purl.org/biotop/biotop.owl +- namespace: http://purl.org/spar/biro/ + prefix: biro + title: The Bibliographic Reference Ontology + uri: http://purl.org/spar/biro +- namespace: http://www.bl.uk/schemas/bibliographic/blterms# + prefix: blt + title: British Library Terms RDF schema + uri: http://www.bl.uk/schemas/bibliographic/blterms +- namespace: http://swa.cefriel.it/ontologies/botdcat-ap# + prefix: bot + title: BotDCAT-AP - Data Catalogue vocabulary Application Profile for chatbots + uri: http://swa.cefriel.it/ontologies/botdcat-ap +- namespace: http://purl.org/NET/biol/botany# + prefix: botany + title: Biological Taxonomy Vocabulary 0.2 (Botany) + uri: http://purl.org/NET/biol/botany# +- namespace: http://data.vlaanderen.be/ns/persoon# + prefix: bperson + title: Person + uri: http://data.vlaanderen.be/ns/persoon +- namespace: http://vocab.deri.ie/br# + prefix: br + title: Brainstorm Ontology + uri: http://vocab.deri.ie/br +- namespace: http://brk.basisregistraties.overheid.nl/def/brk# + prefix: brk + title: Key Register Cadastre (BRK) vocabulary + uri: http://brk.basisregistraties.overheid.nl/def/brk +- namespace: http://brt.basisregistraties.overheid.nl/def/top10nl# + prefix: brt + title: Key Register Topography (BRT) vocabulary + uri: http://brt.basisregistraties.overheid.nl/def/top10nl +- namespace: https://w3id.org/bot# + prefix: bto + title: 'BOT: Building Topology Ontology' + uri: https://w3id.org/bot +- namespace: http://vocab.deri.ie/c4n# + prefix: c4n + title: Call for Anything vocabulary + uri: http://vocab.deri.ie/c4n +- namespace: http://purl.org/spar/c4o/ + prefix: c4o + title: C4O, the Citation Counting and Context Characterization Ontology + uri: http://purl.org/spar/c4o +- namespace: http://www.w3.org/2002/12/cal/ical# + prefix: cal + title: Internet Calendaring and Scheduling Core Object Specification + uri: http://www.w3.org/2002/12/cal/ical +- namespace: http://caressesrobot.org/ontology# + prefix: caresses + title: CARESSES Ontology + uri: http://caressesrobot.org/ontology +- namespace: http://purl.org/net/cartCoord# + prefix: cart + title: cartCoordOnt + uri: http://purl.org/net/cartCoord# +- namespace: http://comicmeta.org/cbo/ + prefix: cbo + title: Comic Book Ontology + uri: http://comicmeta.org/cbo/ +- namespace: http://creativecommons.org/ns# + prefix: cc + title: Creative Commons Rights Expression Language + uri: http://creativecommons.org/ns +- namespace: http://cookingbigdata.com/linkeddata/ccinstances# + prefix: cci + title: Ontology for Cloud Computing instances + uri: http://cookingbigdata.com/linkeddata/ccinstances +- namespace: http://purl.org/ontology/cco/core# + prefix: cco + title: Cognitive Characteristics Ontology + uri: http://purl.org/ontology/cco/core# +- namespace: http://cookingbigdata.com/linkeddata/ccpricing# + prefix: ccp + title: Vocabulary for prices options in Cloud Computing Services + uri: http://cookingbigdata.com/linkeddata/ccpricing +- namespace: http://cookingbigdata.com/linkeddata/ccregions# + prefix: ccr + title: Vocabulary for Regions and Zones on Cloud Computing + uri: http://cookingbigdata.com/linkeddata/ccregions +- namespace: http://cookingbigdata.com/linkeddata/ccsla# + prefix: ccsla + title: Service Level Agreement for Cloud Computing + uri: http://cookingbigdata.com/linkeddata/ccsla +- namespace: https://w3id.org/arco/ontology/context-description/ + prefix: cdesc + title: Context Description Ontology (ArCo network) + uri: https://w3id.org/arco/ontology/context-description +- namespace: http://purl.org/twc/ontology/cdm.owl# + prefix: cdm + title: Conceptual Depth and Momentum + uri: http://purl.org/twc/ontology/cdm.owl# +- namespace: http://purl.org/cld/cdtype/ + prefix: cdtype + title: The Collection Description Type Namespace + uri: http://purl.org/cld/cdtype/ +- namespace: http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1# + prefix: ceo + title: Consumer Electronics Ontology + uri: http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1 +- namespace: http://www.eurocris.org/ontologies/cerif/1.3# + prefix: cerif + title: CERIF Ontology 1.3 + uri: http://www.eurocris.org/ontologies/cerif/1.3 +- namespace: http://www.w3.org/ns/auth/cert# + prefix: cert + title: The Cert Ontology + uri: http://www.w3.org/ns/auth/cert# +- namespace: https://w3id.org/arco/ontology/cultural-event/ + prefix: cevent + title: Cultural Event Ontology (ArCo network) + uri: https://w3id.org/arco/ontology/cultural-event +- namespace: http://purl.oclc.org/NET/ssnx/cf/cf-feature# + prefix: cff + title: Climate and Forecast (CF) features + uri: http://purl.oclc.org/NET/ssnx/cf/cf-feature +- namespace: http://purl.oclc.org/NET/ssnx/cf/cf-property# + prefix: cfp + title: Climate and Forecast (CF) standard names parameter vocabulary + uri: http://purl.oclc.org/NET/ssnx/cf/cf-property +- namespace: http://linkeddata.finki.ukim.mk/lod/ontology/cfrl# + prefix: cfrl + title: Corporate Financial Reports and Loans Ontology + uri: http://linkeddata.finki.ukim.mk/lod/ontology/cfrl# +- namespace: http://reference.data.gov.uk/def/central-government/ + prefix: cgov + title: Central Government Ontology + uri: http://reference.data.gov.uk/def/central-government +- namespace: http://purl.org/ontology/chord/ + prefix: chord + title: The OMRAS2 Chord Ontology + uri: http://purl.org/ontology/chord/ +- namespace: https://privatealpha.com/ontology/content-inventory/1# + prefix: ci + title: A Content Inventory Vocabulary + uri: https://privatealpha.com/ontology/content-inventory/1# +- namespace: http://dati.beniculturali.it/cis/ + prefix: cis + title: 'Cultural-ON (Cultural ONtology): Cultural Institute/Site and Cultural Event Ontology' + uri: http://dati.beniculturali.it/cultural-ON/cultural-ON.owl +- namespace: http://purl.org/spar/cito/ + prefix: cito + title: CiTO, the Citation Typing Ontology + uri: http://purl.org/spar/cito +- namespace: http://www.essepuntato.it/2013/03/cito-functions/ + prefix: citof + title: Functions of Citations + uri: http://www.essepuntato.it/2013/03/cito-functions +- namespace: http://advene.org/ns/cinelab/ld# + prefix: cl + title: Cinelab ontology + uri: http://advene.org/ns/cinelab/ld +- namespace: http://purl.org/cld/terms/ + prefix: cld + title: The Collection Description Terms + uri: http://purl.org/cld/terms/ +- namespace: http://purl.org/twc/ontologies/cmo.owl# + prefix: cmo + title: Conceptual Model Ontology + uri: http://purl.org/twc/ontologies/cmo.owl +- namespace: http://www.w3.org/2011/content# + prefix: cnt + title: Representing Content in RDF + uri: http://www.w3.org/2011/content +- namespace: http://purl.org/ontology/co/core# + prefix: co + title: Counter Ontology + uri: http://purl.org/ontology/co/core# +- namespace: http://data.cochrane.org/ontologies/core/ + prefix: cochrane + title: Cochrane Core Vocabulary Ontology + uri: http://data.cochrane.org/ontologies/core/ +- namespace: https://w3id.org/cocoon/v1.0# + prefix: cocoon + title: Cloud Computing Services Ontology + uri: https://w3id.org/cocoon/v1.0 +- namespace: http://vocab.deri.ie/cogs# + prefix: cogs + title: COGS Vocabulary + uri: http://vocab.deri.ie/cogs +- namespace: http://purl.org/configurationontology# + prefix: cold + title: "'Configuration as Linked Data' ontology" + uri: http://purl.org/configurationontology +- namespace: http://purl.org/co/ + prefix: coll + title: Collections Ontology + uri: http://purl.org/co +- namespace: http://vocab.resc.info/communication# + prefix: comm + title: Vocabulary related to incident communication + uri: http://vocab.resc.info/communication +- namespace: http://www.w3.org/2007/uwa/context/common.owl# + prefix: common + title: The Delivery Context Ontology + uri: http://www.w3.org/2007/uwa/context/deliverycontext.owl +- namespace: http://www.w3.org/2000/10/swap/pim/contact# + prefix: con + title: Contact + uri: http://www.w3.org/2000/10/swap/pim/contact +- namespace: http://purl.org/twc/vocab/conversion/ + prefix: conversion + title: Conversion Ontology + uri: http://purl.org/twc/vocab/conversion/ +- namespace: http://purl.org/coo/ns# + prefix: coo + title: Car Options Ontology + uri: http://purl.org/coo/ns# +- namespace: http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl# + prefix: cpa + title: Content Pattern Annotations + uri: http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl +- namespace: http://www.cidoc-crm.org/cidoc-crm/ + prefix: crm + title: CIDOC Conceptual Reference Model + uri: http://www.cidoc-crm.org/cidoc-crm/ +- namespace: http://rhizomik.net/ontologies/copyrightonto.owl# + prefix: cro + title: Copyright Ontology + uri: http://rhizomik.net/ontologies/copyrightonto.owl +- namespace: http://purl.org/vocab/changeset/schema# + prefix: cs + title: Changeset + uri: http://purl.org/vocab/changeset/schema +- namespace: http://vocab.deri.ie/csp# + prefix: csp + title: Constraint Satisfaction Problems Vocabulary + uri: http://vocab.deri.ie/csp +- namespace: http://www.w3.org/ns/csvw# + prefix: csvw + title: CSV on the Web Vocabulary + uri: http://www.w3.org/ns/csvw# +- namespace: http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl# + prefix: ct + title: Connectivity types + uri: http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl +- namespace: https://w3id.org/arco/ontology/catalogue/ + prefix: ctlog + title: Catalogue Ontology (ArCo network) + uri: https://w3id.org/arco/ontology/catalogue +- namespace: http://purl.org/ctic/infraestructuras/organizacion# + prefix: ctorg + title: Vocabulary for the structure of the public organizations + uri: http://purl.org/ctic/infraestructuras/organizacion +- namespace: https://w3id.org/ibp/CTRLont# + prefix: ctrl + title: CTRLont - An ontology to formally specify the control domain + uri: https://w3id.org/ibp/CTRLont +- namespace: http://www.demcare.eu/ontologies/contextdescriptor.owl# + prefix: ctxdesc + title: Context Descriptor Pattern + uri: http://www.demcare.eu/ontologies/contextdescriptor.owl +- namespace: http://purl.org/cwmo/# + prefix: cwmo + title: Creative Workshop Management Ontology (CWMO) + uri: http://purl.org/cwmo/# +- namespace: http://www.bbc.co.uk/ontologies/creativework/ + prefix: cwork + title: Creative Work Ontology + uri: http://www.bbc.co.uk/ontologies/creativework +- namespace: http://sparql.cwrc.ca/ontologies/cwrc# + prefix: cwrc + title: The CWRC Ontology + uri: http://sparql.cwrc.ca/ontologies/cwrc +- namespace: http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1# + prefix: d2rq + title: D2RQ - Language Specification + uri: http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1 +- namespace: http://purl.org/NET/dady# + prefix: dady + title: Dataset Dynamics (dady) vocabulary + uri: http://vocab.deri.ie/dady +- namespace: http://purl.org/eis/vocab/daq# + prefix: daq + title: Dataset Quality Vocabulary + uri: http://purl.org/eis/vocab/daq# +- namespace: http://dataid.dbpedia.org/ns/core# + prefix: dataid + title: DataID + uri: http://dataid.dbpedia.org/ns/core# +- namespace: http://vocab.datex.org/terms# + prefix: datex + title: Linked Datex II + uri: http://vocab.datex.org/terms# +- namespace: http://theme-e.adaptcentre.ie/dave# + prefix: dave + title: Data Value Vocabulary (DaVe) + uri: http://theme-e.adaptcentre.ie/dave/dave.ttl +- namespace: http://purl.org/net/dbm/ontology# + prefix: dbm + title: DBM Ontology + uri: http://purl.org/net/dbm/ontology# +- namespace: http://ontology.cybershare.utep.edu/dbowl/relational-to-ontology-mapping-primitive.owl# + prefix: dbowl + title: Relational to Ontology Mapping Primitive + uri: http://ontology.cybershare.utep.edu/dbowl +- namespace: http://dbpedia.org/ontology/ + prefix: dbpedia-owl + title: The DBpedia Ontology + uri: http://dbpedia.org/ontology/ +- namespace: http://ontologi.es/doap-bugs# + prefix: dbug + title: DOAP Bugs + uri: http://ontologi.es/doap-bugs# +- namespace: http://purl.org/dc/dcam/ + prefix: dcam + title: DCMI Abstract Model + uri: http://purl.org/dc/dcam/ +- namespace: http://www.w3.org/ns/dcat# + prefix: dcat + title: Data Catalog Vocabulary + uri: http://www.w3.org/ns/dcat +- namespace: http://purl.org/dc/elements/1.1/ + prefix: dce + title: Dublin Core Metadata Element Set + uri: http://purl.org/dc/elements/1.1/ +- namespace: http://purl.org/spar/datacite/ + prefix: dcite + title: The DataCite Ontology + uri: http://purl.org/spar/datacite +- namespace: http://ndl.go.jp/dcndl/terms/ + prefix: dcndl + title: NDL Metadata Terms + uri: http://ndl.go.jp/dcndl/terms/ +- namespace: http://purl.org/dc/terms/ + prefix: dcterms + title: DCMI Metadata Terms + uri: http://purl.org/dc/terms/ +- namespace: http://purl.org/dc/dcmitype/ + prefix: dctype + title: DCMI Type Vocabulary + uri: http://purl.org/dc/dcmitype/ +- namespace: https://w3id.org/arco/ontology/denotative-description/ + prefix: ddesc + title: Denotative Description Ontology (ArCo network) + uri: https://w3id.org/arco/ontology/denotative-description +- namespace: http://www.demcare.eu/ontologies/demlab.owl# + prefix: demlab + title: Dem@Care Lab Ontology for Dementia Assessment + uri: http://www.demcare.eu/ontologies/demlab.owl +- namespace: http://purl.org/spar/deo/ + prefix: deo + title: The Discourse Elements Ontology + uri: http://purl.org/spar/deo +- namespace: http://ontologi.es/doap-deps# + prefix: deps + title: DOAP Dependencies + uri: http://ontologi.es/doap-deps# +- namespace: http://datafoodconsortium.org/ontologies/DFC_FullModel.owl# + prefix: dfc + title: Data Food Consortium Ontology + uri: http://datafoodconsortium.org/ontologies/DFC_FullModel.owl +- namespace: http://datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl# + prefix: dfcb + title: DFC Business Ontology + uri: http://datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl +- namespace: https://w3id.org/dingo# + prefix: dg + title: DINGO Ontology + uri: https://w3id.org/dingo/ +- namespace: http://purl.org/healthcarevocab/v1# + prefix: dicom + title: Healthcare metadata - DICOM ontology + uri: http://purl.org/healthcarevocab/v1 +- namespace: https://w3id.org/dio# + prefix: dio + title: The Design Intent Ontology + uri: https://w3id.org/dio +- namespace: http://purl.org/dita/ns# + prefix: dita + title: DITA RDF ontology + uri: http://purl.org/dita/ns# +- namespace: http://www.data-knowledge.org/dk/ + prefix: dk + title: The Data Knowledge Vocabulary + uri: http://www.data-knowledge.org/dk/ +- namespace: http://d-nb.info/standards/elementset/dnb# + prefix: dnbt + title: DNB Metadata Terms + uri: http://d-nb.info/standards/elementset/dnb +- namespace: http://usefulinc.com/ns/doap# + prefix: doap + title: Description of a Project vocabulary + uri: http://usefulinc.com/ns/doap# +- namespace: http://www.w3.org/2000/10/swap/pim/doc# + prefix: doc + title: Works, licences, derivatives and dependencies + uri: http://www.w3.org/2000/10/swap/pim/doc +- namespace: http://purl.org/spar/doco/ + prefix: doco + title: DoCO, the Document Components Ontology + uri: http://purl.org/spar/doco +- namespace: http://purl.org/ontology/dso# + prefix: docso + title: Document Service Ontology + uri: http://purl.org/ontology/dso +- namespace: http://elite.polito.it/ontologies/dogont + prefix: dogont + title: Ontology Modeling for Intelligent Domotic Environments + uri: http://elite.polito.it/ontologies/dogont.owl +- namespace: http://reference.data.gov.au/def/ont/dataset# + prefix: donto + title: Dataset Ontology + uri: http://reference.data.gov.au/def/ont/dataset +- namespace: http://purl.org/dpn# + prefix: dpn + title: Data Provider Node ontology + uri: http://purl.org/dpn +- namespace: http://promsns.org/def/do# + prefix: dprov + title: Decision Provenance ontology (DecPROV) + uri: http://promsns.org/def/decprov +- namespace: http://semwebquality.org/ontologies/dq-constraints# + prefix: dqc + title: The Data Quality Constraints Library + uri: http://semwebquality.org/ontologies/dq-constraints +- namespace: http://purl.org/dqm-vocabulary/v1/dqm# + prefix: dqm + title: The Data Quality Management Vocabulary + uri: http://purl.org/dqm-vocabulary/v1/dqm +- namespace: http://www.w3.org/ns/dqv# + prefix: dqv + title: Data Quality Vocabulary + uri: http://www.w3.org/ns/dqv +- namespace: http://purl.org/swan/2.0/discourse-relationships/ + prefix: dr + title: Discourse relationships vocabulary + uri: http://purl.org/swan/2.0/discourse-relationships/ +- namespace: http://www.purl.org/drammar# + prefix: drama + title: 'Drammar: a comprehensive ontology of drama' + uri: http://www.purl.org/drammar +- namespace: http://vocab.data.gov/def/drm# + prefix: drm + title: Data Reference Model + uri: http://vocab.data.gov/def/drm +- namespace: http://purl.org/ctic/dcat# + prefix: ds + title: Dataset Catalog Vocabulary + uri: http://purl.org/ctic/dcat# +- namespace: http://purl.org/dsnotify/vocab/eventset/ + prefix: dsn + title: 'DSNotify Eventsets: A vocabulary for change events in linked data sources' + uri: http://purl.org/dsnotify/vocab/eventset/ +- namespace: http://www.linkedmodel.org/schema/dtype# + prefix: dtype + title: Datatype Ontology + uri: http://www.linkedmodel.org/schema/dtype +- namespace: http://www.ontologydesignpatterns.org/ont/dul/DUL.owl# + prefix: dul + title: DOLCE+DnS Ultralite + uri: http://www.ontologydesignpatterns.org/ont/dul/DUL.owl +- namespace: http://www.w3.org/ns/duv# + prefix: duv + title: Dataset Usage Vocabulary + uri: http://www.w3.org/ns/duv +- namespace: http://purl.org/ontology/dvia# + prefix: dvia + title: The visualization vocabulary for LOD applications + uri: http://purl.org/ontology/dvia +- namespace: http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/ + prefix: eac-cpf + title: 'EAC-CPF Descriptions Ontology for Linked Archival Data:' + uri: http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/ +- namespace: http://www.w3.org/ns/earl# + prefix: earl + title: Evaluation and Report Language + uri: http://www.w3.org/ns/earl +- namespace: http://linked.earth/ontology# + prefix: earth + title: The Linked Earth Ontology + uri: http://linked.earth/ontology# +- namespace: http://www.ebu.ch/metadata/ontologies/ebucore/ebucore# + prefix: ebucore + title: EBU Ontology + uri: http://www.ebu.ch/metadata/ontologies/ebucore/ebucore +- namespace: https://vocab.eccenca.com/revision/ + prefix: eccrev + title: RDF changes and revisions vocabulary + uri: https://vocab.eccenca.com/revision/ +- namespace: http://purl.org/ontology/ecpo# + prefix: ecpo + title: Enumeration and Chronology of Periodicals Ontology + uri: http://purl.org/ontology/ecpo +- namespace: http://erlangen-crm.org/current/ + prefix: ecrm + title: Erlangen CRM / OWL + uri: http://erlangen-crm.org/current/ +- namespace: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl# + prefix: edac + title: ELSEWeb EDAC Ontology + uri: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl +- namespace: http://www.europeana.eu/schemas/edm/ + prefix: edm + title: Europeana Data Model vocabulary + uri: http://www.europeana.eu/schemas/edm/ +- namespace: https://schema.edu.ee/ + prefix: edu + title: Education Ontology + uri: https://schema.edu.ee/ +- namespace: http://ns.inria.fr/semed/eduprogression# + prefix: edupro + title: EduProgression Ontology + uri: http://ns.inria.fr/semed/eduprogression/ +- namespace: http://purl.org/eem# + prefix: eem + title: The EPCIS Event Model + uri: http://purl.org/eem +- namespace: https://w3id.org/eepsa# + prefix: eepsa + title: EEPSA (Energy Efficiency Prediction Semantic Assistant) Ontology + uri: https://w3id.org/eepsa +- namespace: http://opendata.aragon.es/def/ei2a# + prefix: ei2a + title: |- + Aragon Interoperable Information Structure Ontology + EI2A + uri: https://opendata.aragon.es/def/ei2a/ei2a.owl +- namespace: http://purl.org/ctic/sector-publico/elecciones# + prefix: elec + title: Vocabulary for Vote Results + uri: http://purl.org/ctic/sector-publico/elecciones +- namespace: http://data.europa.eu/eli/ontology# + prefix: eli + title: The European Legislation Identifier + uri: http://data.europa.eu/eli/ontology +- namespace: http://ns.inria.fr/emoca# + prefix: emotion + title: Emotion Ontology for Context Awareness + uri: http://ns.inria.fr/emoca +- namespace: http://purl.org/ctic/empleo/oferta# + prefix: emp + title: A vocabulary for jobs + uri: http://purl.org/ctic/empleo/oferta +- namespace: http://labs.mondeca.com/vocab/endpointStatus# + prefix: ends + title: Vocabulary of endpoint status (availability, responseTime) + uri: http://labs.mondeca.com/vocab/endpointStatus +- namespace: http://eprints.org/ontology/ + prefix: ep + title: EPrints Ontology + uri: http://eprints.org/ontology/ +- namespace: https://w3id.org/ep-plan# + prefix: eppl + title: The EP-Plan ontology + uri: https://w3id.org/ep-plan +- namespace: http://data.europa.eu/esco/model# + prefix: esco + title: The ESCO ontology + uri: http://data.europa.eu/esco/model +- namespace: http://purl.org/essglobal/vocab/ + prefix: essglobal + title: ESSGlobal Vocabulary + uri: http://purl.org/essglobal/vocab/ +- namespace: http://elite.polito.it/ontologies/eupont.owl# + prefix: eupont + title: 'EUPont: an ontology for End User Programming of the IoT' + uri: http://elite.polito.it/ontologies/eupont.owl +- namespace: http://purl.org/NET/c4dm/event.owl# + prefix: event + title: The Event Ontology + uri: http://purl.org/NET/c4dm/event.owl +- namespace: http://purl.org/net/ns/ex# + prefix: ex + title: Example vocabulary + uri: http://purl.org/net/ns/ex +- namespace: http://www.w3.org/2003/12/exif/ns# + prefix: exif + title: Exif data description vocabulary + uri: http://www.w3.org/2003/12/exif/ns +- namespace: http://purl.org/spar/fabio/ + prefix: fabio + title: FRBR-aligned Bibliographic Ontology + uri: http://purl.org/spar/fabio +- namespace: http://biohackathon.org/resource/faldo# + prefix: faldo + title: Feature Annotation Location Description Ontology + uri: http://biohackathon.org/resource/faldo +- namespace: http://vocab.data.gov/def/fea# + prefix: fea + title: Federal Enterprise Architecture Vocabulary + uri: http://vocab.data.gov/def/fea +- namespace: http://w3id.org/vcb/fel# + prefix: fel + title: A Fine-grained Entity Linking vocabulary + uri: http://w3id.org/vcb/fel# +- namespace: http://purl.org/iot/ontology/fiesta-iot# + prefix: fiesta-iot + title: FIESTA-IoT Ontology + uri: http://purl.org/iot/ontology/fiesta-iot +- namespace: http://purl.org/iot/ontology/fiesta-iot# + prefix: fiesta-priv + title: FIESTA-Priv Ontology + uri: http://purl.org/iot/ontology/fiesta-priv# +- namespace: http://xmlns.com/foaf/0.1/ + prefix: foaf + title: Friend of a Friend vocabulary + uri: http://xmlns.com/foaf/0.1/ +- namespace: https://w3id.org/fog# + prefix: fog + title: 'FOG: File Ontology for Geometry formats' + uri: https://w3id.org/fog +- namespace: https://w3id.org/seas/FeatureOfInterestOntology/ + prefix: foio + title: The SEAS Feature of Interest ontology. + uri: https://w3id.org/seas/FeatureOfInterestOntology +- namespace: http://www.w3.org/TR/2003/PR-owl-guide-20031209/food# + prefix: fowl + title: Food Ontology in OWL + uri: http://www.w3.org/TR/2003/PR-owl-guide-20031215/food +- namespace: http://purl.org/cerif/frapo/ + prefix: frapo + title: Funding, Research Administration and Projects Ontology + uri: http://purl.org/cerif/frapo/ +- namespace: http://streamreasoning.org/ontologies/frappe# + prefix: frappe + title: 'FraPPE: Frame, Pixel, Place, Event vocabulary' + uri: http://streamreasoning.org/ontologies/frappe# +- namespace: http://purl.org/vocab/frbr/core# + prefix: frbr + title: Expression of Core FRBR Concepts in RDF + uri: http://purl.org/vocab/frbr/core +- namespace: http://purl.org/vocab/frbr/extended# + prefix: frbre + title: Extended FRBR + uri: http://purl.org/vocab/frbr/extended +- namespace: http://www.w3.org/2004/09/fresnel# + prefix: fresnel + title: Fresnel Lens and Format Core Vocabulary + uri: http://www.w3.org/2004/09/fresnel +- namespace: http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/ + prefix: g50k + title: 50K Gazetteer Vocabulary + uri: http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/ +- namespace: http://data.totl.net/game/ + prefix: game + title: TotL Game Ontology + uri: http://data.totl.net/game/ +- namespace: http://www.oegov.org/core/owl/gc# + prefix: gc + title: oeGOV Government Core Ontology + uri: http://www.oegov.org/core/owl/gc +- namespace: http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl# + prefix: gci + title: Global City Indicator Foundation Ontology + uri: http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl +- namespace: https://w3id.org/GConsent# + prefix: gcon + title: GConsent - a consent ontology based on the GDPR + uri: https://w3id.org/GConsent +- namespace: http://reference.data.gov/def/govdata/ + prefix: gd + title: Government Data Vocabulary + uri: http://vocab.data.gov/gd +- namespace: https://w3id.org/GDPRov# + prefix: gdprov + title: The GDPR Provenance ontology + uri: https://w3id.org/GDPRov +- namespace: https://w3id.org/GDPRtEXT# + prefix: gdprt + title: GDPR text EXTensions + uri: https://w3id.org/GDPRtEXT +- namespace: http://purl.org/gen/0.1# + prefix: gen + title: Vocabulary for Linked Genealogical Data + uri: http://purl.org/gen/0.1# +- namespace: http://www.w3.org/2003/01/geo/wgs84_pos# + prefix: geo + title: WGS84 Geo Positioning + uri: http://www.w3.org/2003/01/geo/wgs84_pos +- namespace: http://vocab.lenka.no/geo-deling# + prefix: geod + title: Administrative vocabulary for Norway + uri: http://vocab.lenka.no/geo-deling +- namespace: http://data.ign.fr/def/geofla# + prefix: geofla + title: Ontology of administrative units at IGN-France + uri: http://data.ign.fr/def/geofla +- namespace: http://data.ign.fr/def/geometrie# + prefix: geom + title: Ontology for geometry + uri: http://data.ign.fr/def/geometrie +- namespace: https://www.gleif.org/ontology/L1/ + prefix: gleif-L1 + title: Global Legal Entity Identifier Foundation Level 1 Ontology - Who Is Who + uri: https://www.gleif.org/ontology/L1/ +- namespace: https://www.gleif.org/ontology/L2/ + prefix: gleif-L2 + title: Global Legal Entity Identifier Foundation Level 2 Ontology - Who Owns Whom + uri: https://www.gleif.org/ontology/L2/ +- namespace: https://www.gleif.org/ontology/Base/ + prefix: gleif-base + title: Global Legal Entity Identifier Foundation Base Ontology + uri: https://www.gleif.org/ontology/Base/ +- namespace: https://www.gleif.org/ontology/EntityLegalForm/ + prefix: gleif-elf + title: Entity Legal Form Ontology + uri: https://www.gleif.org/ontology/EntityLegalForm/ +- namespace: https://www.gleif.org/ontology/Geocoding/ + prefix: gleif-geo + title: Global Legal Entity Identifier Foundation Geocoding Ontology + uri: https://www.gleif.org/ontology/Geocoding/ +- namespace: https://www.gleif.org/ontology/RegistrationAuthority/ + prefix: gleif-ra + title: Global Legal Entity Identifier Foundation Registration Authority Ontology + uri: https://www.gleif.org/ontology/RegistrationAuthority/ +- namespace: https://www.gleif.org/ontology/ReportingException/ + prefix: gleif-repex + title: Global Legal Entity Identifier Foundation Reporting Exception Ontology + uri: https://www.gleif.org/ontology/ReportingException/ +- namespace: http://www.opengis.net/ont/gml# + prefix: gml + title: OGC Geometry + uri: http://www.opengis.net/ont/gml +- namespace: http://www.geonames.org/ontology# + prefix: gn + title: The Geonames ontology + uri: http://www.geonames.org/ontology +- namespace: http://d-nb.info/standards/elementset/gnd# + prefix: gndo + title: GND Ontology + uri: http://d-nb.info/standards/elementset/gnd# +- namespace: http://purl.org/linguistics/gold/ + prefix: gold + title: General Ontology for Linguistic Description + uri: http://purl.org/linguistics/gold +- namespace: https://w3id.org/gom# + prefix: gom + title: 'GOM: Geometry Metadata Ontology' + uri: https://w3id.org/gom +- namespace: http://gov.genealogy.net/ontology.owl# + prefix: gov + title: Ontology for modelling historic administrative information. + uri: http://gov.genealogy.net/ontology.owl +- namespace: http://purl.org/goodrelations/v1# + prefix: gr + title: The GoodRelations Ontology for Semantic Web-based E-Commerce + uri: http://purl.org/goodrelations/v1 +- namespace: http://www.w3.org/2003/g/data-view# + prefix: grddl + title: Gleaning Resource Descriptions from Dialects of Languages Vocabulary + uri: http://www.w3.org/2003/g/data-view +- namespace: http://www.w3.org/2006/gen/ont# + prefix: gso + title: Generic Specific Ontology + uri: http://www.w3.org/2006/gen/ont +- namespace: http://www.opengis.net/ont/geosparql# + prefix: gsp + title: OGC GeoSPARQL + uri: http://www.opengis.net/ont/geosparql +- namespace: http://vocab.gtfs.org/terms# + prefix: gtfs + title: General Transit Feed Specification + uri: http://vocab.gtfs.org/terms# +- namespace: http://resource.geosciml.org/ontology/timescale/gts# + prefix: gts + title: Geologic Timescale model + uri: http://resource.geosciml.org/ontology/timescale/gts +- namespace: http://vocab.getty.edu/ontology# + prefix: gvp + title: Getty Vocabulary Program ontology + uri: http://vocab.getty.edu/ontology +- namespace: http://sensormeasurement.appspot.com/ont/home/homeActivity# + prefix: ha + title: Home Activity + uri: http://sensormeasurement.appspot.com/ont/home/homeActivity# +- namespace: https://www.w3.org/2019/wot/hypermedia# + prefix: hctl + title: Hypermedia Controls Ontology + uri: https://www.w3.org/2019/wot/hypermedia# +- namespace: http://purl.org/net/hifm/ontology# + prefix: hifm + title: HIFM Ontology + uri: http://purl.org/net/hifm/ontology# +- namespace: http://purl.org/ontology/holding# + prefix: holding + title: Holding Ontology + uri: http://purl.org/ontology/holding +- namespace: http://health.data.gov/def/hospital/ + prefix: hosp + title: Hospital Vocabulary + uri: http://vocab.data.gov/hosp +- namespace: http://vcharpenay.github.io/hto/hto.xml# + prefix: hto + title: Haystack Tagging Ontology + uri: http://vcharpenay.github.io/hto/hto.xml +- namespace: http://www.w3.org/2011/http# + prefix: http + title: HTTP in RDF + uri: http://www.w3.org/2011/http +- namespace: https://privatealpha.com/ontology/ibis/1# + prefix: ibis + title: IBIS Vocabulary + uri: https://privatealpha.com/ontology/ibis/1# +- namespace: http://ontology.eil.utoronto.ca/icontact.owl# + prefix: ic + title: 'International Contact Ontology: Addresses, phone numbers and emails.' + uri: http://ontology.eil.utoronto.ca/icontact.owl +- namespace: http://rdf.insee.fr/def/demo# + prefix: idemo + title: Demographic ontology from the French Statistics Institute + uri: http://rdf.insee.fr/def/demo +- namespace: http://www.identity.org/ontologies/identity.owl# + prefix: identity + title: Ontology of digital identity. + uri: http://www.identity.org/ontologies/identity.owl +- namespace: https://w3id.org/ifc/IFC4_ADD1# + prefix: ifc + title: IFC4_ADD1 + uri: https://w3id.org/ifc/IFC4_ADD1 +- namespace: http://rdf.insee.fr/def/geo# + prefix: igeo + title: French Statistical ontology for geolocation + uri: http://rdf.insee.fr/def/geo +- namespace: http://data.ign.fr/def/ignf# + prefix: ignf + title: Ontology of coordinates reference systems + uri: http://data.ign.fr/def/ignf +- namespace: http://imgpedia.dcc.uchile.cl/ontology# + prefix: imo + title: The IMGpedia Ontology + uri: http://imgpedia.dcc.uchile.cl/ontology +- namespace: http://vocab.resc.info/incident# + prefix: incident + title: Vocabulary to describe incident response by emergency services + uri: http://vocab.resc.info/incident +- namespace: http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl# + prefix: infor + title: Information Realization + uri: http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl +- namespace: http://purl.org/innovation/ns# + prefix: inno + title: Ontology for Innovation + uri: http://purl.org/innovation/ns +- namespace: http://reference.data.gov.uk/def/intervals/ + prefix: interval + title: Intervals Ontology + uri: http://reference.data.gov.uk/def/intervals +- namespace: http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl# + prefix: iol + title: Information Objects ontology + uri: http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl +- namespace: http://purl.oclc.org/NET/UNIS/fiware/iot-lite# + prefix: iot-lite + title: Iot-lite ontology + uri: http://purl.oclc.org/NET/UNIS/fiware/iot-lite# +- namespace: http://www.irit.fr/recherches/MELODI/ontologies/IoT-O# + prefix: ioto + title: IoT-O + uri: http://www.irit.fr/recherches/MELODI/ontologies/IoT-O +- namespace: http://purl.org/iot/vocab/iot-taxonomy-lite# + prefix: iottaxolite + title: The IoTTaxonomy-lite Taxonomy + uri: http://purl.org/iot/vocab/iot-taxonomy-lite# +- namespace: http://purl.org/ipo/core# + prefix: ipo + title: IPO - Issue Procedure Ontology + uri: http://purl.org/ipo/core +- namespace: http://www.ontologydesignpatterns.org/ont/web/irw.owl# + prefix: irw + title: The Identity of Resources on the Web ontology + uri: http://www.ontologydesignpatterns.org/ont/web/irw.owl +- namespace: http://purl.org/ontology/is/core# + prefix: is + title: Info Service Ontology + uri: http://purl.org/ontology/is/core# +- namespace: http://purl.org/iso25964/skos-thes# + prefix: iso-thes + title: ISO 25964 SKOS extension + uri: http://purl.org/iso25964/skos-thes +- namespace: http://ontology.eil.utoronto.ca/ISO37120.owl# + prefix: iso37120 + title: ISO 37120 indicator URIs + uri: http://ontology.eil.utoronto.ca/ISO37120.owl +- namespace: http://reference.data.gov.au/def/ont/iso19160-1-address# + prefix: isoadr + title: ISO19160-1:2015 Address ontology + uri: http://reference.data.gov.au/def/ont/iso19160-1-address +- namespace: http://dati.isprambiente.it/ontology/core# + prefix: ispra + title: Ispra Ontology + uri: http://dati.isprambiente.it/ontology/core# +- namespace: https://data.istex.fr/ontology/istex# + prefix: istex + title: Istex ontology for scholarly documents and extracted entities + uri: https://data.istex.fr/ontology/istex# +- namespace: http://ontology.it/itsmo/v1# + prefix: itsmo + title: IT Service Management Ontology + uri: http://ontology.it/itsmo/v1 +- namespace: https://www.w3.org/2019/wot/json-schema# + prefix: jsonsc + title: JSON Schema in RDF + uri: https://www.w3.org/2019/wot/json-schema# +- namespace: http://w3id.org/charta77/jup/ + prefix: jup + title: Ontology of Building Accessibility + uri: http://w3id.org/charta77/jup +- namespace: http://rdfs.co/juso/ + prefix: juso + title: Juso Ontology + uri: http://rdfs.co/juso/ +- namespace: http://rdfs.co/juso/kr/ + prefix: juso.kr + title: South Korea Extension to Juso Ontology + uri: http://rdfs.co/juso/kr/ +- namespace: http://linkeddata.center/kees/v1# + prefix: kees + title: KEES Ontology + uri: http://linkeddata.center/kees/v1 +- namespace: http://purl.org/NET/c4dm/keys.owl# + prefix: keys + title: Keys Ontology + uri: http://purl.org/NET/c4dm/keys.owl +- namespace: http://www.disit.org/km4city/schema# + prefix: km4c + title: km4city, the DISIT Knowledge Model for City and Mobility + uri: http://www.disit.org/km4city/schema +- namespace: http://purl.org/net/vocab/2004/03/label# + prefix: label + title: label + uri: http://purl.org/net/vocab/2004/03/label +- namespace: http://lawd.info/ontology/ + prefix: lawd + title: Linking Ancient World Data Ontology + uri: http://lawd.info/ontology/ +- namespace: http://purl.org/vocab/lifecycle/schema# + prefix: lcy + title: Lifecycle Schema + uri: http://purl.org/vocab/lifecycle/schema +- namespace: http://www.w3.org/ns/ldp# + prefix: ldp + title: Linked Data Platform + uri: http://www.w3.org/ns/ldp# +- namespace: http://purl.oclc.org/NET/ldr/ns# + prefix: ldr + title: Linked Data Rights (LDR) + uri: http://purl.oclc.org/NET/ldr/ns# +- namespace: http://linked.opendata.cz/ontology/ldvm/ + prefix: ldvm + title: Vocabulary for Linked Data Visualization Model + uri: http://linked.opendata.cz/ontology/ldvm/ +- namespace: http://lemon-model.net/lemon# + prefix: lemon + title: LExicon Model for ONtologies + uri: http://lemon-model.net/lemon +- namespace: http://www.lexinfo.net/ontology/2.0/lexinfo# + prefix: lexinfo + title: LexInfo Ontology + uri: http://www.lexinfo.net/ontology/2.0/lexinfo +- namespace: http://purl.org/library/ + prefix: lib + title: Library extension of schema.org + uri: http://purl.org/library/ +- namespace: http://purl.org/vocab/lifecycle/schema# + prefix: lifecycle + title: IoT-Lifecycle + uri: http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle +- namespace: http://purl.org/limo-ontology/limo# + prefix: limo + title: Linked Statistical Models Vocabulary + uri: http://purl.org/limo-ontology/limo/ +- namespace: http://purl.org/LiMo/0.1# + prefix: limoo + title: License Model Ontology + uri: http://purl.org/LiMo/0.1# +- namespace: https://w3id.org/vocab/lingvoj# + prefix: lingvo + title: The Lingvoj Ontology + uri: https://w3id.org/vocab/lingvoj +- namespace: http://purl.org/net/lio# + prefix: lio + title: Lightweight Image Ontology + uri: http://purl.org/net/lio +- namespace: http://www.linklion.org/ontology# + prefix: llont + title: LinkLion - the Link Discovery Portal + uri: http://www.linklion.org/ontology +- namespace: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl# + prefix: lmm1 + title: Lexical MetaModel Level 1 + uri: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl +- namespace: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl# + prefix: lmm2 + title: Lexical MetaModel Level 2 + uri: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl +- namespace: http://purl.org/ctic/infraestructuras/localizacion# + prefix: loc + title: Location Vocabulary + uri: http://purl.org/ctic/infraestructuras/localizacion +- namespace: http://data.archiveshub.ac.uk/def/ + prefix: locah + title: The LOCAH RDF Vocabulary + uri: http://data.archiveshub.ac.uk/def/ +- namespace: http://www.w3.org/ns/locn# + prefix: locn + title: ISA Programme Location Core Vocabulary + uri: http://www.w3.org/ns/locn +- namespace: http://linkedevents.org/ontology/ + prefix: lode + title: Linking Open Descriptions of Events + uri: http://linkedevents.org/ontology/ +- namespace: http://www.w3.org/2000/10/swap/log# + prefix: log + title: SWAP Logic Ontology + uri: http://www.w3.org/2000/10/swap/log +- namespace: http://data.opendiscoveryspace.eu/lom_ontology_ods.owl# + prefix: lom + title: Learning Object Metadata Ontology + uri: http://data.opendiscoveryspace.eu/lom_ontology_ods.owl +- namespace: http://sparql.sstu.ru:3030/speciality/ + prefix: losp + title: Linked open specialities RF + uri: http://sparql.sstu.ru:3030/speciality/ +- namespace: http://linkedscience.org/lsc/ns# + prefix: lsc + title: Linked Science Core Vocabulary + uri: http://linkedscience.org/lsc/ns# +- namespace: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl# + prefix: lslife + title: ELSEWeb Lifemapper Ontology + uri: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl +- namespace: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl# + prefix: lsmap + title: ELSEWeb Mappings Ontology + uri: http://ontology.cybershare.utep.edu/ELSEWeb/mappings/elseweb-mappings.owl +- namespace: http://lsq.aksw.org/vocab# + prefix: lsq + title: The Linked SPARQL Queries Vocabulary (LSQ(V)) + uri: http://lsq.aksw.org/vocab +- namespace: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl# + prefix: lsweb + title: ELSEWeb Data Ontology + uri: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl +- namespace: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl# + prefix: lswmo + title: ELSEWeb Modelling Ontology + uri: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl +- namespace: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl# + prefix: lswpm + title: ELSEWeb Lifemapper Parameters Ontology + uri: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl +- namespace: http://ns.inria.fr/ludo + prefix: ludo + title: Ludo Ontology + uri: http://ns.inria.fr/ludo +- namespace: http://purl.org/lobid/lv# + prefix: lv + title: lobid vocab + uri: http://purl.org/lobid/lv +- namespace: http://purl.org/linkingyou/ + prefix: lyou + title: Linking-you vocabulary + uri: http://purl.org/linkingyou/ +- namespace: http://purl.org/iot/vocab/m3-lite# + prefix: m3lite + title: The Machine-to-Machine Measurement (M3) Lite Ontology + uri: http://purl.org/iot/vocab/m3-lite# +- namespace: http://www.w3.org/ns/ma-ont# + prefix: ma-ont + title: Ontology for Media Resources + uri: http://www.w3.org/ns/ma-ont +- namespace: http://www.loc.gov/mads/rdf/v1# + prefix: mads + title: Metadata Authority Description Schema + uri: http://www.loc.gov/mads/rdf/v1 +- namespace: http://www.gsi.dit.upm.es/ontologies/marl/ns# + prefix: marl + title: Marl Ontology Specification + uri: http://www.gsi.dit.upm.es/ontologies/marl/ns +- namespace: http://securitytoolbox.appspot.com/MASO# + prefix: maso + title: Mobile Agents Security + uri: http://securitytoolbox.appspot.com/MASO +- namespace: https://w3id.org/multidimensional-interface/ontology# + prefix: mdi + title: RDF vocabulary to describe a Multidimensional Interface. + uri: https://w3id.org/multidimensional-interface/ontology +- namespace: http://purl.org/media# + prefix: media + title: The Media RDF Vocabulary + uri: http://purl.org/media +- namespace: http://w3id.org/medred/medred# + prefix: medred + title: 'MedRed ontology: clinical data acquisition model' + uri: http://w3id.org/medred/medred# +- namespace: http://mex.aksw.org/mex-algo# + prefix: mexalgo + title: MEX Algorithm Ontology + uri: http://mex.aksw.org/mex-algo +- namespace: http://mex.aksw.org/mex-core# + prefix: mexcore + title: MEX Core Vocabulary + uri: http://mex.aksw.org/mex-core +- namespace: http://mex.aksw.org/mex-perf# + prefix: mexperf + title: MEX Performance Ontology + uri: http://mex.aksw.org/mex-perf +- namespace: http://www.w3.org/ns/mls# + prefix: mls + title: Machine Learning Schema + uri: http://www.w3.org/ns/mls +- namespace: http://purl.org/ontology/mo/ + prefix: mo + title: Music Ontology + uri: http://purl.org/ontology/mo/ +- namespace: http://observedchange.com/moac/ns# + prefix: moac + title: Management of a Crisis Vocabulary + uri: http://www.observedchange.com/moac/ns# +- namespace: http://www.isibang.ac.in/ns/mod# + prefix: mod + title: 'MOD: Metadata for Ontology Description and publication' + uri: http://www.isibang.ac.in/ns/mod +- namespace: https://w3id.org/skgo/modsci# + prefix: modsci + title: ModSci, Modern Science Ontology. + uri: https://w3id.org/skgo/modsci# +- namespace: http://id.loc.gov/vocabulary/relators/ + prefix: mrel + title: MARC Code List for Relators + uri: http://id.loc.gov/vocabulary/relators +- namespace: http://iserve.kmi.open.ac.uk/ns/msm# + prefix: msm + title: Minimal Service Model + uri: http://iserve.kmi.open.ac.uk/ns/msm +- namespace: http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl# + prefix: mtlo + title: MarineTLO Ontology + uri: http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl +- namespace: http://ns.inria.fr/munc# + prefix: munc + title: Meta-Uncertainty + uri: http://ns.inria.fr/munc/ +- namespace: http://data.doremus.org/ontology# + prefix: mus + title: DOREMUS is an extension of the FRBRoo model for describing the music. + uri: http://data.doremus.org/ontology# +- namespace: http://www.kanzaki.com/ns/music# + prefix: music + title: Music Vocabulary + uri: http://www.kanzaki.com/ns/music +- namespace: http://purl.org/muto/core# + prefix: muto + title: Modular Unified Tagging Ontology (MUTO) + uri: http://purl.org/muto/core +- namespace: http://schema.mobivoc.org/ + prefix: mv + title: 'MobiVoc: Open Mobility Vocabulary' + uri: http://schema.mobivoc.org/ +- namespace: http://purl.oclc.org/NET/mvco.owl# + prefix: mvco + title: Media Value Chain Ontology + uri: http://purl.oclc.org/NET/mvco.owl +- namespace: http://www.semanticdesktop.org/ontologies/2007/08/15/nao# + prefix: nao + title: NEPOMUK Annotation Ontology + uri: http://www.semanticdesktop.org/ontologies/2007/08/15/nao +- namespace: http://www.semanticdesktop.org/ontologies/2007/04/02/ncal# + prefix: ncal + title: NEPOMUK Calendar Ontology + uri: http://www.semanticdesktop.org/ontologies/2007/04/02/ncal +- namespace: http://www.semanticdesktop.org/ontologies/2007/03/22/nco# + prefix: nco + title: NEPOMUK Contact Ontology + uri: http://www.semanticdesktop.org/ontologies/2007/03/22/nco +- namespace: http://www.semanticdesktop.org/ontologies/2007/03/22/nfo# + prefix: nfo + title: NEPOMUK File Ontology + uri: http://www.semanticdesktop.org/ontologies/2007/03/22/nfo +- namespace: http://geovocab.org/geometry# + prefix: ngeo + title: NeoGeo Geometry Ontology + uri: http://geovocab.org/geometry +- namespace: http://www.semanticdesktop.org/ontologies/2007/01/19/nie# + prefix: nie + title: NEPOMUK Information Element Core Ontology + uri: http://www.semanticdesktop.org/ontologies/2007/01/19/nie +- namespace: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core# + prefix: nif + title: NLP Interchange Format + uri: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core# +- namespace: http://lod.nl.go.kr/ontology/ + prefix: nlon + title: National Library of Korea Ontology + uri: http://lod.nl.go.kr/ontology/ +- namespace: https://w3id.org/nno/ontology# + prefix: nno + title: The Neural Network Ontology + uri: https://w3id.org/nno/ontology +- namespace: http://ns.nature.com/terms/ + prefix: npg + title: Nature.com Core Ontology + uri: http://ns.nature.com/terms/ +- namespace: http://www.semanticdesktop.org/ontologies/2007/08/15/nrl# + prefix: nrl + title: NEPOMUK Representational Language + uri: http://www.semanticdesktop.org/ontologies/2007/08/15/nrl +- namespace: http://ns.inria.fr/nrv# + prefix: nrv + title: Normative Requirements Vocabulary + uri: http://ns.inria.fr/nrv +- namespace: http://purl.org/ontology/storyline/ + prefix: nsl + title: A News Storyline Ontology + uri: http://purl.org/ontology/storyline +- namespace: http://ns.inria.fr/nicetag/2010/09/09/voc# + prefix: ntag + title: Nice Tag Ontology + uri: http://ns.inria.fr/nicetag/2010/09/09/voc +- namespace: http://www.w3.org/ns/oa# + prefix: oa + title: Open Annotation Data Model + uri: http://www.w3.org/ns/oa# +- namespace: http://culturalis.org/oad# + prefix: oad + title: Ontology for archival description + uri: http://culturalis.org/oad# +- namespace: http://www.ics.forth.gr/isl/oae/core# + prefix: oae + title: Open NEE Model + uri: http://www.ics.forth.gr/isl/oae/core +- namespace: http://purl.obolibrary.org/obo/ + prefix: obo + title: Ontology for Biomedical Investigation + uri: http://purl.obolibrary.org/obo/obi.owl +- namespace: http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl# + prefix: obws + title: Object with states ontology + uri: http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl +- namespace: http://dati.camera.it/ocd/ + prefix: ocd + title: Ontology of Italian Deputy Chamber + uri: http://dati.camera.it/ocd/ +- namespace: http://purl.org/onto-ocds/ocds# + prefix: ocds + title: Schema for an Open Contracting Release (OCDS) + uri: http://purl.org/onto-ocds/ocds +- namespace: http://vocab.deri.ie/odapp# + prefix: odapp + title: Open Data Applications Vocabulary + uri: http://vocab.deri.ie/odapp +- namespace: http://semweb.mmlab.be/ns/odapps# + prefix: odapps + title: The vocabulary for (L)OD ideas and applications + uri: http://semweb.mmlab.be/ns/odapps +- namespace: http://www.ontologydesignpatterns.org/cp/owl/participation.owl# + prefix: odpart + title: Ontology Design Pattern Participation + uri: http://www.ontologydesignpatterns.org/cp/owl/participation.owl +- namespace: http://www.w3.org/ns/odrl/2/ + prefix: odrl + title: The Open Digital Rights Language (ODRL) Ontology + uri: http://www.w3.org/ns/odrl/2/ +- namespace: http://schema.theodi.org/odrs# + prefix: odrs + title: Open Data Rights Statement Vocabulary + uri: http://schema.theodi.org/odrs +- namespace: http://www.oegov.org/core/owl/cc# + prefix: oecc + title: Extended Creative Commons Ontology + uri: http://www.oegov.org/core/owl/cc +- namespace: http://owlrep.eu01.aws.af.cm/fridge# + prefix: of + title: Open Fridge vocabulary + uri: http://owlrep.eu01.aws.af.cm/fridge +- namespace: http://purl.org/opdm/refrigerator# + prefix: ofrd + title: Fridge and Freezer Vocabulary + uri: http://purl.org/opdm/refrigerator# +- namespace: http://ogp.me/ns# + prefix: og + title: Open Graph Protocol Vocabulary + uri: http://ogp.me/ns +- namespace: http://semweb.mmlab.be/ns/oh# + prefix: oh + title: The Opening Hours vocabulary + uri: http://semweb.mmlab.be/ns/oh +- namespace: https://w3id.org/vocab/olca# + prefix: olca + title: Ontology Loose Coupling Annotation + uri: https://w3id.org/vocab/olca +- namespace: http://purl.org/ontology/olo/core# + prefix: olo + title: Ordered List Ontology + uri: http://purl.org/ontology/olo/core# +- namespace: https://w3id.org/omg# + prefix: omg + title: 'OMG: Ontology for Managing Geometry' + uri: https://w3id.org/omg +- namespace: http://open-multinet.info/ontology/omn# + prefix: omn + title: Open-Multinet Upper Ontology + uri: http://open-multinet.info/ontology/omn +- namespace: http://open-multinet.info/ontology/omn-federation# + prefix: omnfed + title: Open-Multinet Upper Federation Ontology + uri: http://open-multinet.info/ontology/omn-federation +- namespace: http://open-multinet.info/ontology/omn-lifecycle# + prefix: omnlc + title: Open-Multinet Upper Lifecycle Ontology + uri: http://open-multinet.info/ontology/omn-lifecycle +- namespace: http://www.ics.forth.gr/isl/oncm/core# + prefix: onc + title: Open NEE Configuration Model + uri: http://www.ics.forth.gr/isl/oncm/core +- namespace: http://purl.org/net/ns/ontology-annot# + prefix: ont + title: Ontology annotation DLiser vocabulary + uri: http://purl.org/net/ns/ontology-annot +- namespace: http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl# + prefix: ontopic + title: Ontopic Ontology + uri: http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl +- namespace: http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl# + prefix: ontosec + title: Ontology Security + uri: http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl +- namespace: http://www.gsi.dit.upm.es/ontologies/onyx/ns# + prefix: onyx + title: Onyx Emotion Ontology + uri: http://www.gsi.dit.upm.es/ontologies/onyx/ns +- namespace: http://environment.data.gov.au/def/op# + prefix: op + title: Observable properties + uri: http://environment.data.gov.au/def/op +- namespace: http://ontology.eil.utoronto.ca/open311# + prefix: open311 + title: "Open 311 Ontology: An Ontology for publishing a city's non-emergency events." + uri: http://ontology.eil.utoronto.ca/open311.owl +- namespace: https://w3id.org/opm# + prefix: opm + title: 'OPM: Ontology for Property Management' + uri: https://w3id.org/opm +- namespace: http://openprovenance.org/model/opmo# + prefix: opmo + title: Open Provenance Model + uri: http://openprovenance.org/model/opmo +- namespace: http://purl.org/net/opmv/ns# + prefix: opmv + title: Open Provenance Model Vocabulary + uri: http://purl.org/net/opmv/ns# +- namespace: http://www.opmw.org/ontology/ + prefix: opmw + title: The OPMW Ontology + uri: http://www.opmw.org/ontology/ +- namespace: http://vocab.deri.ie/orca# + prefix: orca + title: orca, the Ontology of Reasoning, Certainty and Attribution + uri: http://vocab.deri.ie/orca +- namespace: http://www.openarchives.org/ore/terms/ + prefix: ore + title: The OAI ORE terms vocabulary + uri: http://www.openarchives.org/ore/terms/ +- namespace: http://www.w3.org/ns/org# + prefix: org + title: Core organization ontology + uri: http://www.w3.org/ns/org# +- namespace: http://datos.gob.es/def/sector-publico/organizacion# + prefix: orges + title: Ontology about Spanish public organizations + uri: http://datos.gob.es/def/sector-publico/organizacion# +- namespace: http://data.ordnancesurvey.co.uk/ontology/admingeo/ + prefix: osadm + title: The administrative geography and civil voting area ontology + uri: http://data.ordnancesurvey.co.uk/ontology/admingeo/ +- namespace: http://data.ordnancesurvey.co.uk/ontology/geometry/ + prefix: osgeom + title: Ordnance Survey Geometry Ontology + uri: http://data.ordnancesurvey.co.uk/ontology/geometry/ +- namespace: http://open-services.net/ns/core# + prefix: oslc + title: OSLC Core Vocabulary + uri: http://open-services.net/ns/core# +- namespace: http://purl.org/oslo/ns/localgov# + prefix: oslo + title: OSLO Exchange Standard + uri: http://purl.org/oslo/ns/localgov +- namespace: http://data.ordnancesurvey.co.uk/ontology/spatialrelations/ + prefix: osspr + title: Spatial Relations Ontology + uri: http://data.ordnancesurvey.co.uk/ontology/spatialrelations/ +- namespace: http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl# + prefix: ostop + title: Ordnance Survey Topography Ontology + uri: http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl +- namespace: https://w3id.org/opentrafficlights# + prefix: otl + title: The Open Traffic Lights ontology + uri: https://w3id.org/opentrafficlights +- namespace: http://open.vocab.org/terms/ + prefix: ov + title: OpenVocab + uri: http://open.vocab.org/terms +- namespace: http://www.w3.org/2002/07/owl# + prefix: owl + title: The OWL 2 Schema vocabulary + uri: http://www.w3.org/2002/07/owl +- namespace: http://purl.org/net/p-plan# + prefix: p-plan + title: The P-PLAN Ontology + uri: http://purl.org/net/p-plan# +- namespace: http://purl.org/vocab/participation/schema# + prefix: part + title: Participation Schema + uri: http://purl.org/vocab/participation/schema +- namespace: http://purl.org/hpi/patchr# + prefix: pat + title: Patch Request Ontology + uri: http://purl.org/hpi/patchr# +- namespace: http://www.essepuntato.it/2008/12/pattern# + prefix: pattern + title: The Pattern Ontology + uri: http://www.essepuntato.it/2008/12/pattern +- namespace: http://purl.org/pav/ + prefix: pav + title: Provenance, Authoring and Versioning + uri: http://purl.org/pav/ +- namespace: http://purl.org/ontology/pbo/core# + prefix: pbo + title: Play Back Ontology + uri: http://purl.org/ontology/pbo/core# +- namespace: http://purl.org/procurement/public-contracts# + prefix: pc + title: Public Contracts Ontology + uri: http://purl.org/procurement/public-contracts +- namespace: http://ontologies.smile.deri.ie/pdo# + prefix: pdo + title: Project Documents Ontology + uri: http://vocab.deri.ie/pdo +- namespace: https://w3id.org/pep/ + prefix: pep + title: Process Execution ontology. + uri: https://w3id.org/pep/ +- namespace: http://www.w3.org/ns/person# + prefix: person + title: ISA Programme Person Core Vocabulary + uri: http://www.w3.org/ns/person +- namespace: http://www.ontotext.com/proton/protonext# + prefix: pext + title: PROTON Extent module + uri: http://www.ontotext.com/proton/protonext +- namespace: https://w3id.org/pfeepsa# + prefix: pfeepsa + title: The PFEEPSA Ontology. + uri: https://w3id.org/pfeepsa# +- namespace: http://data.cochrane.org/ontologies/pico/ + prefix: pico + title: Cochrane PICO Ontology + uri: http://data.cochrane.org/ontologies/pico/ +- namespace: http://purl.org/ontology/places# + prefix: place + title: The Places Ontology + uri: http://purl.org/ontology/places +- namespace: http://cedric.cnam.fr/isid/ontologies/PersonLink.owl# + prefix: plink + title: PersonLink Ontology + uri: http://cedric.cnam.fr/isid/ontologies/PersonLink.owl +- namespace: http://purl.org/net/po# + prefix: plo + title: Playlist Ontology + uri: http://purl.org/net/po# +- namespace: http://premon.fbk.eu/ontology/fn# + prefix: pmofn + title: Predicate Model for Ontologies (PreMOn) - FrameNet ontology module + uri: http://premon.fbk.eu/ontology/fn +- namespace: http://premon.fbk.eu/ontology/nb# + prefix: pmonb + title: Predicate Model for Ontologies (PreMOn) - NomBank ontology module + uri: http://premon.fbk.eu/ontology/nb +- namespace: http://premon.fbk.eu/ontology/pb# + prefix: pmopb + title: Predicate Model for Ontologies (PreMOn) - PropBank ontology module + uri: http://premon.fbk.eu/ontology/pb +- namespace: http://premon.fbk.eu/ontology/vn# + prefix: pmovn + title: Predicate Model for Ontologies (PreMOn) - VerbNet ontology module + uri: http://premon.fbk.eu/ontology/vn +- namespace: http://purl.org/ontology/po/ + prefix: po + title: Programmes ontology + uri: http://purl.org/ontology/po/ +- namespace: http://dev.poderopedia.com/vocab/ + prefix: poder + title: Poder Vocabulary + uri: http://dev.poderopedia.com/vocab/schema +- namespace: http://data.ordnancesurvey.co.uk/ontology/postcode/ + prefix: postcode + title: Postcode Ontology + uri: http://data.ordnancesurvey.co.uk/ontology/postcode/ +- namespace: http://vocab.deri.ie/ppo# + prefix: ppo + title: Privacy Preference Ontology + uri: http://vocab.deri.ie/ppo +- namespace: http://contsem.unizar.es/def/sector-publico/pproc# + prefix: pproc + title: PPROC ontology + uri: http://contsem.unizar.es/def/sector-publico/pproc +- namespace: http://purl.org/ontology/prv/core# + prefix: pr + title: Property Reification Vocabulary + uri: http://purl.org/ontology/prv/core# +- namespace: http://www.loc.gov/premis/rdf/v1# + prefix: premis + title: PREMIS Ontology + uri: http://www.loc.gov/premis/rdf/v1 +- namespace: http://ns.inria.fr/prissma/v2# + prefix: prissma + title: Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability + uri: http://ns.inria.fr/prissma/v2# +- namespace: http://purl.org/spar/pro/ + prefix: pro + title: The Publishing Roles Ontology + uri: http://purl.org/spar/pro +- namespace: http://www.w3.org/ns/dx/prof/ + prefix: prof + title: Profiles Vocabulary + uri: http://www.w3.org/ns/dx/prof +- namespace: http://www.w3.org/ns/prov# + prefix: prov + title: W3C PROVenance Interchange + uri: http://www.w3.org/ns/prov# +- namespace: http://ns.inria.fr/provoc# + prefix: provoc + title: Product Vocabulary + uri: http://ns.inria.fr/provoc +- namespace: http://purl.org/net/provenance/ns# + prefix: prv + title: Provenance Vocabulary Core Ontology + uri: http://purl.org/net/provenance/ns# +- namespace: http://purl.org/net/provenance/types# + prefix: prvt + title: Provenance Vocabulary types + uri: http://purl.org/net/provenance/types# +- namespace: http://purl.org/spar/pso/ + prefix: pso + title: The Publishing Status Ontology + uri: http://purl.org/spar/pso +- namespace: http://www.ontotext.com/proton/protontop# + prefix: ptop + title: PROTON (Proto Ontology), Top Module + uri: http://www.ontotext.com/proton/protontop +- namespace: https://vocab.eccenca.com/pubsub/ + prefix: pubsub + title: Eccenca Publish-Subscribe Vocabulary + uri: https://vocab.eccenca.com/pubsub/ +- namespace: http://purl.org/spar/pwo/ + prefix: pwo + title: The Publishing Workflow Ontology + uri: http://purl.org/spar/pwo +- namespace: http://purl.org/linked-data/cube# + prefix: qb + title: The data cube vocabulary + uri: http://purl.org/linked-data/cube +- namespace: http://purl.org/qb4olap/cubes# + prefix: qb4o + title: Vocabulary for publishing OLAP data cubes + uri: http://purl.org/qb4olap/cubes +- namespace: http://purl.oclc.org/NET/ssnx/qu/qu# + prefix: qu + title: Quantity Kinds and Units + uri: http://purl.oclc.org/NET/ssnx/qu/qu +- namespace: http://qudt.org/schema/qudt/ + prefix: qudt + title: Quantities, Units, Dimensions and Types + uri: http://qudt.org/schema/qudt +- namespace: https://w3id.org/arco/ontology/arco/ + prefix: r-arco + title: ArCo Ontology (ArCo network) + uri: https://w3id.org/arco/ontology/arco +- namespace: http://guava.iis.sinica.edu.tw/r4r/ + prefix: r4r + title: Relations for Reusing (R4R) Ontology + uri: http://guava.iis.sinica.edu.tw/r4r +- namespace: http://www.w3.org/ns/radion# + prefix: radion + title: Repository Asset Distribution + uri: http://www.w3.org/ns/radion# +- namespace: http://iais.fraunhofer.de/vocabs/rami# + prefix: rami + title: rami - Reference Architecture Model + uri: https://w3id.org/i40/rami/ +- namespace: http://purl.org/NET/raul# + prefix: raul + title: RAUL Vocabulary + uri: http://vocab.deri.ie/raul +- namespace: http://rdvocab.info/uri/schema/FRBRentitiesRDA/ + prefix: rdafrbr + title: FRBR Entities for RDA + uri: http://rdvocab.info/uri/schema/FRBRentitiesRDA +- namespace: http://rdvocab.info/Elements/ + prefix: rdag1 + title: RDA Group 1 Elements + uri: http://rdvocab.info/Elements +- namespace: http://rdvocab.info/ElementsGr2/ + prefix: rdag2 + title: RDA Group 2 Elements + uri: http://rdvocab.info/ElementsGr2 +- namespace: http://rdvocab.info/ElementsGr3/ + prefix: rdag3 + title: RDA Group 3 Elements + uri: http://rdvocab.info/ElementsGr3 +- namespace: http://rdvocab.info/RDARelationshipsWEMI/ + prefix: rdarel + title: RDA Relationships for Works, Expressions, Manifestations, Items + uri: http://rdvocab.info/RDARelationshipsWEMI +- namespace: http://metadataregistry.org/uri/schema/RDARelationshipsGR2/ + prefix: rdarel2 + title: RDA Relationships GR2 + uri: http://metadataregistry.org/uri/schema/RDARelationshipsGR2 +- namespace: http://rdvocab.info/roles/ + prefix: rdarole + title: RDA Roles + uri: http://rdvocab.info/roles +- namespace: http://www.w3.org/1999/02/22-rdf-syntax-ns# + prefix: rdf + title: The RDF Concepts Vocabulary + uri: http://www.w3.org/1999/02/22-rdf-syntax-ns# +- namespace: http://www.w3.org/ns/rdfa# + prefix: rdfa + title: RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting + uri: http://www.w3.org/ns/rdfa# +- namespace: http://www.w3.org/2004/03/trix/rdfg-1/ + prefix: rdfg + title: Graph + uri: http://www.w3.org/2004/03/trix/rdfg-1/ +- namespace: https://w3id.org/rdfp/ + prefix: rdfp + title: The RDF Presentation ontology + uri: https://w3id.org/rdfp/ +- namespace: http://www.w3.org/2000/01/rdf-schema# + prefix: rdfs + title: The RDF Schema vocabulary + uri: http://www.w3.org/2000/01/rdf-schema# +- namespace: http://purl.org/ontology/rec/core# + prefix: rec + title: Recommendation Ontology + uri: http://purl.org/ontology/rec/core# +- namespace: http://www.w3.org/2001/02pd/rec54# + prefix: rec54 + title: Model of the W3C Process + uri: http://www.w3.org/2001/02pd/rec54# +- namespace: http://purl.org/reco# + prefix: reco + title: RECommendations Ontology + uri: http://purl.org/reco# +- namespace: http://reegle.info/schema# + prefix: reegle + title: Renewable Energy and Energy Efficiency + uri: http://reegle.info/schema +- namespace: http://purl.org/vocab/relationship/ + prefix: rel + title: Relationship + uri: http://purl.org/vocab/relationship/ +- namespace: http://www.purl.org/net/remetca# + prefix: remetca + title: ReMetCa Ontology + uri: http://www.purl.org/net/remetca# +- namespace: http://purl.org/stuff/rev# + prefix: rev + title: Review Vocabulary + uri: http://purl.org/stuff/rev# +- namespace: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog# + prefix: rlog + title: RDF Logging Ontology + uri: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog# +- namespace: http://purl.org/wf4ever/ro# + prefix: ro + title: The Research Object Ontology + uri: http://purl.org/wf4ever/ro +- namespace: http://vocab.deri.ie/rooms# + prefix: rooms + title: Buildings and Rooms Vocabulary + uri: http://vocab.deri.ie/rooms +- namespace: http://www.w3.org/ns/regorg# + prefix: rov + title: Registered Organization Vocabulary + uri: http://www.w3.org/ns/regorg +- namespace: http://www.w3.org/ns/r2rml# + prefix: rr + title: RDB to RDF Mapping Language Schema + uri: http://www.w3.org/ns/r2rml# +- namespace: http://softeng.polito.it/rsctx# + prefix: rsctx + title: Recommender System Context + uri: http://softeng.polito.it/rsctx +- namespace: http://purl.org/rss/1.0/ + prefix: rss + title: Vocabulary for Rich Site Summary (RSS) 1.0 + uri: http://purl.org/rss/1.0 +- namespace: http://purl.org/imbi/ru-meta.owl# + prefix: ru + title: Representational Units Metadata Ontology + uri: http://purl.org/imbi/ru-meta.owl +- namespace: http://rdfunit.aksw.org/ns/core# + prefix: ruto + title: Test-Driven Data Debugging Ontology + uri: http://rdfunit.aksw.org/ns/core# +- namespace: http://ns.inria.fr/s4ac/v2# + prefix: s4ac + title: Social Semantic SPARQL Security For Access Control Ontology + uri: http://ns.inria.fr/s4ac/v2 +- namespace: https://w3id.org/def/saref4bldg# + prefix: s4bldg + title: SAREF extension for building devices + uri: https://w3id.org/def/saref4bldg +- namespace: https://w3id.org/saref4ee# + prefix: s4ee + title: 'SAREF4EE: the EEbus/Energy@home extension of SAREF' + uri: https://w3id.org/saref4ee +- namespace: http://dati.san.beniculturali.it/SAN/ + prefix: san-lod + title: SAN Ontologia + uri: http://dati.san.beniculturali.it/SAN/ +- namespace: https://w3id.org/saref# + prefix: saref + title: 'SAREF: the Smart Appliances REFerence ontology' + uri: https://w3id.org/saref +- namespace: https://w3id.org/def/saref4agri# + prefix: saref4agri + title: SAREF extension for Agriculture + uri: https://w3id.org/def/saref4agri +- namespace: http://purl.org/saws/ontology# + prefix: saws + title: Sharing Ancient Wisdoms Ontology + uri: http://purl.org/saws/ontology +- namespace: http://schema.org/ + prefix: schema + title: Schema.org vocabulary + uri: http://schema.org/ +- namespace: http://lod.taxonconcept.org/ontology/sci_people.owl# + prefix: scip + title: Scientific People Ontology + uri: http://lod.taxonconcept.org/ontology/sci_people.owl +- namespace: http://purl.org/spar/scoro/ + prefix: scoro + title: Scholarly Contributions and Roles Ontology + uri: http://purl.org/spar/scoro/ +- namespace: http://rdfs.org/scot/ns# + prefix: scot + title: Social Semantic Cloud of Tags + uri: http://rdfs.org/scot/ns# +- namespace: http://purl.org/NET/scovo# + prefix: scovo + title: The Statistical Core Vocabulary + uri: http://vocab.deri.ie/scovo +- namespace: http://purl.org/NET/schema-org-csv# + prefix: scsv + title: Schema.org CSV + uri: http://vocab.deri.ie/scsv +- namespace: http://www.w3.org/ns/sparql-service-description# + prefix: sd + title: SPARQL 1.1 Service Description + uri: http://www.w3.org/ns/sparql-service-description +- namespace: https://w3id.org/vocab/sdm# + prefix: sdm + title: SPARQL endpoint metadata + uri: https://w3id.org/vocab/sdm +- namespace: http://purl.org/linked-data/sdmx# + prefix: sdmx + title: SDMX-RDF vocabulary + uri: http://purl.org/linked-data/sdmx +- namespace: http://purl.org/linked-data/sdmx/2009/code# + prefix: sdmx-code + title: SDMX Code + uri: http://purl.org/linked-data/sdmx/2009/code +- namespace: http://purl.org/linked-data/sdmx/2009/dimension# + prefix: sdmx-dimension + title: SDMX Dimension + uri: http://purl.org/linked-data/sdmx/2009/dimension +- namespace: http://sindice.com/vocab/search# + prefix: search + title: Sindice Search Vocabulary + uri: http://vocab.deri.ie/search +- namespace: https://w3id.org/seas/ + prefix: seas + title: SEAS ontology + uri: https://w3id.org/seas/ +- namespace: https://w3id.org/seas/ + prefix: seas-eval + title: The SEAS Evaluation ontology + uri: https://w3id.org/seas/EvaluationOntology +- namespace: https://w3id.org/seas/ + prefix: seas-op + title: The SEAS Failable System ontology + uri: https://w3id.org/seas/OperatingOntology +- namespace: https://w3id.org/seas/ + prefix: seas-qudt + title: QUDT Alignment. + uri: https://w3id.org/seas/QUDTAlignment +- namespace: https://w3id.org/seas/ + prefix: seas-stats + title: The SEAS Statistics ontology. + uri: https://w3id.org/seas/StatisticsOntology +- namespace: https://w3id.org/seas/ + prefix: seas-sys + title: The SEAS System ontology + uri: https://w3id.org/seas/SystemOntology +- namespace: https://w3id.org/seas/ + prefix: seasb + title: The SEAS Battery ontology. + uri: https://w3id.org/seas/BatteryOntology +- namespace: https://w3id.org/seas/ + prefix: seasbo + title: The SEAS Building Ontology + uri: https://w3id.org/seas/BuildingOntology +- namespace: https://w3id.org/seas/ + prefix: seasd + title: The SEAS Device ontology + uri: https://w3id.org/seas/DeviceOntology +- namespace: https://w3id.org/seas/ + prefix: seasfo + title: The SEAS Forecasting ontology + uri: https://w3id.org/seas/ForecastingOntology +- namespace: https://w3id.org/seas/ + prefix: seast + title: The SEAS Time Ontology. + uri: https://w3id.org/seas/TimeOntology +- namespace: https://w3id.org/seas/ + prefix: seasto + title: The SEAS Trading ontology + uri: https://w3id.org/seas/TradingOntology +- namespace: http://securitytoolbox.appspot.com/securityMain# + prefix: security + title: Security Ontology + uri: http://securitytoolbox.appspot.com/securityMain +- namespace: http://semanticweb.cs.vu.nl/2009/11/sem/ + prefix: sem + title: The SEM Ontology + uri: http://semanticweb.cs.vu.nl/2009/11/sem/ +- namespace: http://purl.org/SemSur/ + prefix: semsur + title: The Semantic Survey Ontology (semsur) + uri: http://purl.org/SemSur/ +- namespace: http://purl.org/seo/ + prefix: seo + title: The Scientific Events Ontology + uri: http://purl.org/seo/ +- namespace: http://www.ontologydesignpatterns.org/cp/owl/sequence.owl# + prefix: seq + title: Sequence Pattern + uri: http://www.ontologydesignpatterns.org/cp/owl/sequence.owl +- namespace: http://purl.org/ontology/service# + prefix: service + title: The Service Ontology + uri: http://purl.org/ontology/service +- namespace: http://www.opengis.net/ont/sf# + prefix: sf + title: Simplified Features Geometry + uri: http://www.opengis.net/ont/sf +- namespace: http://www.w3.org/ns/shacl# + prefix: sh + title: W3C Shapes Constraint Language (SHACL) Vocabulary + uri: http://www.w3.org/ns/shacl# +- namespace: http://dati.cdec.it/lod/shoah/ + prefix: shoah + title: Shoah Vocabulary Specification + uri: http://dati.cdec.it/lod/shoah/ +- namespace: http://paul.staroch.name/thesis/SmartHomeWeather.owl# + prefix: shw + title: Smart Home Weather + uri: http://paul.staroch.name/thesis/SmartHomeWeather.owl# +- namespace: http://purl.org/ontology/similarity/ + prefix: sim + title: The Similarity Ontology + uri: http://purl.org/ontology/similarity/ +- namespace: http://semanticscience.org/resource/ + prefix: sio + title: Semanticscience Integrated Ontology + uri: http://semanticscience.org/ontology/sio.owl +- namespace: http://rdfs.org/sioc/ns# + prefix: sioc + title: Semantically-Interlinked Online Communities + uri: http://rdfs.org/sioc/ns# +- namespace: http://www.ontologydesignpatterns.org/cp/owl/situation.owl# + prefix: situ + title: Situation Pattern + uri: http://www.ontologydesignpatterns.org/cp/owl/situation.owl +- namespace: http://www.w3.org/2004/02/skos/core# + prefix: skos + title: Simple Knowledge Organization System + uri: http://www.w3.org/2004/02/skos/core +- namespace: http://www.w3.org/2008/05/skos-xl# + prefix: skosxl + title: SKOS eXtension for Labels + uri: http://www.w3.org/2008/05/skos-xl +- namespace: http://www.w3.org/ns/solid/terms# + prefix: solid + title: Solid terms + uri: http://www.w3.org/ns/solid/terms +- namespace: http://purl.org/net/soron/ + prefix: sor + title: 'SORON: Social Relationships ONtology' + uri: http://purl.org/net/soron +- namespace: http://www.w3.org/ns/sosa/ + prefix: sosa + title: Sensor, Observation, Sample, and Actuator (SOSA) Ontology + uri: http://www.w3.org/ns/sosa/ +- namespace: http://spinrdf.org/sp# + prefix: sp + title: SPIN SPARQL Syntax + uri: http://spinrdf.org/sp +- namespace: http://geovocab.org/spatial# + prefix: spatial + title: NeoGeo Spatial Ontology + uri: http://geovocab.org/spatial +- namespace: http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl# + prefix: spfood + title: SmartProducts Food Domain Model + uri: http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl +- namespace: http://spinrdf.org/spin# + prefix: spin + title: SPIN Inferencing Vocabulary + uri: http://spinrdf.org/spin +- namespace: http://www.bbc.co.uk/ontologies/sport/ + prefix: sport + title: BBC Sport Ontology + uri: http://www.bbc.co.uk/ontologies/sport +- namespace: http://spitfire-project.eu/ontology/ns/ + prefix: spt + title: SPITFIRE Ontology + uri: http://spitfire-project.eu/ontology/ns +- namespace: http://ns.inria.fr/ast/sql# + prefix: sql + title: SQL Abstract Syntax Trees Vocabulary + uri: http://ns.inria.fr/ast/sql# +- namespace: http://purl.oclc.org/NET/ssnx/ssn# + prefix: ssn + title: Semantic Sensor Network Ontology + uri: http://www.w3.org/2005/Incubator/ssn/ssnx/ssn +- namespace: http://www.w3.org/ns/ssn/ + prefix: ssno + title: Semantic Sensor Network Ontology + uri: http://www.w3.org/ns/ssn/ +- namespace: http://purl.org/ontology/ssso# + prefix: ssso + title: Simple Service Status Ontology + uri: http://purl.org/ontology/ssso +- namespace: http://semweb.mmlab.be/ns/stoptimes# + prefix: st + title: The Stop Times ontology + uri: http://semweb.mmlab.be/ns/stoptimes#Ontology +- namespace: http://securitytoolbox.appspot.com/stac# + prefix: stac + title: 'Security Toolbox : Attacks and Countermeasures' + uri: http://securitytoolbox.appspot.com/stac +- namespace: http://purl.org/net/step# + prefix: step + title: Semantic Trajectory Episodes + uri: http://purl.org/net/step +- namespace: https://w3id.org/i40/sto# + prefix: sto + title: i40 Standards Lanscape Vocabulary + uri: https://w3id.org/i40/sto# +- namespace: https://w3id.org/survey-ontology# + prefix: sur + title: The Survey Ontology + uri: https://www.w3id.org/survey-ontology +- namespace: https://w3id.org/squap/SoftwareQuality/ + prefix: sw-quality + title: SQuAP Ontology + uri: https://w3id.org/squap/ +- namespace: http://www.w3.org/2004/03/trix/swp-1/ + prefix: swp + title: Graph Authority + uri: http://www.w3.org/2004/03/trix/swp-1 +- namespace: http://swrc.ontoware.org/ontology# + prefix: swrc + title: Semantic Web for Research Communities + uri: http://swrc.ontoware.org/ontology-07 +- namespace: http://www.w3.org/2003/11/swrl# + prefix: swrl + title: Semantic Web Rule Language + uri: http://www.w3.org/2003/11/swrl +- namespace: http://ns.bergnet.org/tac/0.1/triple-access-control# + prefix: tac + title: TripleAccessControl Ontology + uri: http://ns.bergnet.org/tac/0.1/triple-access-control +- namespace: http://vocab.deri.ie/tao# + prefix: tao + title: Trust Assertion Ontology + uri: http://vocab.deri.ie/tao +- namespace: http://purl.org/biodiversity/taxon/ + prefix: taxon + title: TaxonMap Ontology + uri: http://purl.org/biodiversity/taxon/ +- namespace: https://w3id.org/timebank# + prefix: tb + title: Timebank Ontology + uri: https://w3id.org/timebank +- namespace: http://www.w3.org/2006/time-entry# + prefix: te + title: Time Entry + uri: http://www.w3.org/2006/time-entry +- namespace: http://linkedscience.org/teach/ns# + prefix: teach + title: Teaching Core Vocabulary Specification + uri: http://linkedscience.org/teach/ns# +- namespace: http://www.w3.org/2006/03/test-description# + prefix: test + title: Test Metadata + uri: http://www.w3.org/2006/03/test-description +- namespace: https://privatealpha.com/ontology/transformation/1# + prefix: tfo + title: Transformation Functions Ontology + uri: https://privatealpha.com/ontology/transformation/1# +- namespace: http://purl.org/theatre# + prefix: theatre + title: Theatre Ontology + uri: http://purl.org/theatre# +- namespace: http://resource.geosciml.org/ontology/timescale/thors# + prefix: thors + title: The Temporal Ordinal Reference Systems + uri: http://resource.geosciml.org/ontology/timescale/thors +- namespace: http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl# + prefix: ti + title: The Time Interval Pattern + uri: http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl +- namespace: http://www.w3.org/2006/time# + prefix: time + title: Time Ontology + uri: http://www.w3.org/2006/time +- namespace: http://purl.org/tio/ns# + prefix: tio + title: The Tickets Ontology + uri: http://purl.org/tio/ns# +- namespace: http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl + prefix: tis + title: Time Indexed Situation + uri: http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl +- namespace: http://observedchange.com/tisc/ns# + prefix: tisc + title: Open Time and Space Core Vocabulary + uri: http://www.observedchange.com/tisc/ns# +- namespace: http://purl.org/NET/c4dm/timeline.owl# + prefix: tl + title: The Timeline Ontology + uri: http://purl.org/NET/c4dm/timeline.owl +- namespace: http://www.w3.org/2001/sw/hcls/ns/transmed/ + prefix: tmo + title: Translational Medicine Ontology + uri: http://www.w3.org/2001/sw/hcls/ns/transmed/ +- namespace: http://purl.org/toco/ + prefix: toco + title: Toucan Ontology + uri: http://purl.org/toco/ +- namespace: http://data.ign.fr/def/topo# + prefix: topo + title: An ontology for describing territory elements an infrastructure at French Mapping Agency. + uri: http://data.ign.fr/def/topo +- namespace: http://tour-pedia.org/download/tp.owl# + prefix: tp + title: Tourpedia Ontology + uri: http://tour-pedia.org/download/tp.owl +- namespace: http://www.sensormeasurement.appspot.com/ont/transport/traffic# + prefix: traffic + title: Road Traffic Management + uri: http://www.sensormeasurement.appspot.com/ont/transport/traffic +- namespace: http://vocab.org/transit/terms/ + prefix: transit + title: TRANSIT + uri: http://vocab.org/transit/terms/ +- namespace: http://linkeddata.finki.ukim.mk/lod/ontology/tao# + prefix: trao + title: Transport Administration Ontology + uri: http://linkeddata.finki.ukim.mk/lod/ontology/tao# +- namespace: http://rdfs.org/sioc/types# + prefix: tsioc + title: SIOC Types Ontology Module + uri: http://rdfs.org/sioc/types# +- namespace: http://purl.org/net/tsn# + prefix: tsn + title: Territorial Statistical Nomenclature Ontology + uri: http://purl.org/net/tsn# +- namespace: http://purl.org/net/tsnchange# + prefix: tsnc + title: Territorial Statistical Nomenclature Change Ontology + uri: http://purl.org/net/tsnchange# +- namespace: http://www.essepuntato.it/2012/04/tvc/ + prefix: tvc + title: The Time-indexed Value in Context + uri: http://www.essepuntato.it/2012/04/tvc +- namespace: http://lod.taxonconcept.org/ontology/txn.owl# + prefix: txn + title: TaxonConcept Ontology + uri: http://lod.taxonconcept.org/ontology/txn.owl +- namespace: http://www.w3.org/2006/timezone# + prefix: tzont + title: Time Zone Ontology + uri: http://www.w3.org/2006/timezone +- namespace: http://purl.org/olia/ubyCat.owl# + prefix: uby + title: ubyCat.owl + uri: http://purl.org/olia/ubyCat.owl +- namespace: http://purl.org/uco/ns# + prefix: uco + title: Used Cars Ontology + uri: http://purl.org/uco/ns# +- namespace: http://purl.oclc.org/NET/muo/ucum/ + prefix: ucum + title: Units of measurement ontology + uri: http://purl.oclc.org/NET/muo/ucum/ +- namespace: http://www.w3.org/ns/ui# + prefix: ui + title: A user interface ontology + uri: http://www.w3.org/ns/ui +- namespace: http://purl.org/umu/uneskos# + prefix: uneskos + title: UNESKOS Vocabulary + uri: http://purl.org/umu/uneskos +- namespace: http://purl.uniprot.org/core/ + prefix: uniprot + title: Uniprot Core Ontology + uri: http://purl.uniprot.org/core/ +- namespace: http://uri4uri.net/vocab# + prefix: uri4uri + title: URI Vocabulary + uri: http://uri4uri.net/vocab +- namespace: https://w3id.org/usability# + prefix: usability + title: Usability + uri: https://w3id.org/usability +- namespace: http://www.linkedmodel.org/schema/vaem# + prefix: vaem + title: Vocabulary for Attaching Essential Metadata + uri: http://www.linkedmodel.org/schema/vaem +- namespace: http://www.essepuntato.it/2013/10/vagueness/ + prefix: vag + title: The Vagueness Ontology + uri: http://www.essepuntato.it/2013/10/vagueness +- namespace: http://purl.org/vocab/vann/ + prefix: vann + title: 'VANN: A vocabulary for annotating vocabulary descriptions' + uri: http://purl.org/vocab/vann/ +- namespace: http://www.w3.org/2006/vcard/ns# + prefix: vcard + title: An Ontology for vCards + uri: http://www.w3.org/2006/vcard/ns +- namespace: http://linkeddata.finki.ukim.mk/lod/ontology/veo# + prefix: veo + title: Vehicle Emissions Ontology + uri: http://linkeddata.finki.ukim.mk/lod/ontology/veo# +- namespace: http://purl.org/net/VideoGameOntology# + prefix: vgo + title: The Video Game Ontology + uri: http://purl.org/net/VideoGameOntology +- namespace: http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine# + prefix: vin + title: Wine Ontology + uri: http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine +- namespace: http://w3id.org/vir# + prefix: vir + title: VIR - Visual Representation ontology + uri: http://w3id.org/vir# +- namespace: http://vivoweb.org/ontology/core# + prefix: vivo + title: VIVO Core Ontology + uri: http://vivoweb.org/ontology/core +- namespace: http://purl.org/vocommons/voaf# + prefix: voaf + title: Vocabulary of a Friend + uri: http://purl.org/vocommons/voaf +- namespace: http://w3id.org/rsp/vocals# + prefix: vocals + title: 'VoCaLS: A Vocabulary and Catalog for Linked Streams' + uri: http://w3id.org/rsp/vocals# +- namespace: http://rdfs.org/ns/void# + prefix: void + title: Vocabulary of Interlinked Datasets + uri: http://vocab.deri.ie/void +- namespace: http://purl.org/query/voidext# + prefix: voidext + title: Extended Vocabulary of Interlinked Datasets (VoIDext) + uri: http://purl.org/query/voidext +- namespace: http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl + prefix: voidwh + title: Void Warehouse Ontology + uri: http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl +- namespace: http://purl.org/voc/vrank# + prefix: vrank + title: Vocabulary for Ranking + uri: http://vocab.sti2.at/vrank +- namespace: http://www.w3.org/2003/06/sw-vocab-status/ns# + prefix: vs + title: SemWeb Vocab Status ontology + uri: http://www.w3.org/2003/06/sw-vocab-status/ns +- namespace: http://purl.org/vso/ns# + prefix: vso + title: Vehicle Sales Ontology + uri: http://purl.org/vso/ns +- namespace: http://purl.org/vvo/ns# + prefix: vvo + title: Volkswagen Vehicles Ontology + uri: http://purl.org/vvo/ns# +- namespace: https://www.w3.org/ns/ssn/ + prefix: w3c-ssn + title: Semantic Sensor Network Ontology + uri: https://www.w3.org/ns/ssn +- namespace: http://purl.org/wai# + prefix: wai + title: Roles and Profiles Ontology + uri: http://purl.org/wai# +- namespace: http://www.w3.org/2007/05/powder-s# + prefix: wdrs + title: Protocol for Web Description Resources + uri: http://www.w3.org/2007/05/powder-s +- namespace: http://purl.org/net/wf-invocation# + prefix: wf-invoc + title: Workflow Invocation Ontology + uri: http://purl.org/net/wf-invocation +- namespace: http://purl.org/wf4ever/wfdesc# + prefix: wfdesc + title: The Wfdesc ontology + uri: http://purl.org/wf4ever/wfdesc +- namespace: http://purl.org/net/wf-motifs# + prefix: wfm + title: The Workflow Motif Ontology + uri: http://purl.org/net/wf-motifs +- namespace: http://purl.org/wf4ever/wfprov# + prefix: wfprov + title: The Wfprov Ontology + uri: http://purl.org/wf4ever/wfprov +- namespace: http://vocab.org/whisky/terms/ + prefix: whisky + title: Whisky Ontology + uri: http://vocab.org/whisky/terms +- namespace: http://www.kanzaki.com/ns/whois# + prefix: whois + title: Who's who description vocabulary + uri: http://www.kanzaki.com/ns/whois +- namespace: http://purl.org/ontology/wi/core# + prefix: wi + title: The Weighted Interests Vocabulary + uri: http://purl.org/ontology/wi/core# +- namespace: http://www.wsmo.org/ns/wsmo-lite# + prefix: wl + title: WSMO-Lite Ontology + uri: http://www.wsmo.org/ns/wsmo-lite# +- namespace: http://purl.org/ontology/wo/ + prefix: wlo + title: BBC Wildlife Ontology + uri: http://purl.org/ontology/wo/ +- namespace: http://purl.org/ontology/wo/core# + prefix: wo + title: Weighting Ontology + uri: http://purl.org/ontology/wo/core# +- namespace: http://xmlns.com/wot/0.1/ + prefix: wot + title: Web Of Trust + uri: http://xmlns.com/wot/0.1/ +- namespace: https://www.w3.org/2019/wot/security# + prefix: wotsec + title: Security mechanisms for the Web of Things + uri: https://www.w3.org/2019/wot/security# +- namespace: http://purl.org/xapi/ontology# + prefix: xapi + title: xAPI Controlled Vocabulary Ontology + uri: http://purl.org/xapi/ontology# +- namespace: https://w3id.org/vocab/xbrll# + prefix: xbrll + title: A lightweight XBRL vocabulary + uri: https://w3id.org/vocab/xbrll +- namespace: http://www.w3.org/1999/xhtml/vocab# + prefix: xhv + title: XHTML Vocabulary + uri: http://www.w3.org/1999/xhtml/vocab +- namespace: http://www.w3.org/2001/XMLSchema# + prefix: xsd + title: XML Schema + uri: http://www.w3.org/2001/XMLSchema +- namespace: http://zbw.eu/namespaces/zbw-extensions/ + prefix: zbwext + title: ZBW Extensions + uri: http://zbw.eu/namespaces/zbw-extensions +- namespace: http://www4.wiwiss.fu-berlin.de/gutendata/resource/ + prefix: fu-berlin-project-gutenberg + title: Project Gutenberg in RDF (FU Berlin) + uri: http://www4.wiwiss.fu-berlin.de/gutendata/ +- namespace: http://colinda.org/resource/ + prefix: colinda + title: COLINDA - Conference Linked Data + uri: http://colinda.org +- namespace: http://datos.eurohelp.es/PruebasFinales/ + prefix: gipuzkoademografia + title: Gipuzkoa Demografia + uri: http://datahub.io/dataset/GipuzkoaDemografia +- namespace: http://data.totl.net/ + prefix: temple-ov-thee-lemur-datasets + title: Temple ov thee Lemur + uri: http://data.totl.net/ +- namespace: http://curriculum.rkbexplorer.com/id/ + prefix: rkb-explorer-curriculum + title: ReSIST MSc in Resilient Computing Curriculum (RKBExplorer) + uri: http://curriculum.rkbexplorer.com +- namespace: http://linked.opendata.cz/resource/domain/coi.cz/confiscation/ + prefix: cz-ctia-confiscations + title: Confiscations of the Czech Trade Inspection Authority + uri: http://linked.opendata.cz/resource/dataset/coi.cz/zajisteni +- namespace: http://comsode.eu/resource/ + prefix: comsode-d3-2 + title: Requirements on the COMSODE project based on selected datasets + uri: http://comsode.eu/resource/dataset/COMSODE_D3.2 +- namespace: http://diavgeia.math.auth.gr/resource/ + prefix: diavgeia + title: Diavgeia + uri: http://opendata.diavgeia.gov.gr/?lang=en +- namespace: http://purl.org/vocabularies/cornetto/ + prefix: cornetto + title: Cornetto1.2 + uri: http://www2.let.vu.nl/oz/cltl/cornetto/ +- namespace: http://ft.rkbexplorer.com/id/ + prefix: rkb-explorer-ft + title: France Telecom Recherche et Développement (RKBExplorer) + uri: http://ft.rkbexplorer.com +- namespace: http://collection.britishmuseum.org/id/ + prefix: british-museum-collection + title: British Museum Collection + uri: http://collection.britishmuseum.org +- namespace: http://data.bib.uni-mannheim.de/data/ + prefix: ub-mannheim-linked-data + title: Linked Data Service der Universitätsbibliothek Mannheim + uri: http://data.bib.uni-mannheim.de/ +- namespace: http://yago-knowledge.org/resource/ + prefix: yago + title: YAGO + uri: http://yago-knowledge.org +- namespace: http://www.rdfabout.com/rdf/usgov/sec/id/ + prefix: sec-rdfabout + title: U.S. Securities and Exchange Commission Corporate Ownership RDF Data (rdfabout) + uri: http://www.rdfabout.com/demo/sec/ +- namespace: http://crime.rkbexplorer.com/id/ + prefix: rkb-explorer-crime + title: Street level crime reports for England and Wales + uri: http://crime.rkbexplorer.com/ +- namespace: http://ld.panlex.org/plx/ + prefix: panlex + title: PanLex + uri: http://panlex.org +- namespace: http://data.open.ac.uk/resource/ + prefix: data-open-ac-uk + title: data.open.ac.uk, Linked Data from the Open University + uri: http://data.open.ac.uk/ +- namespace: http://www.theses.fr/ + prefix: thesesfr + title: theses.fr + uri: http://www.theses.fr +- namespace: http://rdf.farmbio.uu.se/chembl/ + prefix: farmbio-chembl + title: ChEMBL-RDF (@ Uppsala University) + uri: https://github.com/egonw/chembl.rdf +- namespace: http://eur-lex.publicdata.eu/ontology/ + prefix: eur-lex-rdf + title: EUR-Lex as Linked Data + uri: http://eur-lex.publicdata.eu/ +- namespace: https://linkedsoftwaredependencies.org/ + prefix: npm + title: NPM + uri: https://github.com/LinkedSoftwareDependencies/npm-extraction-server +- namespace: http://www.kanzaki.com/works/2011/stat/ra/ + prefix: japan-radioactivity-stat + title: National Radioactivity Stat as Linked Data + uri: http://www.kanzaki.com/works/2011/stat/ra/ +- namespace: http://www.bedlamtheatre.co.uk/ + prefix: eutc-productions + title: Edinburgh University Theatre Company Productions + uri: http://www.bedlamtheatre.co.uk/ +- namespace: http://zhishi.me/ + prefix: zhishi-me + title: Zhishi.me + uri: http://zhishi.me +- namespace: http://chronos.org/janusamp/ + prefix: oceandrilling-janusamp + title: Ocean Drilling - Janus Age Models + uri: http://chronos.org/janusAmp/ +- namespace: http://nl.dbpedia.org/resource/ + prefix: dbpedia-nl + title: DBpedia in Dutch + uri: http://nl.dbpedia.org +- namespace: http://w3id.org/foodie/atlas/ + prefix: Urban Atlas Dataset + title: Urban Atlas dataset + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://ruian.linked.opendata.cz/resource/ + prefix: cz-cuzk-cadastre-offices + title: Cadastre offices from Czech land registry + uri: http://ruian.linked.opendata.cz/resource/dataset/cuzk/pracoviste-resortu +- namespace: http://id.sgcb.mcu.es/ + prefix: lista-encabezamientos-materia + title: Lista de Encabezamientos de Materia as Linked Open Data + uri: http://id.sgcb.mcu.es +- namespace: http://ineverycrea.net/en/community/ineverycreaargentina + prefix: ineverycrea-argentina + title: IneveryCREA Argentina, la comunidad de la creatividad educativa + uri: http://ineverycrea.net/en/community/ineverycreaargentina +- namespace: Americka Foka + prefix: Uros Susa + title: Legija + uri: http://www.facebook.com +- namespace: http://www.snik.eu/ontology/ + prefix: snik + title: SNIK + uri: https://www.snik.eu +- namespace: http://eumida.publicdata.eu/data/ + prefix: eumida-linked-data + title: EUMIDA as Linked Data + uri: http://eumida.publicdata.eu/ +- namespace: http://www4.wiwiss.fu-berlin.de/drugbank/resource/ + prefix: fu-berlin-drugbank + title: DrugBank + uri: http://www4.wiwiss.fu-berlin.de/drugbank/ +- namespace: http://dartmouth.eagle-i.net/i/ + prefix: eagle-i-dartmouth + title: eagle-i @ Dartmouth College + uri: http://dartmouth.eagle-i.net +- namespace: http://www.yovisto.com/resource + prefix: yovisto + title: Yovisto - academic video search + uri: http://www.yovisto.com/ontology/ +- namespace: http://gnoss.com/comunidad/nextweb + prefix: nextweb-gnoss + title: Next Web, a global knowledge network of semantic technology and Web 3.0 (GNOSS) + uri: http://gnoss.com/comunidad/nextweb +- namespace: http://w3id.org/foodie/open/cz/Soil_maps_BPEJ_WGSc/ + prefix: Soil maps + title: Erosion-endangered soil zones dataset from Czech Republic + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://www.yso.fi/onto/kunnat/ + prefix: finnish-municipalities + title: Finnish municipalities and regional classifications + uri: http://onki.fi/en/browser/overview/kunnat +- namespace: http://mismuseos.net/ + prefix: mismuseos-gnoss + title: Mis Museos, índice semántico de museos, artistas y obras de arte (GNOSS) + uri: http://mismuseos.net/ +- namespace: http://rae2001.rkbexplorer.com/id/ + prefix: rkb-explorer-rae2001 + title: Research Assessment Exercise 2001 (RKBExplorer) + uri: http://rae2001.rkbexplorer.com +- namespace: http://id.ndl.go.jp/auth/ndlsh/ + prefix: national-diet-library-subject-headings + title: National Diet Library of Japan subject headings + uri: http://id.ndl.go.jp/auth/ndlsh +- namespace: http://linked.opendata.cz/resource/domain/coi.cz/check-action/ + prefix: cz-ctia-inspections + title: Inspections of the Czech Trade Inspection Authority + uri: http://linked.opendata.cz/resource/dataset/coi.cz/kontroly +- namespace: https://linked.opendata.cz/zdroj/datová-schránka/ + prefix: cz-list-of-databoxes + title: List of Czech data boxes + uri: https://linked.opendata.cz/zdroj/datová-sada/datové-schránky +- namespace: http://www.gutenberg.org/ + prefix: gutenberg + title: Project Gutenberg + uri: http://www.gutenberg.org/ +- namespace: http://data.nku.cz/resource/ + prefix: cz-sao-audited-subjects + title: Audited subjects of Supreme Audit Office of the Czech Republic + uri: http://data.nku.cz/resource/dataset/audited-subjects +- namespace: http://dbtune.org/bbc/peel/ + prefix: dbtune-john-peel-sessions + title: DBTune.org John Peel sessions RDF server + uri: http://dbtune.org/bbc/peel/ +- namespace: http://data.kasabi.com/dataset/un-hazardous-material-numbers + prefix: un-hazardous-numbers + title: UN Hazardous Materials Numbers + uri: http://kasabi.com/dataset/un-hazardous-material-numbers +- namespace: http://red.gnoss.com/en/community/greencompetitiveness + prefix: green-competitiveness-gnoss + title: Green Competitiveness (GNOSS) + uri: http://red.gnoss.com/en/community/greencompetitiveness +- namespace: http://lod.gesis.org/thesoz/ + prefix: gesis-thesoz + title: TheSoz Thesaurus for the Social Sciences (GESIS) + uri: http://lod.gesis.org/thesoz/ +- namespace: http://www.fao.org/aims/aos/fi/taxonomic/ + prefix: FAO species + title: FAO ASFIS classification of biological entities + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://aims.fao.org/aos/jita/ + prefix: jita + title: JITA Classification System of Library and Information Science + uri: http://www.destin-informatique.com/ASKOSI/Wiki.jsp?page=JITA%20Maintenance +- namespace: http://red.gnoss.com/comunidad/buscaempresas + prefix: aegp-spanish-textile-and-clothing-association + title: AEGP, Spanish Textile and Clothing Association + uri: http://red.gnoss.com/comunidad/buscaempresas +- namespace: http://www.yso.fi/onto/yso/ + prefix: yso + title: YSO - General Finnish Ontology + uri: http://finto.fi/yso/ +- namespace: http://opencorporates.com/companies + prefix: opencorporates + title: OpenCorporates - The Open Database Of The Corporate World + uri: http://opencorporates.com/ +- namespace: http://msm.eagle-i.net/i/ + prefix: eagle-i-msm + title: eagle-i @ Morehouse School of Medicine + uri: http://msm.eagle-i.net +- namespace: http://core.kmi.open.ac.uk/data/ + prefix: core + title: CORE - Semantic Similarity of Open Access publications + uri: http://core-project.kmi.open.ac.uk/ +- namespace: http://ja.dbpedia.org/resource/ + prefix: dbpedia-ja + title: DBpedia in Japanese + uri: http://ja.dbpedia.org/ +- namespace: http://rod.eionet.europa.eu + prefix: eea-rod + title: EEA Reporting Obligations Database + uri: http://rod.eionet.europa.eu/ +- namespace: http://d-nb.info/ + prefix: deutsche-nationalbibliografie-dnb + title: Deutsche Nationalbibliografie (DNB) + uri: http://www.dnb.de/EN/lds +- namespace: http://linkeddata.uriburner.com/ + prefix: uriburner + title: URIBurner + uri: http://uriburner.com/ +- namespace: http://linkeddata.ge.imati.cnr.it/resource/ThIST/ + prefix: thist + title: ThIST + uri: http://purl.org/NET/ThISTWebPage +- namespace: http://datos.bcn.cl/recurso/ + prefix: datos-bcn-cl + title: Datos.bcn.cl + uri: https://datos.bcn.cl/es/ +- namespace: pm + prefix: premon + title: PreMOn + uri: http://premon.fbk.eu +- namespace: http://purl.org/science/plasmid/addgene/ + prefix: addgene + title: Addgene + uri: http://www.addgene.org/ +- namespace: http://museos.gnoss.com/comunidad/mismuseos/ + prefix: museosespania-gnoss + title: Museos de España, colección de museos públicos y privados españoles (GNOSS) + uri: http://museos.gnoss.com/comunidad/mismuseos/ +- namespace: http://institutions.publicdata.eu/# + prefix: eu-institutions + title: Institutions and Bodies of the European Union + uri: http://institutions.publicdata.eu/ +- namespace: http://uccaribe.eagle-i.net/i/ + prefix: eagle-i-uccaribe + title: eagle-i @ Universidad Central del Caribe + uri: http://uccaribe.eagle-i.net +- namespace: http://purl.org/weso/pscs/naics/2007/resource + prefix: naics-2007 + title: NAICS 2007 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: https://linked.opendata.cz/zdroj/ovm/ + prefix: cz-ovm + title: Institutions of public power of the Czech Republic + uri: https://linked.opendata.cz/zdroj/datová-sada/ovm +- namespace: http://data.kasabi.com/dataset/pali-english-lexicon + prefix: pali-english-lexicon + title: Pali English Lexicon + uri: http://kasabi.com/dataset/pali-english-lexicon +- namespace: http://statistics.data.gov.uk/id/ + prefix: statistics-data-gov-uk + title: statistics.data.gov.uk + uri: http://statistics.data.gov.uk/ +- namespace: http://purl.org/ASN/schema/core/ + prefix: asn-us + title: ASN:US + uri: http://asn.jesandco.org +- namespace: http://ibm.rkbexplorer.com/id/ + prefix: rkb-explorer-ibm + title: IBM Research GmbH (RKBExplorer) + uri: http://ibm.rkbexplorer.com +- namespace: https://w3id.org/framester + prefix: framester + title: Framester + uri: https://w3id.org/framester +- namespace: http://eprints.rkbexplorer.com/id/ + prefix: rkb-explorer-eprints + title: ePrints3 Institutional Archive Collection (RKBExplorer) + uri: http://eprints.rkbexplorer.com/ +- namespace: http://purl.org/weso/pscs/cpa/2008/resource + prefix: cpa-2008 + title: CPA 2008 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://www.icane.es + prefix: icane + title: ICANE + uri: http://www.icane.es/semantic-web +- namespace: http://irit.rkbexplorer.com/id/ + prefix: rkb-explorer-irit + title: Université Paul Sabatier - Toulouse 3 (RKB Explorer) + uri: http://irit.rkbexplorer.com +- namespace: http://lod.taxonconcept.org/ + prefix: taxonconcept + title: TaxonConcept Knowledge Base + uri: http://lod.taxonconcept.org/ +- namespace: http://n-lex.publicdata.eu/ontology + prefix: n-lex-as-linked-data + title: N-Lex as Linked Data + uri: http://n-lex.publicdata.eu/ +- namespace: http://utep.eagle-i.net/i/ + prefix: eagle-i-utep + title: eagle-i @ University of Texas at El Paso + uri: http://utep.eagle-i.net +- namespace: https://bibsonomy.org/ + prefix: BibSonomy + title: BibSonomy - The blue social bookmark and publication sharing system. + uri: https://www.bibsonomy.org/ +- namespace: http://budapest.rkbexplorer.com/id/ + prefix: rkb-explorer-budapest + title: Budapest University of Technology and Economics (RKBExplorer) + uri: http://budapest.rkbexplorer.com/ +- namespace: http://data.nku.cz/resource/ + prefix: cz-sao-check-actions-law + title: List of laws used in inspection reports of SAO + uri: http://data.nku.cz/resource/dataset/check-actions-law +- namespace: http://slod.fiz-karlsruhe.de + prefix: slod + title: Linked Stage Graph + uri: http://slod.fiz-karlsruhe.de/ +- namespace: http://data.linkededucation.org/resource/ + prefix: lak-dataset + title: Learning Analytics and Knowledge (LAK) Dataset + uri: http://www.solaresearch.org/resources/lak-dataset/ +- namespace: Moje Ime je Legija + prefix: Uros Legija Susa + title: Legija Stranaca + uri: http://www.legion-etrangere.com +- namespace: https://data.muziekweb.nl/Link/ + prefix: muziekweb + title: Muziekweb + uri: https://data.muziekweb.nl/ +- namespace: http://data.kasabi.com/dataset/sanskrit-english-lexicon + prefix: sanskrit-english-lexicon + title: Sanskrit English Lexicon + uri: http://kasabi.com/dataset/sanskrit-english-lexicon +- namespace: http://www4.wiwiss.fu-berlin.de/factbook/resource/ + prefix: world-factbook-fu-berlin + title: World Factbook (FU Berlin) + uri: http://www4.wiwiss.fu-berlin.de/factbook/ +- namespace: http://nlg.okfn.gr/resource/authority/ + prefix: national-library-of-greece-authority-records + title: National Library of Greece Authority Records + uri: http://nlg.okfn.gr +- namespace: http://linked.opendata.cz/resource/sukl/medicinal-product-packaging/ + prefix: cz-sidc-drug-prices + title: List of prices of reimbursed medicinal products marketed in Czech republic + uri: http://linked.opendata.cz/resource/dataset/sukl/drug-prices +- namespace: http://purl.org/weso/pscs/cpv/2008/resource + prefix: cpv-2008 + title: CPV 2008 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://howard.eagle-i.net/i/ + prefix: eagle-i-howard + title: eagle-i @ Howard University + uri: http://howard.eagle-i.net +- namespace: http://psi.oasis-open.org/iso/639/ + prefix: iso-639-oasis + title: Published subjects for languages in ISO 639 + uri: http://psi.oasis-open.org/iso/639/ +- namespace: http://resex.rkbexplorer.com/id/ + prefix: rkb-explorer-resex + title: ReSIST Resilience Mechanisms (RKBExplorer.com) + uri: http://resex.rkbexplorer.com +- namespace: http://stitch.cs.vu.nl/vocabularies/rameau/ + prefix: stitch-rameau + title: RAMEAU subject headings (STITCH) + uri: http://stitch.cs.vu.nl/rameau/ +- namespace: http://finance.data.gov.uk/def/coins/ + prefix: coins-openuplabs + title: OpenUpLabs COINS + uri: http://data.gov.uk/resources/coins +- namespace: http://w3id.org/foodie/olu/ + prefix: Open Land Use + title: Open Land Use + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://id.ndl.go.jp/auth/ndlna/ + prefix: national-diet-library-authorities + title: Web NDL Authorities - National Diet Library of Japan + uri: http://id.ndl.go.jp/auth/ndla +- namespace: http://os.rkbexplorer.com/id/ + prefix: rkb-explorer-os + title: Ordnance Survey (RKBExplorer) + uri: http://os.rkbexplorer.com +- namespace: http://purl.org/collections/nl/am/ + prefix: amsterdam-museum-as-edm-lod + title: Amsterdam Museum as Linked Open Data in the Europeana Data Model + uri: http://semanticweb.cs.vu.nl/lod/am/ +- namespace: http://linked.opendata.cz/resource/domain/irz/ + prefix: cz-cenia-irz-chemicals + title: Chemicals reported to the Integrated register of pollution + uri: http://linked.opendata.cz/resource/dataset/cenia-irz-chemicals +- namespace: http://linked.opendata.cz/resource/es/msssi + prefix: es-msssi-drug-prices + title: List of prices of medicinal products marketed in Kingdom of Spain + uri: http://linked.opendata.cz/resource/dataset/es/msssi/drug-prices +- namespace: http://utsa.eagle-i.net/i/ + prefix: eagle-i-utsa + title: eagle-i @ University of Texas at San Antonio + uri: http://utsa.eagle-i.net +- namespace: http://data.nobelprize.org/resource/ + prefix: nobelprizes + title: Nobel Prizes + uri: http://www.nobelprize.org/nobel_organizations/nobelmedia/nobelprize_org/developer/manual-linkeddata/terms.html +- namespace: http://www4.wiwiss.fu-berlin.de/eccompetition/resource/ + prefix: fu-berlin-ec-competition + title: European Commission Competition data set (FU Berlin) + uri: http://www4.wiwiss.fu-berlin.de/eccompetition/ +- namespace: http://data.linkedopendata.it/scuole/resource/ + prefix: italian-public-schools-linkedopendata-it + title: Italian public schools (LinkedOpenData.it) + uri: http://www.linkedopendata.it/datasets/scuole +- namespace: http:miuras.inf.um.es/ogolod/resource/Gene/67440 + prefix: ogolod + title: Orthology and Diseases Information - OGO + uri: http://miuras.inf.um.es/~ogo/ogolod.html +- namespace: http://sws.geonames.org/ + prefix: geonames-semantic-web + title: GeoNames Semantic Web + uri: http://www.geonames.org/ontology/ +- namespace: http://viaf.org/viaf/ + prefix: viaf + title: 'VIAF: The Virtual International Authority File' + uri: http://viaf.org/viaf/data/ +- namespace: http://bibliotecaescolardigital.es + prefix: biblioteca-escolar-digital-cita + title: Biblioteca Escolar Digital CITA + uri: http://red.gnoss.com/comunidad/Biblioteca-Escolar-Digital +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-projects + title: R&D Projects + uri: http://linked.opendata.cz/resource/dataset/vavai/projects +- namespace: http://deusto.gnoss.com/en/community/deustoEntrepreneurship + prefix: deustoentrepreneurship + title: 'Deusto Entrepreneurship: sharing business knowledge' + uri: http://deusto.gnoss.com/en/community/deustoEntrepreneurship +- namespace: http://linkedlifedata.com/resource/ + prefix: linked-life-data + title: Linked Life Data + uri: http://linkedlifedata.com/ +- namespace: http://lov.okfn.org/dataset/lov/lov# + prefix: linked-open-vocabularies-lov + title: Linked Open Vocabularies (LOV) + uri: http://lov.okfn.org/dataset/lov/index.html +- namespace: http://webisa.webdatacommons.org/ + prefix: webisalod + title: WebIsALOD + uri: http://webisa.webdatacommons.org +- namespace: https://betweenourworlds.org/ + prefix: betweenourworlds + title: Between Our Worlds + uri: https://betweenourworlds.org +- namespace: http://linked.opendata.cz/resource/sukl/medicinal-product-packaging/ + prefix: cz-sidc-drugs + title: Medicinal products marketed in Czech Republic + uri: http://linked.opendata.cz/resource/dataset/sukl/drugs +- namespace: https://w3id.org/jp-textbook/ + prefix: jp-textbook + title: Japanese Textbook LOD + uri: https://w3id.org/jp-textbook/ +- namespace: http://www.surgeradio.co.uk/ + prefix: surge-radio + title: Surge Radio + uri: http://www.surgeradio.co.uk/ +- namespace: http://www4.wiwiss.fu-berlin.de/bookmashup/ + prefix: rdf-book-mashup + title: RDF Book Mashup + uri: http://www4.wiwiss.fu-berlin.de/bizer/bookmashup/ +- namespace: http://citeseer.rkbexplorer.com/id/ + prefix: rkb-explorer-citeseer + title: CiteSeer (Research Index) (RKBExplorer) + uri: http://citeseer.rkbexplorer.com/ +- namespace: http://data.bnf.fr/ + prefix: data-bnf-fr + title: data.bnf.fr - Bibliothèque nationale de France + uri: http://data.bnf.fr +- namespace: http://fr.dbpedia.org/resource/ + prefix: dbpedia-fr + title: DBpedia in French + uri: http://fr.dbpedia.org +- namespace: http://linked.opendata.cz/resource/sukl/active-ingredient/ + prefix: cz-sidc-drug-ingredients + title: Active ingredients of medicinal products available in Czech Republic + uri: http://linked.opendata.cz/resource/dataset/sukl/drug-ingredients +- namespace: http://smartlink.open.ac.uk/smartlink/resource/ + prefix: smartlink + title: 'SmartLink: Linked Services Non-Functional Properties' + uri: http://purl.org/smartlink +- namespace: http://purl.org/allie/ + prefix: allie-abbreviation-and-long-form-database-in-life-science + title: Allie Abbreviation And Long Form Database in Life Science + uri: http://allie.dbcls.jp/ +- namespace: http://digitaleconomy.rkbexplorer.com/id/ + prefix: rkb-explorer-digitaleconomy + title: digitaleconomy + uri: http://digitaleconomy.rkbexplorer.com +- namespace: http://gnoss.com/ + prefix: gnoss-com-a-social-and-semantic-platform + title: GNOSS.com, a Social and Semantic Platform + uri: http://gnoss.com/en/home +- namespace: http://w3id.org/foodie/open/pl/LPIS/ + prefix: LPIS (Poland) + title: Polish Land Parcel Information System (LPIS) dataset + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://keithalexander.co.uk/pbac + prefix: printed-book-auction-catalogues + title: English Language Books listed in Printed Book Auction Catalogues from 17th Century Holland + uri: http://keithalexander.co.uk/pbac +- namespace: http://www4.wiwiss.fu-berlin.de/diseasome/resource/ + prefix: fu-berlin-diseasome + title: Diseasome + uri: http://www4.wiwiss.fu-berlin.de/diseasome/ +- namespace: http://gnoss.com/comunidad/MPV-APADRINA + prefix: proyectoapadrina + title: Proyecto Apadrina, Marketing Punto de Venta + uri: http://gnoss.com/comunidad/MPV-APADRINA +- namespace: http://ec.europa.eu/eurostat/ + prefix: eurostat-rdf + title: Eurostat RDF datasets + uri: http://ec.europa.eu/eurostat/ramon/rdfdata/ +- namespace: http://theviewfrom.org/things/ + prefix: the-view-from + title: The View From + uri: http://theviewfrom.org/ +- namespace: https://linked.opendata.cz/zdroj/ovm/ + prefix: cz-souhrnne-typy-ovm + title: Summary types of Czech institutions of public power + uri: https://linked.opendata.cz/zdroj/datová-sada/souhrnné-typy-ovm +- namespace: http://purl.org/weso/nomenclator/ + prefix: nomenclator-asturias + title: Nomenclator Asturias + uri: http://www.josemalvarez.es/web/2011/11/01/nomenclator-asturias-2010/ +- namespace: http://unodc.publicdata.eu/r/ + prefix: unodc + title: UNODC - Statistics on criminal justice + uri: http://unodc.publicdata.eu/ +- namespace: http://resource.geolba.ac.at/ + prefix: geological-survey-of-austria-thesaurus + title: Geological Survey of Austria (GBA) - Thesaurus + uri: http://resource.geolba.ac.at/ +- namespace: http://dbtune.org/classical/resource/ + prefix: dbtune-classical + title: DBTune.org/classical + uri: http://dbtune.org/classical/ +- namespace: https://data.cultureelerfgoed.nl/term/id/cht/ + prefix: cht + title: Cultural Heritage Thesaurus + uri: https://data.cultureelerfgoed.nl/ +- namespace: http://ohsu.eagle-i.net/i/ + prefix: eagle-i-ohsu + title: eagle-i @ Oregon Health and Science University + uri: http://ohsu.eagle-i.net +- namespace: http://www.data.gov/semantic/data/ + prefix: data-gov + title: Data.gov + uri: http://data.gov/ +- namespace: http://jisc.rkbexplorer.com/id/ + prefix: rkb-explorer-jisc + title: UK JISC (RKBExplorer) + uri: http://jisc.rkbexplorer.com +- namespace: http://zitgist.com/music + prefix: zitgist-musicbrainz + title: MusicBrainz (zitgist.com) + uri: http://fgiasson.com/blog/index.php/2007/05/22/browsing-musicbrainzs-dataset-via-uri-dereferencing/ +- namespace: http://rhizomik.net/semanticxbrl/ + prefix: semantic-xbrl + title: Semantic XBRL Financial Data + uri: http://rhizomik.net/semanticxbrl/ +- namespace: http://es.dbpedia.org/resource/ + prefix: dbpedia-es + title: DBpedia in Spanish + uri: http://es.dbpedia.org +- namespace: http://linkedgeodata.org/ + prefix: linkedgeodata + title: LinkedGeoData + uri: http://linkedgeodata.org/ +- namespace: http://business.data.gov.uk/id/company/ + prefix: business-data-gov-uk + title: business.data.gov.uk + uri: http://business.data.gov.uk/ +- namespace: http://dbtune.org/myspace/ + prefix: dbtune-myspace + title: DBTune.org MySpace RDF Service + uri: http://dbtune.org/myspace/ +- namespace: http://psh.ntkcz.cz/ + prefix: psh-subject-headings + title: Polythematic Structured Subject Heading System + uri: http://psh.ntkcz.cz/skos/home/html/en +- namespace: http://bnb.bibliographica.org/ + prefix: jiscopenbib-bl_bnb-1 + title: JISC Open Bibliography British National Bibliography dataset + uri: http://openbiblio.net/2010/11/17/jisc-openbibliography-british-library-data-release/ +- namespace: http://dotac.rkbexplorer.com/id/ + prefix: rkb-explorer-dotac + title: dotAC (RKBExplorer) + uri: http://dotac.rkbexplorer.com +- namespace: http://www.openmobilenetwork.org/resource/ + prefix: openmobilenetwork + title: OpenMobileNetwork + uri: http://www.openmobilenetwork.org +- namespace: http://sociallink.futuro.media/ontology + prefix: SocialLink + title: SocialLink + uri: http://sociallink.futuro.media +- namespace: http://standardgraphs.ices.dk/stocks/ + prefix: Fishery Stock Dataset + title: Norway fishery stocks dataset + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://data.linkedevents.org/ + prefix: event-media + title: EventMedia + uri: http://eventmedia.eurecom.fr/ +- namespace: http://micka.lesprojekt.cz/catalog/dataset/ + prefix: EO metadata + title: Micka (EO metadata) + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://pisa.rkbexplorer.com/id/ + prefix: rkb-explorer-pisa + title: Università di Pisa (RKBExplorer) + uri: http://pisa.rkbexplorer.com +- namespace: http://data.odw.tw/record + prefix: ' data.odw.tw' + title: Open Data Web + uri: http://data.odw.tw/ +- namespace: http://nsf.rkbexplorer.com/id/ + prefix: rkb-explorer-nsf + title: National Science Foundation (RKBExplorer) + uri: http://nsf.rkbexplorer.com +- namespace: http://data.hnm.hu/id/colls/lib/bib/Instance/ + prefix: data-hnm-hu + title: data-hnm-hu - Hungarian National Museum Datasets + uri: http://hnm.hu +- namespace: http://www.cnr.it/ontology/cnr/individuo/ + prefix: data-cnr-it + title: Open Data from the Italian National Research Council + uri: http://data.cnr.it/site/ +- namespace: http://www.legislation.gov.uk/ + prefix: uk-legislation-api + title: UK Legislation + uri: http://www.legislation.gov.uk/ +- namespace: http://www.london-gazette.co.uk/ + prefix: london-gazette + title: The London Gazette - Gazettes Data + uri: http://www.london-gazette.co.uk/mashup/gazettesdata.htm +- namespace: http://data.szepmuveszeti.hu/id/collections/ + prefix: data-szepmuveszeti-hu + title: data-szepmuveszeti-hu + uri: http://www.szepmuveszeti.hu +- namespace: http://onto.fel.cvut.cz/ontologies/ufo/ + prefix: ufo + title: Unified Foundational Ontology + uri: http://onto.fel.cvut.cz/ontologies/ufo/current/index-en.html +- namespace: http://nuts.psi.enakting.org/id/ + prefix: linked-nuts + title: Linked NUTS + uri: http://nuts.psi.enakting.org/ +- namespace: http://dbtune.org/jamendo/ + prefix: jamendo-dbtune + title: DBTune.org Jamendo RDF Server + uri: http://dbtune.org/jamendo/ +- namespace: http://www4.wiwiss.fu-berlin.de/cordis/resource/ + prefix: fu-berlin-cordis + title: Community Research and Development Information Service (CORDIS) + uri: http://www4.wiwiss.fu-berlin.de/cordis/ +- namespace: http://vocabulary.semantic-web.at/OpenData/ + prefix: open-data-thesaurus + title: Open Data Thesaurus + uri: http://vocabulary.semantic-web.at/PoolParty/wiki/OpenData +- namespace: http://www.archivesdefrance.culture.gouv.fr/thesaurus/resource/ + prefix: thesaurus-w + title: Thesaurus W for Local Archives + uri: http://www.archivesdefrance.culture.gouv.fr/thesaurus/ +- namespace: http://zbw.eu/beta/p20/ + prefix: zbw-pressemappe20 + title: 20th Century Press Archives + uri: http://zbw.eu/beta/p20 +- namespace: ' http://linked.opendata.cz/resource/business-entity/' + prefix: cz-ares-or + title: Data about business entities from the ARES system - business registry of the Czech Republic + uri: http://linked.opendata.cz/resource/dataset/ares/or +- namespace: http://italy.rkbexplorer.com/id/ + prefix: rkb-explorer-italy + title: Diverse Italian ReSIST Partner Institutions (RKBExplorer) + uri: http://italy.rkbexplorer.com +- namespace: http://cau.eagle-i.net/i/ + prefix: eagle-i-cau + title: eagle-i @ Clark Atlanta University + uri: http://cau.eagle-i.net/ +- namespace: http://linked.opendata.cz/resource/domain/seznam.gov.cz/agendy/ + prefix: cz-ovm-agendas + title: Agendas of institutions of public power of the Czech Republic + uri: http://linked.opendata.cz/resource/dataset/seznam.gov.cz/agendy +- namespace: http://www.rdfabout.com/rdf/usgov/ + prefix: govtrack + title: GovTrack.us U.S Congress Legislative Data + uri: http://www.govtrack.us +- namespace: http://era.rkbexplorer.com/id/ + prefix: rkb-explorer-era + title: ERA - Australian Research Council publication ratings (RKBExplorer) + uri: http://era.rkbexplorer.com +- namespace: http://www4.wiwiss.fu-berlin.de/dailymed/resource/ + prefix: fu-berlin-dailymed + title: DailyMed + uri: http://www4.wiwiss.fu-berlin.de/dailymed/ +- namespace: http://newcastle.rkbexplorer.com/id/ + prefix: rkb-explorer-newcastle + title: University of Newcastle upon Tyne (RKBExplorer) + uri: http://newcastle.rkbexplorer.com +- namespace: http://lobid.org/resource/ + prefix: lobid-resources + title: lobid-Bibliographic Resources + uri: http://lobid.org/resource +- namespace: http://data.kasabi.com/dataset/bricklink/ + prefix: bricklink + title: Bricklink + uri: http://kasabi.com/dataset/bricklink +- namespace: http://purl.org/lu/uni/alma/swift + prefix: Swift + title: Swift Vocabulary + uri: http://purl.org/lu/uni/alma/swift +- namespace: http://transport.data.gov.uk/id/ + prefix: transport-data-gov-uk + title: transport.data.gov.uk + uri: http://transport.data.gov.uk/ +- namespace: http://umbel.org/umbel/ + prefix: umbel + title: UMBEL (Upper Mapping and Binding Exchange Layer) + uri: http://umbel.org +- namespace: http://www4.wiwiss.fu-berlin.de/medicare/resource/ + prefix: fu-berlin-medicare + title: MediCare + uri: http://www4.wiwiss.fu-berlin.de/medicare/ +- namespace: http://www.ntnu.no/ub/data/nvd/2003/ + prefix: nvd + title: Norsk inndeling av vitenskapsdisipliner + uri: http://www.ntnu.no/ub/data/nvd/about +- namespace: http://tsu.eagle-i.net/i/ + prefix: eagle-i-tsu + title: eagle-i @ Texas Southern University + uri: http://tsu.eagle-i.net +- namespace: http://ulm.rkbexplorer.com/id/ + prefix: rkb-explorer-ulm + title: Universität Ulm (RKBExplorer) + uri: http://ulm.rkbexplorer.com +- namespace: open data + prefix: The Respublic of Uzbekistan + title: Open data of Uzbekistan + uri: https://data.gov.uz/en +- namespace: http://organogram.data.gov.uk/data/thurrocktgdc + prefix: staff-organograms-and-pay-thurrock-thames-gateway-development-corporation + title: Organogram and staff pay data for Thurrock Thames Gateway Development Corporation + uri: http://data.gov.uk/dataset/staff-organograms-and-pay-thurrock-thames-gateway-development-corporation +- namespace: http://upr.eagle-i.net/i/ + prefix: eagle-i-upr + title: eagle-i@ University of Puerto Rico - Medical Sciences Campus + uri: http://upr.eagle-i.net +- namespace: http://telegraphis.net/ + prefix: telegraphis + title: Telegraphis Linked Data + uri: http://telegraphis.net/data/ +- namespace: http://linked.opendata.cz/resource/domain/coi.cz/check-action/ + prefix: cz-ctia-focus + title: Focus of the Czech Trade Inspection Authority's inspections + uri: http://linked.opendata.cz/resource/dataset/coi.cz/zamereni +- namespace: http://xula.eagle-i.net/i/ + prefix: eagle-i-xula + title: eagle-i @ Xavier University of Louisiana + uri: http://xula.eagle-i.net +- namespace: http://linked.opendata.cz/resource/domain/coi.cz/sanction/ + prefix: cz-ctia-sanctions + title: Sanctions of the Czech Trade Inspection Authority + uri: http://linked.opendata.cz/resource/dataset/coi.cz/sankce +- namespace: http://purl.org/weso/pscs/sitc/v4/resource + prefix: sitc-v4 + title: SITC-V4 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://ruian.linked.opendata.cz/resource/ + prefix: cz-cuzk-legal-relationships-documents + title: Code lists of the legal relationships and documents + uri: http://ruian.linked.opendata.cz/resource/dataset/cuzk/pravni-vztahy-listiny +- namespace: http://rdf.freebase.com/ + prefix: freebase + title: Freebase + uri: http://freebase.com/ +- namespace: http://education.data.gov.uk/doc/institution + prefix: education-data-gov-uk + title: education.data.gov.uk + uri: http://education.data.gov.uk/ +- namespace: http://zbw.eu/stw/ + prefix: stw-thesaurus-for-economics + title: STW Thesaurus for Economics + uri: http://zbw.eu/stw +- namespace: http://pleiades.stoa.org/places/ http://pleiades.stoa.org/places/vocab# http://atlantides.org/capgrids/ + prefix: pleiades + title: Pleiades + uri: http://pleiades.stoa.org/ +- namespace: http://www.rdfabout.com/rdf/usgov/geo/ + prefix: 2000-us-census-rdf + title: 2000 U.S. Census in RDF (rdfabout.com) + uri: http://www.rdfabout.com/demo/census/ +- namespace: http://purl.uniprot.org/uniprot/ + prefix: uniprotkb + title: UniProtKB + uri: https://www.uniprot.org/uniprot/ +- namespace: http://kasabi.com/dataset/discogs + prefix: data-incubator-discogs + title: Discogs in RDF + uri: http://kasabi.com/dataset/discogs +- namespace: http://resourcelists.st-andrews.ac.uk/ + prefix: st-andrews-resource-lists + title: St. Andrews University Resource Lists + uri: http://resourcelists.st-andrews.ac.uk/ +- namespace: http://schemapedia.com/ + prefix: schemapedia + title: 'Schemapedia: RDF schema compendium' + uri: http://schemapedia.com/ +- namespace: http://purl.uniprot.org/ + prefix: uniprot + title: UniProt + uri: http://www.uniprot.org/ +- namespace: http://linked.opendata.cz/resource/domain/seznam.gov.cz/rejstriky/plneni/ + prefix: cz-fulfillments + title: Registry of contracts of the Czech Republic - Financial fulfillments + uri: http://linked.opendata.cz/resource/dataset/seznam.gov.cz/rejstriky/plneni +- namespace: http://id.loc.gov/ + prefix: lcsh + title: Library of Congress Subject Headings + uri: http://id.loc.gov/authorities/ +- namespace: http://data.odw.tw/record/ + prefix: data.odw.tw + title: Open Data Web + uri: http://data.odw.tw/ +- namespace: http://www.fao.org/countryprofiles/geoinfo/geopolitical/resource/ + prefix: fao-geopolitical-ontology + title: FAO geopolitical ontology + uri: http://www.fao.org/countryprofiles/geoinfo.asp?lang=en +- namespace: http://lisbon.rkbexplorer.com/id/ + prefix: rkb-explorer-lisbon + title: Fundação da Faculdade de Ciencas da Universidade de Lisboa (RKBExplorer) + uri: http://lisbon.rkbexplorer.com +- namespace: http://purl.org/weso/pscs/resource + prefix: pscs-catalogue + title: Product Scheme Classifications Catalogue + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://www.eea.europa.eu/publications + prefix: eea + title: European Environment Agency Published Products + uri: http://www.eea.europa.eu/ +- namespace: http://www.eionet.europa.eu/gemet/ + prefix: gemet + title: GEneral Multilingual Environmental Thesaurus + uri: http://www.eionet.europa.eu/gemet/ +- namespace: http://www.wikidata.org/entity/ + prefix: wikidata + title: Wikidata + uri: https://www.wikidata.org/ +- namespace: http://my-family-lineage.com/wiki/ + prefix: my-family-lineage + title: My Family Lineage + uri: http://my-family-lineage.com/wiki/Main_Page +- namespace: id.agrisemantics.org/gacs + prefix: GACS + title: Global Agricultural Concept Space + uri: https://agrisemantics.org/#GACShome/ +- namespace: http://taxref.mnhn.fr/lod/ + prefix: taxref-ld + title: 'TAXREF-LD: Linked Data French Taxonomic Register' + uri: https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref?lg=en +- namespace: http://whoiswho.publicdata.eu/data/ + prefix: eu-who-is-who + title: EU Who Is Who + uri: http://whoiswho.publicdata.eu/ +- namespace: http://www.sudoc.fr/ + prefix: sudocfr + title: Sudoc bibliographic data + uri: http://punktokomo.abes.fr/2011/07/04/le-sudoc-sur-le-web-de-donnees/ +- namespace: http://linked.opendata.cz/resource/domain/coi.cz/ban/ + prefix: cz-ctia-bans + title: Bans of the Czech Trade Inspection Authority + uri: http://linked.opendata.cz/resource/dataset/coi.cz/zakazy +- namespace: http://data.kasabi.com/dataset/yahoo-geoplanet + prefix: yahoo_geoplanet + title: Yahoo Geoplanet RDF + uri: http://kasabi.com/dataset/yahoo-geoplanet +- namespace: http://www.ntnu.no/ub/data/tekord + prefix: tekord + title: TEKORD + uri: http://www.ntnu.no/ub/data/tekord/about +- namespace: http://unlocode.rkbexplorer.com/id/ + prefix: rkb-explorer-unlocode + title: UN/LOCODE (RKBExplorer) + uri: http://unlocode.rkbexplorer.com +- namespace: http://purl.org/net7/vocab/locs/v1# + prefix: linked-open-camera + title: Linked Open Camera (LinkedOpenData.it) + uri: http://www.linkedopendata.it/datasets/loc +- namespace: http://population.psi.enakting.org/id/ + prefix: enakting-population + title: EnAKTing Population Dataset + uri: http://population.psi.enakting.org/ +- namespace: http://semanticscience.org/resource/ + prefix: bioportal-sio + title: SemanticScience Integrated Ontology + uri: http://bioportal.bioontology.org/ontologies/1532 +- namespace: http://ec.europa.eu/agriculture/FADN/ + prefix: FADN (2019) + title: Farm Accountancy Data Network (FADN) linked dataset from 2019 + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://dbtune.org/magnatune/artist/ + prefix: dbtune-magnatune + title: DBTune.org Magnatune RDF server + uri: http://dbtune.org/magnatune/ +- namespace: http://chroniclingamerica.loc.gov/ + prefix: chronicling-america + title: Chronicling America + uri: http://chroniclingamerica.loc.gov/about/api/ +- namespace: http://purl.org/vocabularies/princeton/wn30 + prefix: vu-wordnet + title: WordNet 3.0 (VU Amsterdam) + uri: http://semanticweb.cs.vu.nl/lod/wn30/ +- namespace: http://deusto.gnoss.com + prefix: deustotech + title: DeustoTech (Deusto Institute of Technology) + uri: http://deusto.gnoss.com +- namespace: http://purl.org/weso/pscs/cn/2012/resource + prefix: combined-nomenclature-2012 + title: CN 2012 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://pt.dbpedia.org/resource/ + prefix: dbpedia-pt + title: DBpedia in Portuguese + uri: http://pt.dbpedia.org +- namespace: http://cordis.rkbexplorer.com/id/ + prefix: rkb-explorer-cordis + title: Community R&D Information Service (CORDIS) (RKBExplorer) + uri: http://cordis.rkbexplorer.com +- namespace: http://ns.inria.fr/covid19/ + prefix: Covid-on-the-Web + title: Covid-on-the-Web Dataset + uri: https://github.com/Wimmics/CovidOnTheWeb +- namespace: http://www.pokepedia.fr/ + prefix: pokepedia-fr + title: Poképédia + uri: http://www.pokepedia.fr +- namespace: http://santillana.linkeddata.es/elviajero/resource + prefix: santillana_guide_dataset + title: Santillana Guide Dataset + uri: http://webenemasuno.linkeddata.es/ +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-results + title: Results of R&D + uri: http://linked.opendata.cz/resource/dataset/vavai/results +- namespace: http://kaunas.rkbexplorer.com/id/ + prefix: rkb-explorer-kaunas + title: Vytautas Magnus University, Kaunas (RKBExplorer) + uri: http://kaunas.rkbexplorer.com +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-evaluation-2013 + title: Evaluation of VaVaI results for 2013 + uri: http://linked.opendata.cz/resource/dataset/vavai/evaluation/2013 +- namespace: http://lod.hebis.de/resource/ + prefix: hebis-bibliographic-resources + title: HeBIS - Bibliographic Resources of the Library Union Catalogues of Hessen and parts of the Rhineland Palatinate + uri: http://www.hebis.de +- namespace: http://harvard.eagle-i.net/i/ + prefix: eagle-i-harvard + title: eagle-i @ Harvard University + uri: http://harvard.eagle-i.net +- namespace: http://psm.eagle-i.net/i/ + prefix: eagle-i-psm + title: eagle-i @ Ponce School of Medicine + uri: http://psm.eagle-i.net/ +- namespace: http://packages.qa.debian.org/ + prefix: debian-package-tracking-system + title: Debian Package Tracking System + uri: http://packages.qa.debian.org/common/RDF.html +- namespace: http://ecs.rkbexplorer.com/id/ + prefix: rkb-explorer-ecs + title: School of Electronics and Computer Science, University of Southampton + uri: http://ecs.rkbexplorer.com +- namespace: http://www.idref.fr/ + prefix: idreffr + title: 'IdRef: Sudoc authority data' + uri: http://punktokomo.abes.fr/2011/07/05/idref-des-pages-html-et-rdf-plus-riches/ +- namespace: ttp://opendatacommunities.org/id/IMD/2010/IMD-rank/LSOA/ + prefix: english-index-of-multiple-deprivation-ranking-2010 + title: English Index of Multiple Deprivation Ranking 2010 + uri: http://opendatacommunities.org/data/imd-rank-2010 +- namespace: http://www4.wiwiss.fu-berlin.de/dblp/resource/ + prefix: fu-berlin-dblp + title: DBLP Bibliography Database in RDF (FU Berlin) + uri: http://www4.wiwiss.fu-berlin.de/dblp/ +- namespace: http://us.patents.aksw.org + prefix: linked-uspto-patent-data + title: USPTO Patent data + uri: http://aksw.org/Projects/USPatents.html +- namespace: http://data.kasabi.com/dataset/global-hunger-index + prefix: global-hunger-index-2011 + title: Global Hunger Index (2011) + uri: http://www.ifpri.org/publication/2011-global-hunger-index +- namespace: http://w3id.org/foodie/open/catchrecord/norway/ + prefix: Catch Record (2014- 2019) + title: Norway catch records dataset + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://w3id.org/foodie/open/cz/water_buffer25/ + prefix: Water Buffer + title: Water buffer dataset from Czech Republic + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://corporateexcellence.net/en/community/patronato + prefix: ce4r + title: CE4R Knowledge Centre Corporate Excellence – Centre for Reputation Leadership + uri: http://corporateexcellence.net/en/community/patronato +- namespace: http://elections.publicdata.eu/data/ + prefix: european-election-results + title: European Election Results + uri: http://elections.publicdata.eu +- namespace: 'http://msc2010.org/resources/MSC/2010/msc2010/ ' + prefix: msc + title: Mathematics Subject Classification + uri: http://msc2010.org/mscwork/ +- namespace: http://www.morelab.deusto.es/resource/ + prefix: morelab + title: MORElab + uri: http://www.morelab.deusto.es +- namespace: http://nomisma.org/ + prefix: nomisma_org + title: 'Nomisma.org ' + uri: http://nomisma.org +- namespace: http://linked.opendata.cz/resource/domain/seznam.gov.cz/rejstriky/smlouvy/ + prefix: cz-contracts + title: Registry of contracts of the Czech Republic - Contracts + uri: http://linked.opendata.cz/resource/dataset/seznam.gov.cz/rejstriky/smlouvy +- namespace: http://mortality.psi.enakting.org/id/ + prefix: enakting-mortality + title: EnAKTing Mortality Dataset + uri: http://mortality.psi.enakting.org/ +- namespace: http://reference.data.gov.uk/id/ + prefix: reference-data-gov-uk + title: reference.data.gov.uk + uri: http://reference.data.gov.uk/ +- namespace: http://data.europeana.eu + prefix: europeana-lod-v1 + title: Europeana Linked Open Data V1.0 + uri: http://data.europeana.eu/ +- namespace: http://dbtropes.org/resource/ + prefix: dbtropes + title: DBTropes + uri: http://dbtropes.org/ +- namespace: http://logd.tw.rpi.edu/source/congress-gov/dataset/biographical-directory-of-the-united-states-congress/version/2012-Jan-04/ + prefix: biographical-directory-of-the-united-states-congress + title: Biographical Directory of the United States Congress + uri: http://bioguide.congress.gov/biosearch/biosearch.asp +- namespace: http://data.ordnancesurvey.co.uk/doc/postcodeunit/ + prefix: ordnance-survey-linked-data + title: Ordnance Survey Linked Data + uri: http://data.ordnancesurvey.co.uk/ +- namespace: http://www.lotico.com/resource/ + prefix: lotico + title: Lotico + uri: http://www.lotico.com/ +- namespace: http://ineverycrea.net/ + prefix: ineverycrea + title: IneveryCREA, la comunidad de la creatividad educativa + uri: http://ineverycrea.net/ +- namespace: http://www4.wiwiss.fu-berlin.de/eures/resource/ + prefix: fu-berlin-eures + title: European Employment Services (EURES) + uri: http://www4.wiwiss.fu-berlin.de/eures/ +- namespace: http://wordnet.rkbexplorer.com/id/ + prefix: rkb-explorer-wordnet + title: WordNet (RKBExplorer) + uri: http://wordnet.rkbexplorer.com +- namespace: http://reegle.info + prefix: clean-energy-data-reegle + title: Linked Clean Energy Data (reegle.info) + uri: http://data.reegle.info/ +- namespace: http://fun.rkbexplorer.com/id/ + prefix: rkb-explorer-fun + title: fun + uri: http://fun.rkbexplorer.com +- namespace: http://kulturarvsdata.se/ + prefix: swedish-open-cultural-heritage + title: Swedish Open Cultural Heritage + uri: http://www.ksamsok.se/in-english/ +- namespace: Legija Stranaca + prefix: LEGIJA STRANACA + title: U ime Legije + uri: http://www.legion-etrangere.com +- namespace: https://linkeddata.cultureelerfgoed.nl/def/ceo + prefix: ceo + title: Linked Data Cultural Heritage Agency of the Netherlands + uri: https://linkeddata.cultureelerfgoed.nl/ +- namespace: http://ccny-cuny.eagle-i.net/i/ + prefix: eagle-i-ccny-cuny + title: eagle-i @ The City College of New York + uri: http://ccny-cuny.eagle-i.net +- namespace: ttp://rdfohloh.wikier.org/ + prefix: rdfohloh + title: RDFohloh + uri: http://rdfohloh.wikier.org +- namespace: http://darmstadt.rkbexplorer.com/id/ + prefix: rkb-explorer-darmstadt + title: Technische Universität Darmstadt (RKBExplorer) + uri: http://darmstadt.rkbexplorer.com +- namespace: http://prelex.publicdata.eu/r/ + prefix: prelex + title: PreLex + uri: http://prelex.publicdata.eu/ +- namespace: http://libris.kb.se/bib/ + prefix: libris + title: LIBRIS + uri: http://libris.kb.se +- namespace: http://www.yso.fi/onto/ysa/ + prefix: ysa + title: YSA - General Finnish Thesaurus + uri: http://finto.fi/ysa/ +- namespace: http://logd.tw.rpi.edu/source/contactingthecongress/dataset/directory-for-the-112th-congress/ + prefix: congresspeople + title: 2011 US Congress People + uri: http://www.contactingthecongress.org/ +- namespace: http://dbtune.org/last-fm/ + prefix: dbtune-audioscrobbler + title: DBTune.org AudioScrobbler RDF Service + uri: http://dbtune.org/last-fm/ +- namespace: http://data.nku.cz/resource/ + prefix: cz-sao-check-actions + title: Inspections of the Supreme Audit Office of the Czech Republic + uri: http://data.nku.cz/resource/dataset/check-actions +- namespace: http://roma.rkbexplorer.com/id/ + prefix: rkb-explorer-roma + title: Università degli studi di Roma "La Sapienza" (RKBExplorer) + uri: http://roma.rkbexplorer.com +- namespace: http://lobid.org/organisation/ + prefix: lobid-organisations + title: lobid-organisations + uri: http://lobid.org/organisation +- namespace: http://hawaii.eagle-i.net/i/ + prefix: eagle-i-hawaii + title: eagle-i @ University of Hawai’i at Mānoa + uri: http://hawaii.eagle-i.net +- namespace: http://linked.opendata.cz/resource/domain/seznam.gov.cz/rejstriky/objednavky/ + prefix: cz-orders + title: Registry of contracts of the Czech Republic - Orders + uri: http://linked.opendata.cz/resource/dataset/seznam.gov.cz/rejstriky/objednavky +- namespace: http://opendatacommunities.org/id/geography/lsoa/ + prefix: odc-lsoa + title: Open Data Communities - Lower layer Super Output Areas + uri: http://opendatacommunities.org/datasets/geography +- namespace: http://geo.linkeddata.es/resource/ + prefix: geolinkeddata + title: GeoLinkedData + uri: http://geo.linkeddata.es/ +- namespace: http://linked.opendata.cz/resource/es/msssi + prefix: it-aifa-drug-prices + title: List of prices of medicinal products marketed in Italian Republic + uri: http://linked.opendata.cz/resource/dataset/it/aifa/drug-prices +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-funding-providers + title: State funding providers + uri: http://linked.opendata.cz/resource/dataset/vavai/funding-providers +- namespace: http://researchgroups.gnoss.com + prefix: dblp-deusto-gnoss + title: DBLP Research Groups (University of Deusto-GNOSS) + uri: http://researchgroups.gnoss.com +- namespace: http://aemet.linkeddata.es/resource/ + prefix: aemet + title: AEMET metereological dataset + uri: http://aemet.linkeddata.es/ +- namespace: http://d-nb.info/gnd/ + prefix: 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Drew University + uri: http://cdrewu.eagle-i.net +- namespace: cv.iptc.org + prefix: iptc-newscodes + title: IPTC NewsCodes + uri: http://newscodes.org +- namespace: http://oai.rkbexplorer.com/id/ + prefix: rkb-explorer-oai + title: Open Archive Initiative Harvest over OAI-PMH (RKBExplorer) + uri: http://oai.rkbexplorer.com +- namespace: http://eunis.eea.europa.eu/ + prefix: eunis + title: European Nature Information System + uri: http://eunis.eea.europa.eu +- namespace: http://deepblue.rkbexplorer.com/id/ + prefix: rkb-explorer-deepblue + title: Deep Blue (RKBExplorer) + uri: http://deepblue.rkbexplorer.com +- namespace: http://wiki.rkbexplorer.com/id/ + prefix: rkb-explorer-wiki + title: ReSIST Project Wiki (RKBExplorer) + uri: http://wiki.rkbexplorer.com +- namespace: http://ibl.mdanderson.org/TCGA/ + prefix: tcga + title: The Cancer Genome Atlas + uri: http://tcga.s3db.org/ +- namespace: http://dbkwik.webdatacommons.org + prefix: dbkwik + title: DBkWik + uri: http://dbkwik.webdatacommons.org +- namespace: http://southampton.rkbexplorer.com/id/ + prefix: rkb-explorer-southampton + title: School of Electronics and Computer Science, University of Southampton (RKBExplorer) + uri: http://southampton.rkbexplorer.com +- namespace: http://aliada.scanbit.net:8891/id/collections/ + prefix: aliada-scanbit-net + title: aliada-scanbit-net + uri: http://biblioteca.artium.org +- namespace: http://webscience.rkbexplorer.com/id/ + prefix: rkb-explorer-webscience + title: Web Science Conference (RKBExplorer) + uri: http://webscience.rkbexplorer.com +- namespace: http://data.theeuropeanlibrary.org/BibliographicResource/ + prefix: the-european-library-open-dataset + title: The European Library Open Dataset + uri: https://lod-cloud.net/edit-dataset/the-european-library-open-dataset +- namespace: http://data.cervantesvirtual.com/ + prefix: BVMC + title: Biblioteca Virtual Miguel de Cervantes + uri: http://data.cervantesvirtual.com +- namespace: http://liblists.sussex.ac.uk/items/ + prefix: university-sussex-reading-lists + title: University of Sussex Reading Lists + uri: http://liblists.sussex.ac.uk +- namespace: ' http://linked.opendata.cz/resource/business-entity/' + prefix: cz-ares-rzp + title: Data about Czech business entities from the ARES system - Trade Licensing Register + uri: http://linked.opendata.cz/resource/dataset/ares/rzp +- namespace: http://chem2bio2rdf.org/bindingdb/ + prefix: chem2bio2rdf + title: Chem2Bio2RDF + uri: http://chem2bio2rdf.org +- namespace: http://photos.rkbexplorer.com/id/ + prefix: rkb-explorer-photos + title: photos + uri: http://photos.rkbexplorer.com +- namespace: http://thes.bncf.firenze.sbn.it + prefix: bncf-ns + title: Thesaurus BNCF + uri: http://thes.bncf.firenze.sbn.it/ +- namespace: http://www4.wiwiss.fu-berlin.de/eurostat/resource/ + prefix: fu-berlin-eurostat + title: Eurostat in RDF (FU Berlin) + uri: http://www4.wiwiss.fu-berlin.de/eurostat/ +- namespace: http://vocab.nerc.ac.uk/ + prefix: nvs + title: NERC Vocabulary Server 2.0 + uri: http://vocab.nerc.ac.uk/ +- namespace: http://dbtune.org/musicbrainz/ + prefix: dbtune-musicbrainz + title: DBTune.org Musicbrainz D2R Server + uri: http://dbtune.org/musicbrainz/ +- namespace: http://w3id.org/foodie/otm/ + prefix: OTM + title: Open Transport Map + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://didactalia.net + prefix: didactalia + title: Didactalia, índice de recursos educativos para profesores, padres y alumnos (GNOSS) + uri: http://didactalia.net +- namespace: http://purl.org/tcga/core# + prefix: tcga-roadmap + title: TCGA Roadmap + uri: http://tcga.github.com/Roadmap/ +- namespace: http://vivo.cornell.edu/ + prefix: vivo-cornell-university + title: VIVO Cornell + uri: http://vivo.cornell.edu/ +- namespace: http://data.linkedopendata.it/data/musei/resource/ + prefix: museums-in-italy + title: Italian Museums + uri: http://www.linkedopendata.it/datasets/musei +- namespace: http://lod.ac/bdls/ + prefix: lodac-bdls + title: LODAC BDLS + uri: http://lod.ac/wiki/LODAC_BDLS +- namespace: http://www4.wiwiss.fu-berlin.de/stitch/resource/ + prefix: fu-berlin-stitch + title: 'STITCH: Chemical-Protein Interactions' + uri: http://www4.wiwiss.fu-berlin.de/stitch/ +- namespace: http://www.calames.abes.fr/pub/ms/ + prefix: calames + title: Calames + uri: http://www.calames.abes.fr/ +- namespace: http://alaska.eagle-i.net/i/ + prefix: eagle-i-alaska + title: eagle-i @ University of Alaska Fairbanks + uri: http://alaska.eagle-i.net +- namespace: http://www.bbc.co.uk/music/artist/ + prefix: bbc-music + title: BBC Music + uri: http://www.bbc.co.uk/music +- namespace: http://lod.geospecies.org/ + prefix: geospecies + title: GeoSpecies Knowledge Base + uri: http://lod.geospecies.org/ +- namespace: http://www.bbc.co.uk/programmes + prefix: bbc-programmes + title: BBC Programmes + uri: http://www.bbc.co.uk/programmes +- namespace: http://id.esd.org.uk/ + prefix: esd-standards + title: 'ESD Standards: Controlled lists for the UK public sector' + uri: http://standards.esd.org.uk/ +- namespace: http://rdfdata.eionet.europa.eu/ + prefix: eionet-rdf + title: EIONET RDF Data + uri: http://rdfdata.eionet.europa.eu/ +- namespace: http://onto.beef.org.pl/domain/ + prefix: ontobeef-domain + title: OntoBeef Domain + uri: http://onto.beef.org.pl/ontobeef +- namespace: http://km.aifb.kit.edu/projects/numbers/web/ + prefix: linked-open-numbers + title: Linked Open Numbers + uri: http://km.aifb.kit.edu/projects/numbers/ +- namespace: http://prefix.cc/ + prefix: prefix-cc + title: prefix.cc + uri: http://prefix.cc/ +- namespace: http://purl.org/NET/lccn/ + prefix: linkedlccn + title: LinkedLCCN + uri: http://purl.org/NET/lccn/ +- namespace: http://data.archiveshub.ac.uk/ + prefix: archiveshub-linkeddata + title: Archives Hub Linked Data + uri: http://data.archiveshub.ac.uk +- namespace: http://w3id.org/foodie/olu/ + prefix: 'OLU ' + title: Open Land Use + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://aims.fao.org/aos/agrovoc/ + prefix: agrovoc + title: AGROVOC + uri: http://aims.fao.org/vest-registry/vocabularies/agrovoc +- namespace: http://data.kasabi.com/dataset/foodista + prefix: foodista + title: Foodista + uri: http://kasabi.com/dataset/foodista +- namespace: http://www.rubensworks.net/ + prefix: rubentaelman + title: Ruben Taelman's Data + uri: https://github.com/rubensworks/rubensworks.net +- namespace: ei2a + prefix: ei2a + title: Aragon Interoperable Information Structure EI2A - aragon open data + uri: https://opendata.aragon.es +- namespace: http://rdf.corpora.uni-leipzig.de/resources/xho/inventory/ + prefix: open-bantu-isixhosa-lexicon + title: Open Bantu isiXhosa Lexicon + uri: https://github.com/MMoOn-Project/OpenBantu/tree/master/xho +- namespace: http://crime.psi.enakting.org/id/ + prefix: enakting-crime + title: EnAKTing Crime Dataset + uri: http://crime.psi.enakting.org/ +- namespace: http://agencies.publicdata.eu/r/ + prefix: eu-agencies-bodies + title: EU Agencies and decentralized bodies (Agencies) + uri: http://agencies.publicdata.eu/ +- namespace: http://linkeddata.few.vu.nl/rechtspraak/ + prefix: rechtspraak + title: Rechtspraak.nl + uri: http://www.best-project.nl +- namespace: http://spatial.ucd.ie/lod/osn + prefix: osm-semantic-network + title: OSM Semantic Network + uri: http://wiki.openstreetmap.org/wiki/OSM_Semantic_Network +- namespace: http://gnoss.com/comunidad/Arthroscopy + prefix: arthroscopy + title: Arthroscopy community + uri: http://gnoss.com/comunidad/Arthroscopy +- namespace: http://purl.org/net/tcm/ + prefix: tcmgenedit_dataset + title: TCMGeneDIT Dataset + uri: http://code.google.com/p/junsbriefcase/wiki/TGDdataset +- namespace: http://www.zaragoza.es/datosabiertos/id/ + prefix: zaragoza-datosabiertos + title: Datos Abiertos de Zaragoza + uri: http://www.zaragoza.es/ciudad/risp/presentacion.htm +- namespace: http://edgarwrap.ontologycentral.com/ + prefix: linked-edgar + title: Linked EDGAR (OntologyCentral) + uri: http://edgarwrap.ontologycentral.com/ +- namespace: https://linked.opendata.cz/zdroj/ekonomický-subjekt/ + prefix: cz-ic + title: Czech Business Entity identification numbers and names + uri: https://linked.opendata.cz/zdroj/datová-sada/seznam-ič +- namespace: http://eurecom.rkbexplorer.com/id/ + prefix: rkb-explorer-eurecom + title: Institut Eurécom (RKBExplorer) + uri: http://eurecom.rkbexplorer.com +- namespace: http://data.kasabi.com/dataset/ecco-tcp-eighteenth-century-collections-online-texts/ + prefix: ecco-tcp-linked-data + title: ECCO-TCP Eighteenth Century Texts Linked Data + uri: http://kasabi.com/dataset/ecco-tcp-eighteenth-century-collections-online-texts +- namespace: http://publications.europa.eu/resource/authority/language + prefix: language-authority-list + title: ' Language Name Authority List ' + uri: https://op.europa.eu/en/web/eu-vocabularies/at-dataset/-/resource/dataset/language +- namespace: https://linked.opendata.cz/zdroje + prefix: cz-nace + title: Czech statistical classification of economic activities in the European Community (CZ-NACE) + uri: https://linked.opendata.cz/zdroje/datové-sady/čsú/číselníky/cz-nace +- namespace: http://miguiadeviajes.net + prefix: miguiadeviajes-gnoss + title: Mi Guía de Viajes, colección de guías de viaje para viajeros (GNOSS) + uri: http://miguiadeviajes.net +- namespace: http://jsu.eagle-i.net/i/ + prefix: eagle-i-jsu + title: eagle-i @ Jackson State University + uri: http://jsu.eagle-i.net +- namespace: http://pgxlod.loria.fr/resource/ + prefix: PGxLOD + title: PGxLOD + uri: https://pgxlod.loria.fr/ +- namespace: http://eprints.ecs.soton.ac.uk/id/eprint/ + prefix: southampton-ecs-eprints + title: ECS Southampton EPrints + uri: http://eprints.ecs.soton.ac.uk/ +- namespace: http://data.kasabi.com/dataset/prelinger-archives + prefix: prelinger_archives + title: Prelinger Archives + uri: http://kasabi.com/dataset/prelinger-archives +- namespace: http://energy.psi.enakting.org/def/ + prefix: enakting-energy + title: EnAKTing Energy Dataset + uri: http://energy.psi.enakting.org/ +- namespace: http://vivo.cornell.edu/individual/ + prefix: vivo + title: VIVO + uri: http://vivoweb.org/ +- namespace: http://en.openei.org/ + prefix: open-energy-info-wiki + title: OpenEI - Open Energy Info + uri: http://en.openei.org/ +- namespace: http://kisti.rkbexplorer.com/id/ + prefix: rkb-explorer-kisti + title: Korean Institute of Science Technology and Information (RKBExplorer) + uri: http://kisti.rkbexplorer.com +- namespace: http://fintrans.publicdata.eu/ec/resource/ + prefix: beneficiaries-of-the-european-commission + title: 'EU: fintrans.publicdata.eu' + uri: http://fintrans.publicdata.eu/ +- namespace: http://bnb.data.bl.uk/id/ + prefix: bluk-bnb + title: British National Bibliography (BNB) - Linked Open Data + uri: http://bnb.data.bl.uk +- namespace: http://id.worldcat.org/fast/ + prefix: oclc-fast + title: Faceted Application of Subject Terminology + uri: http://id.worldcat.org/fast/ +- namespace: http://www.sdi4apps.eu/poi.rdf + prefix: Smart POI dataset + title: Smart Point Of Interest + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://lod.b3kat.de/title/ + prefix: b3kat + title: B3Kat - Library Union Catalogues of Bavaria, Berlin and Brandenburg + uri: http://lod.b3kat.de +- namespace: https://w3id.org/associations/ + prefix: associations + title: associations + uri: https://w3id.org/associations +- namespace: http://www.w3.org/2006/03/wn/wn20/ + prefix: w3c-wordnet + title: WordNet 2.0 (W3C) + uri: http://www.w3.org/TR/wordnet-rdf +- namespace: http://hunter-cuny.eagle-i.net/i/ + prefix: eagle-i-hunter-cuny + title: eagle-i @ Hunter College + uri: http://hunter-cuny.eagle-i.net +- namespace: http://risks.rkbexplorer.com/id/ + prefix: rkb-explorer-risks + title: RISKS Digest (RKBExplorer) + uri: http://risks.rkbexplorer.com +- namespace: http://ecb.publicdata.eu/ + prefix: ecb-statistics-linked-data + title: European Central Bank Statistics (PublicData.eu) + uri: http://ecb.publicdata.eu +- namespace: http://mapasinteractivos.didactalia.net/comunidad/mapasflashinteractivos + prefix: interactivemaps-gnoss + title: Interactive Maps, a collection of interactive flash maps (GNOSS) + uri: http://mapasinteractivos.didactalia.net/comunidad/mapasflashinteractivos +- namespace: http://www.bbc.co.uk/nature/ + prefix: bbc-wildlife-finder + title: BBC Wildlife Finder + uri: http://www.bbc.co.uk/wildlifefinder/ +- namespace: http://purl.org/weso/pscs/cpa/2008/resource + prefix: cpc-2008 + title: CPC 2008 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-organizations + title: Organizations active in R&D + uri: http://linked.opendata.cz/resource/dataset/vavai/organizations +- namespace: http://purl.org/NET/marccodes/ + prefix: marc-codes + title: MARC Codes List + uri: http://purl.org/NET/marccodes/ +- namespace: http://data.linkedmdb.org/resource/ + prefix: linkedmdb + title: Linked Movie DataBase + uri: http://linkedmdb.org/ +- namespace: http://www.t4gm.info/ + prefix: t4gm-info + title: Thesaurus for Graphic Materials (t4gm.info) + uri: http://www.t4gm.info/ +- namespace: http://nektar.oszk.hu/ + prefix: hungarian-national-library-catalog + title: Hungarian National Library (NSZL) catalog + uri: http://nektar.oszk.hu/wiki/Semantic_web +- namespace: http://famu.eagle-i.net/i/ + prefix: eagle-i-famu + title: eagle-i @ Florida Agricultural and Mechanical University + uri: http://famu.eagle-i.net +- namespace: http://w3id.org/foodie/corine/ + prefix: Corine linked dataset + title: Corine linked dataset + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://ieee.rkbexplorer.com/id/ + prefix: rkb-explorer-ieee + title: IEEE Papers (RKBExplorer) + uri: http://ieee.rkbexplorer.com +- namespace: http://acm.rkbexplorer.com/id/ + prefix: rkb-explorer-acm + title: Association for Computing Machinery (ACM) (RKBExplorer) + uri: http://acm.rkbexplorer.com/ +- namespace: http://red.gnoss.com/comunidad/OpenData + prefix: open-data-risp + title: Open Data RISP, the Spanish Open Data community + uri: http://red.gnoss.com/comunidad/OpenData +- namespace: http://dbpedia.org/resource/ + prefix: dbpedia + title: DBpedia + uri: http://dbpedia.org/ +- namespace: http://standardgraphs.ices.dk/stocks/ + prefix: 'Norway Fishery ' + title: Norway fishery stocks dataset + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://eurobarometer.publicdata.eu/data/ + prefix: eurobarometer-standard + title: Standard Eurobarometer + uri: http://eurobarometer.publicdata.eu +- namespace: http://webconf.rkbexplorer.com/id/ + prefix: rkb-explorer-webconf + title: webconf + uri: http://webconf.rkbexplorer.com +- namespace: http://laas.rkbexplorer.com/id/ + prefix: rkb-explorer-laas + title: LAAS-CNRS (RKBExplorer) + uri: http://laas.rkbexplorer.com +- namespace: http://gnoss.com/comunidad/prospectivatecnologica + prefix: prospects-and-trends-gnoss + title: Prospects and Trends (GNOSS) + uri: http://gnoss.com/comunidad/prospectivatecnologica +- namespace: http://purl.org/weso/pscs/isic/v4/resource + prefix: isic-v4 + title: ISIC V4 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-programmes + title: R&D Programmes + uri: http://linked.opendata.cz/resource/dataset/vavai/programmes +- namespace: http://data.kasabi.com/dataset/renewable-energy-generators + prefix: renewable_energy_generators + title: Renewable Energy Generators + uri: http://kasabi.com/dataset/renewable-energy-generators +- namespace: http://purl.org/weso/pscs/cpv/2003/resource + prefix: cpv-2003 + title: CPV 2003 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://el.dbpedia.org/resource/ + prefix: dbpedia-el + title: DBpedia in Greek + uri: http://wiki.el.dbpedia.org +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-tenders + title: Tenders in R&D + uri: http://linked.opendata.cz/resource/dataset/vavai/tenders +- namespace: http://data.linkedopendata.it/grrt/resource/ + prefix: grrt + title: Accommodations in Tuscany (LinkedOpenData.it) + uri: http://www.linkedopendata.it/datasets/grrt +- namespace: http://datos.bne.es/resource/ + prefix: datos-bne-es + title: datos.bne.es + uri: http://datos.bne.es +- namespace: http://estatwrap.ontologycentral.com/id/ + prefix: linked-eurostat + title: Linked Eurostat (OntologyCentral) + uri: http://ontologycentral.com/2009/01/eurostat/ +- namespace: http://eupmedia.publicdata.eu/data/ + prefix: eu-parliament-media + title: EU Parliament Media Library + uri: http://eupmedia.publicdata.eu/ +- namespace: http://nhs.psi.enakting.org/id/nhs/ + prefix: enakting-nhs + title: EnAKTing NHS Dataset + uri: http://nhs.psi.enakting.org/ +- namespace: http://linked.opendata.cz/resource/domain/vavai/ + prefix: cz-vavai-research-plans + title: Institutional research plans + uri: http://linked.opendata.cz/resource/dataset/vavai/research-plans +- namespace: http://courseware.rkbexplorer.com/id/ + prefix: rkb-explorer-courseware + title: Resilient Computing Courseware (RKBExplorer) + uri: http://courseware.rkbexplorer.com +- namespace: http://webenemasuno.linkeddata.es/elviajero/resource/ + prefix: elviajero + title: El Viajero's tourism dataset + uri: http://webenemasuno.linkeddata.es/ +- namespace: http://scholarometer.indiana.edu/namespaces/ + prefix: scholarometer + title: Scholarometer + uri: http://scholarometer.indiana.edu/data.html +- namespace: http://www.fao.org/aims/aos/fi/water_FAO_areas/ + prefix: Water Areas Classification + title: FAO water areas classification as linked data + uri: https://www.foodie-cloud.org/fct/ +- namespace: http://www.dbacademic.tech/resource + prefix: dbacademic + title: dbacademic + uri: http://sparql.dbacademic.tech/ +- namespace: http://www.readinglists.manchester.ac.uk/ + prefix: manchester-university-reading-lists + title: Manchester University Reading Lists + uri: http://www.readinglists.manchester.ac.uk/ +- namespace: http://gnoss.com/comunidad/Interactivos + prefix: artenuevosmedios-gnoss + title: Entornos interactivos. Arte en los nuevos medios (GNOSS) + uri: http://gnoss.com/comunidad/Interactivos +- namespace: http://caligraph.org + prefix: CaLiGraph + title: CaLiGraph + uri: http://caligraph.org +- namespace: http://logd.tw.rpi.edu/ + prefix: twc-logd + title: 'TWC: Linking Open Government Data' + uri: http://logd.tw.rpi.edu +- namespace: http://www.johngoodwin.me.uk/family/ + prefix: john-goodwins-family-tree + title: John Goodwin's Family Tree + uri: http://www.johngoodwin.me.uk/family/ +- namespace: http://openlibrary.org/ + prefix: open-library + title: Open Library + uri: http://openlibrary.org/ +- namespace: http://datos.artium.org/id/collections/ + prefix: datos-artium-org + title: datos-artium-org + uri: http://biblioteca.artium.org +- namespace: http://eurovoc.europa.eu + prefix: eurovoc + title: EuroVoc + uri: https://op.europa.eu/en/web/eu-vocabularies/th-dataset/-/resource/dataset/eurovoc +- namespace: http://linked.opendata.cz/resource/atc/ + prefix: cz-eh-1-atc + title: ATC groups + uri: http://linked.opendata.cz/resource/dataset/atc +- namespace: http://data.kasabi.com/dataset/chempedia-rdf/ + prefix: chempedia-rdf + title: ChemPedia RDF + uri: http://figshare.com/articles/ChemPedia_as_RDF/681678 +- namespace: http://co2emission.psi.enakting.org/id/ + prefix: enakting-co2emission + title: EnAKTing CO2 Emission Dataset + uri: http://co2emission.psi.enakting.org/ +- namespace: http://www4.wiwiss.fu-berlin.de/flickrwrappr/photos/ + prefix: flickr-wrappr + title: flickr? wrappr + uri: http://www4.wiwiss.fu-berlin.de/flickrwrappr +- namespace: http://deploy.rkbexplorer.com/id/ + prefix: rkb-explorer-deploy + title: DEPLOY (RKBExplorer) + uri: http://deploy.rkbexplorer.com +- namespace: http://purl.org/weso/pscs/naics/2012/resource + prefix: naics-2012 + title: NAICS 2012 + uri: http://www.josemalvarez.es/web/2011/11/16/product-scheme-classifications/ +- namespace: http://epsrc.rkbexplorer.com/id/ + prefix: rkb-explorer-epsrc + title: epsrc + uri: http://epsrc.rkbexplorer.com +- namespace: http://vocabulary.semantic-web.at/semweb/ + prefix: socialsemweb-thesaurus + title: Social Semantic Web Thesaurus + uri: http://vocabulary.semantic-web.at/PoolParty/wiki/semweb +- namespace: http://www4.wiwiss.fu-berlin.de/sider/resource/ + prefix: fu-berlin-sider + title: 'SIDER: Side Effect Resource' + uri: http://www4.wiwiss.fu-berlin.de/sider/ +- namespace: http://opendatacommunities.org/id/IMD/2010/IMD-score/LSOA/ + prefix: english-index-of-multiple-deprivation-score-2010 + title: English Index of Multiple Deprivation Score 2010 + uri: http://opendatacommunities.org/datasets/imd-score-2010 +- namespace: http://linked.opendata.cz/resource/domain/cenia.cz/ + prefix: cz-cenia-pollution + title: Integrated pollution registry + uri: http://linked.opendata.cz/resource/dataset/cenia.cz/irz +- namespace: http://iserve.kmi.open.ac.uk/iserve/ + prefix: iserve + title: 'iServe: Linked Services Registry' + uri: http://iserve.kmi.open.ac.uk/ +- namespace: http://www4.wiwiss.fu-berlin.de/euraxess/resource/ + prefix: fu-berlin-euraxess + title: EURAXESS - Researchers in Motion + uri: http://www4.wiwiss.fu-berlin.de/euraxess/ +- namespace: http://tuskegee.eagle-i.net/i/ + prefix: eagle-i-tuskegee + title: eagle-i @ Tuskegee University + uri: http://tuskegee.eagle-i.net +- namespace: http://eudbpedia.deusto.es/resource/ + prefix: dbpedia-eu + title: DBpedia in Basque + uri: http://eudbpedia.deusto.es +- namespace: https://w3id.org/foodie/open/cz/pLPIS_180616_WGS/ + prefix: LPIS Czech Republic + title: Land parcel dataset (LPIS) from Czech Republic + uri: https://www.foodie-cloud.org/fct/ diff --git a/fuji_server/data/linked_vocabs/bioportal_ontologies.json b/fuji_server/data/linked_vocabs/bioportal_ontologies.json deleted file mode 100644 index 4f7885ed..00000000 --- a/fuji_server/data/linked_vocabs/bioportal_ontologies.json +++ /dev/null @@ -1,9224 +0,0 @@ -{ - "bioportal.aba-amb": { - "bioportal": { - "name": "Allen Brain Atlas (ABA) Adult Mouse Brain Ontology", - "prefix": "ABA-AMB", - "subjects": [ - "Mouse Anatomy" - ], - "uri_format": "http://mouse.brain-map.org/atlas/index.html#$1" - 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"bioportal": { - "name": "Nurse triage", - "prefix": "TRIAGE", - "subjects": [ - "Health" - ], - "uri_format": "http://www.semanticweb.org/philshields/ontologies/2015/4/untitled-ontology-59#$1" - } - }, - "bioportal.tron": { - "bioportal": { - "name": "Tribolium Ontology", - "prefix": "TRON", - "subjects": [ - "Anatomy", - "Development" - ], - "uri_format": "http://purl.obolibrary.org/obo/TrOn_$1" - } - }, - "bioportal.tto": { - "bioportal": { - "name": "Teleost Taxonomy Ontology", - "prefix": "TTO", - "subjects": [ - "Taxonomic Classification" - ], - "uri_format": "http://purl.obolibrary.org/obo/TTO_$1" - } - }, - "bioportal.txpo": { - "bioportal": { - "name": "Toxic Process Ontology", - "prefix": "TXPO", - "subjects": [ - "Dysfunction", - "Biological Process" - ], - "uri_format": "http://purl.obolibrary.org/obo/TXPO_$1" - } - }, - "bioportal.typon": { - "bioportal": { - "name": "Microbial Typing Ontology", - "prefix": "TYPON", - "subjects": [], - "uri_format": "http://purl.phyloviz.net/ontology/typon#$1" - 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"prefix": "VIVO", - "subjects": [ - "Other" - ], - "uri_format": "http://vivoweb.org/ontology/core#$1" - } - }, - "bioportal.vivo-isf": { - "bioportal": { - "name": "VIVO-Integrated Semantic Framework", - "prefix": "VIVO-ISF", - "subjects": [ - "Other" - ], - "uri_format": "http://www.w3.org/2006/vcard/ns#$1" - } - }, - "bioportal.vo": { - "bioportal": { - "name": "Vaccine Ontology", - "prefix": "VO", - "subjects": [ - "All Organisms", - "Immunology", - "Health" - ], - "uri_format": "http://purl.obolibrary.org/obo/VO_$1" - } - }, - "bioportal.vodana-general": { - "bioportal": { - "name": "VODANATERMS", - "prefix": "VODANA-GENERAL", - "subjects": [ - "Vocabularies" - ], - "uri_format": "http://www.vodan-totafrica.info/vocs/vgt$1" - } - }, - "bioportal.vodana-mi": { - "bioportal": { - "name": "VODANA-MIGRANTS-INTERVIEWS", - "prefix": "VODANA-MI", - "subjects": [ - "Health", - "Vocabularies" - ], - "uri_format": "https://www.vodan-totafrica.info/vocs/miv$1" - } - }, - "bioportal.vodana-migrants": { - "bioportal": { - "name": "VODANA MIGRANTS VOCABULARY", - "prefix": "VODANA-MIGRANTS", - "subjects": [ - "Health", - "Vocabularies" - ], - "uri_format": "https://www.vodan-totafrica.info/vocs/vodan-migrant-content$1" - } - }, - "bioportal.vodana-mpa": { - "bioportal": { - "name": "VODANA-MIGRANTS-PRESS ARTICLES", - "prefix": "VODANA-MPA", - "subjects": [ - "Health", - "Vocabularies" - ], - "uri_format": "https://www.vodan-totafrica.info/vocs/mnv$1" - } - }, - "bioportal.vodanacovid": { - "bioportal": { - "name": "VODANA-COVIDTERMS", - "prefix": "VODANACOVID", - "subjects": [ - "Health" - ], - "uri_format": "https://github.com/mariambasajja$1" - } - }, - "bioportal.vodanadiseases": { - "bioportal": { - "name": "VODANADiseases", - "prefix": "VODANADISEASES", - "subjects": [ - "Vocabularies" - ], - "uri_format": "http://vocab.vodan-totafrica.info/vodana-terms/vdiseases$1" - } - }, - "bioportal.vodanakenya": { - "bioportal": { - "name": "VODANA KENYA", - "prefix": "VODANAKENYA", - "subjects": [ - "Vocabularies" - ], - "uri_format": "http://www.vodan-totafrica.info/vodana-terms$1" - } - }, - "bioportal.vodanamflcode": { - "bioportal": { - "name": "VODANAFACILITIESLIST", - "prefix": "VODANAMFLCODE", - "subjects": [ - "Vocabularies" - ], - "uri_format": "http://vocab.vodana.org/vmfl$1" - } - }, - "bioportal.vodananigeria": { - "bioportal": { - "name": "VODANANIGERIA", - "prefix": "VODANANIGERIA", - "subjects": [ - "Health" - ], - "uri_format": "https://github.com/mariambasajja$1" - } - }, - "bioportal.vodanauganda": { - "bioportal": { - "name": "VODANAUGANDA", - "prefix": "VODANAUGANDA", - "subjects": [], - "uri_format": "https://github.com/mariambasajja/vocablary1$1" - } - }, - "bioportal.vsao": { - "bioportal": { - "name": "Vertebrate Skeletal Anatomy Ontology", - "prefix": "VSAO", - "subjects": [ - "Fish Anatomy", - "Gross Anatomy", - "Anatomy", - "Animal Gross Anatomy" - ], - "uri_format": "http://purl.obolibrary.org/obo/VSAO_$1" - } - }, - "bioportal.vso": { - "bioportal": { - "name": "Vital Sign Ontology", - "prefix": "VSO", - "subjects": [ - "Health" - ], - "uri_format": "http://purl.obolibrary.org/obo/VSO_$1" - } - }, - "bioportal.vt": { - "bioportal": { - "name": "Vertebrate Trait Ontology", - "prefix": "VT", - "subjects": [], - "uri_format": "http://purl.obolibrary.org/obo/VT_$1" - } - }, - "bioportal.vto": { - "bioportal": { - "name": "Vertebrate Taxonomy Ontology", - "prefix": "VTO", - "subjects": [ - "Taxonomic Classification" - ], - "uri_format": "http://purl.obolibrary.org/obo/VTO_$1" - } - }, - "bioportal.wb-bt": { - "bioportal": { - "name": "C. elegans Gross Anatomy Vocabulary", - "prefix": "WB-BT", - "subjects": [ - "Gross Anatomy", - "Anatomy", - "Animal Gross Anatomy" - ], - "uri_format": "http://purl.obolibrary.org/obo/WBbt_$1" - } - }, - "bioportal.wb-ls": { - "bioportal": { - "name": "C. elegans Development Vocabulary", - "prefix": "WB-LS", - "subjects": [ - "Development", - "Animal Development" - ], - "uri_format": "http://purl.obolibrary.org/obo/WBls_$1" - } - }, - "bioportal.wb-phenotype": { - "bioportal": { - "name": "C. elegans Phenotype Vocabulary", - "prefix": "WB-PHENOTYPE", - "subjects": [ - "Phenotype" - ], - "uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1" - } - }, - "bioportal.wc": { - "bioportal": { - "name": "Whole-cell modeling ontology", - "prefix": "WC", - "subjects": [ - "Molecule", - "Other", - "Cell" - ], - "uri_format": "http://purl.obolibrary.org/obo/WC_$1" - } - }, - "bioportal.wear": { - "bioportal": { - "name": "WEAR: Wind Energy mAteRials Taxonomy", - "prefix": "WEAR", - "subjects": [], - "uri_format": "http://purl.org/wear$1" - } - }, - "bioportal.weave": { - "bioportal": { - "name": "WEAVE: Wind Energy ActiVitiEs", - "prefix": "WEAVE", - "subjects": [], - "uri_format": "http://purl.org/weave$1" - } - }, - "bioportal.wetaxtopics": { - "bioportal": { - "name": "NEAT: wiNd Energy tAxonomy of Topics", - "prefix": "WETAXTOPICS", - "subjects": [ - "Taxonomic Classification" - ], - "uri_format": "http://purl.org/neat$1" - } - }, - "bioportal.who-art": { - "bioportal": { - "name": "World Health Organization (WHO) Adverse Reaction Terminology", - "prefix": "WHO-ART", - "subjects": [ - "Health" - ], - "uri_format": "http://purl.bioontology.org/ontology/WHO$1" - } - }, - "bioportal.wikipathways": { - "bioportal": { - "name": "WikiPathways", - "prefix": "WIKIPATHWAYS", - "subjects": [ - "Biological Process", - "Vocabularies" - ], - "uri_format": "http://vocabularies.wikipathways.org/wp#$1" - } - }, - "bioportal.wsio": { - "bioportal": { - "name": "Web-Service Interaction Ontology", - "prefix": "WSIO", - "subjects": [ - "Other" - ], - "uri_format": "http://purl.obolibrary.org/obo/WSIO_$1" - } - }, - "bioportal.xao": { - "bioportal": { - "name": "Xenopus Anatomy Ontology", - "prefix": "XAO", - "subjects": [ - "Anatomy", - "Development" - ], - "uri_format": "http://purl.obolibrary.org/obo/XAO_$1" - } - }, - "bioportal.xco": { - "bioportal": { - "name": "Experimental Conditions Ontology", - "prefix": "XCO", - "subjects": [ - "Experimental Conditions", - "Phenotype" - ], - "uri_format": "http://purl.obolibrary.org/obo/XCO_$1" - } - }, - "bioportal.xeo": { - "bioportal": { - "name": "XEML Environment Ontology", - "prefix": "XEO", - "subjects": [ - "Other" - ], - "uri_format": "http://purl.obolibrary.org/obo/XEO_$1" - } - }, - "bioportal.xlmod": { - "bioportal": { - "name": "mass spectrometry cross-linking and derivatization reagents", - "prefix": "XLMOD", - "subjects": [ - "Genomic and Proteomic" - ], - "uri_format": "http://purl.obolibrary.org/obo/XLMOD_$1" - } - }, - "bioportal.xpo": { - "bioportal": { - "name": "Xenopus Phenotype Ontology", - "prefix": "XPO", - "subjects": [ - "Phenotype" - ], - "uri_format": "http://purl.obolibrary.org/obo/XPO_$1" - } - }, - "bioportal.xref-funder-reg": { - "bioportal": { - "name": "CrossRef Funder Registry", - "prefix": "XREF-FUNDER-REG", - "subjects": [ - "Other" - ], - "uri_format": "http://dx.doi.org/10.13039$1" - } - }, - "bioportal.zea": { - "bioportal": { - "name": "Maize Gross Anatomy Ontology", - "prefix": "ZEA", - "subjects": [ - "Plant Anatomy" - ], - "uri_format": "http://purl.obolibrary.org/obo/ZEA_$1" - } - }, - "bioportal.zeco": { - "bioportal": { - "name": "Zebrafish Experimental Conditions Ontology", - "prefix": "ZECO", - "subjects": [ - "Experimental Conditions" - ], - "uri_format": "http://purl.obolibrary.org/obo/ZECO_$1" - } - }, - "bioportal.zfa": { - "bioportal": { - "name": "Zebrafish Anatomy and Development Ontology", - "prefix": "ZFA", - "subjects": [ - "Fish Anatomy", - "Gross Anatomy", - "Anatomy", - "Animal Gross Anatomy" - ], - "uri_format": "http://purl.obolibrary.org/obo/ZFA_$1" - } - }, - "bioportal.zonmw-admin-md": { - "bioportal": { - "name": "ZonMW Administrative Metadata Vocabulary", - "prefix": "ZONMW-ADMIN-MD", - "subjects": [], - "uri_format": "http://www.fair-data-collective.com/zonmw/projectadmin$1" - } - }, - "bioportal.zonmw-content": { - "bioportal": { - "name": "ZonMW COVID-19", - "prefix": "ZONMW-CONTENT", - "subjects": [], - "uri_format": "http://purl.org/zonmw/covid19$1" - } - }, - "bioportal.zonmw-generic": { - "bioportal": { - "name": "ZonMw Generic Terms", - "prefix": "ZONMW-GENERIC", - "subjects": [ - "Other" - ], - "uri_format": "http://purl.org/zonmw/generic$1" - } - }, - "bioportal.zp": { - "bioportal": { - "name": "Zebrafish Phenotype Ontology", - "prefix": "ZP", - "subjects": [ - "Phenotype" - ], - "uri_format": "http://purl.obolibrary.org/obo/ZP_$1" - } - } -} diff --git a/fuji_server/data/linked_vocabs/bioportal_ontologies.yaml b/fuji_server/data/linked_vocabs/bioportal_ontologies.yaml new file mode 100644 index 00000000..86a42063 --- /dev/null +++ b/fuji_server/data/linked_vocabs/bioportal_ontologies.yaml @@ -0,0 +1,6717 @@ +bioportal.aba-amb: + bioportal: + name: Allen Brain Atlas (ABA) Adult Mouse Brain Ontology + prefix: ABA-AMB + subjects: + - Mouse Anatomy + uri_format: http://mouse.brain-map.org/atlas/index.html#$1 +bioportal.abd: + bioportal: + name: Anthology of Biosurveillance Diseases + prefix: ABD + subjects: + - All Organisms + - Health + - Plant + - Human + uri_format: http://brd.bsvgateway.org/api/organism$1 +bioportal.aceso: + bioportal: + name: Adverse Childhood Experiences Ontology + prefix: ACESO + subjects: [] + uri_format: http://www.semanticweb.org/cbmi/ontologies/2018/10/aceso#$1 +bioportal.acgt-mo: + bioportal: + name: Cancer Research and Management ACGT Master Ontology + prefix: ACGT-MO + subjects: + - Health + uri_format: http://www.ifomis.org/acgt/1.0#$1 +bioportal.ad-drop: + bioportal: + name: Alzheimer Disease Relevance Ontology by Process + prefix: AD-DROP + subjects: + - Biomedical Resources + uri_format: http://www.semanticweb.org/AD-DROP#$1 +bioportal.adalab: + bioportal: + name: AdaLab ontology + prefix: ADALAB + subjects: + - Biological Process + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.adalab-meta: + bioportal: + name: AdaLab-meta ontology + prefix: ADALAB-META + subjects: + - Biomedical Resources + - Other + - Vocabularies + uri_format: http://rdf.adalab-project.org/ontology/adalab-meta$1 +bioportal.adar: + bioportal: + name: Autism DSM-ADI-R ontology + prefix: ADAR + subjects: + - Health + uri_format: http://purl.org/autism-ontology/1.0/autism-rules.owl#$1 +bioportal.adcad: + bioportal: + name: Arctic Data Center Academic Disciplines Ontology + prefix: ADCAD + subjects: [] + uri_format: https://purl.dataone.org/odo/ADCAD_$1 +bioportal.adher_intcare_en: + bioportal: + name: Adherence and Integrated Care + prefix: ADHER_INTCARE_EN + subjects: + - Taxonomic Classification + - Health + - Biomedical Resources + - Other + - Vocabularies + uri_format: http://www.semanticweb.org/parracarlos/ontologies/2019/3/untitled-ontology-31#$1 +bioportal.adher_intcare_sp: + bioportal: + name: Adherence and Integrated Care in Spanish + prefix: ADHER_INTCARE_SP + subjects: + - Taxonomic Classification + - Health + - Biomedical Resources + - Other + - Vocabularies + uri_format: http://www.semanticweb.org/parracarlosl27f/ontologies/2019/4/untitled-ontology-64#$1 +bioportal.admin: + bioportal: + name: Nurse Administrator + prefix: ADMIN + subjects: + - Health + uri_format: http://www.semanticweb.org/philshields/ontologies/2015/4/Administrator.owl#$1 +bioportal.admo: + bioportal: + name: Alzheimer Disease Map Ontology + prefix: ADMO + subjects: + - Biological Process + - Human + uri_format: http://www.semanticweb.org/ADMO#$1 +bioportal.ado: + bioportal: + name: Alzheimer's disease ontology + prefix: ADO + subjects: + - Health + - Neurologic Disease + - Neurological Disorder + - Human + uri_format: http://scai.fraunhofer.de/AlzheimerOntology#$1 +bioportal.adw: + bioportal: + name: Animal Natural History and Life History Ontology + prefix: ADW + subjects: + - Anatomy + uri_format: http://www.owl-ontologies.com/unnamed.owl#$1 +bioportal.aeo: + bioportal: + name: Anatomical Entity Ontology + prefix: AEO + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/AEO_$1 +bioportal.aero: + bioportal: + name: Adverse Event Reporting Ontology + prefix: AERO + subjects: + - Health + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/AERO_$1 +bioportal.afo: + bioportal: + name: Allotrope Merged Ontology Suite + prefix: AFO + subjects: + - Chemical + uri_format: http://purl.allotrope.org/ontologies/result#$1 +bioportal.agro: + bioportal: + name: AGRonomy Ontology + prefix: AGRO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/AGRO_$1 +bioportal.agrocymac: + bioportal: + name: Control y Monitoreo de afecciones en los cultivos + prefix: AGROCYMAC + subjects: + - Other + - Plant + - Vocabularies + - Plant Development + uri_format: http://www.semanticweb.org/yali/ontologies/2019/0/cultivos#$1 +bioportal.agromop: + bioportal: + name: Control de Cacao + prefix: AGROMOP + subjects: + - Plant + - Plant Development + uri_format: http://www.semanticweb.org/vera/ontologies/2020/1/untitled-ontology-5#$1 +bioportal.ahol: + bioportal: + name: Animal Health Ontology for Livestock + prefix: AHOL + subjects: [] + uri_format: http://opendata.inra.fr/AHOL/AHOL_$1 +bioportal.ahso: + bioportal: + name: Animal Health Surveillance Ontology + prefix: AHSO + subjects: + - Health + - Biomedical Resources + uri_format: https://w3id.org/ahso#$1 +bioportal.ai-rheum: + bioportal: + name: Artificial Intelligence Rheumatology Consultant System Ontology + prefix: AI-RHEUM + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/AIR$1 +bioportal.aio: + bioportal: + name: Artificial Intelligence Ontology + prefix: AIO + subjects: + - Other + uri_format: https://w3id.org/aio$1 +bioportal.airbus: + bioportal: + name: Airbus + prefix: AIRBUS + subjects: [] + uri_format: http://protege.stanford.edu/thesauri/aero$1 +bioportal.aism: + bioportal: + name: Ontology for the Anatomy of the Insect SkeletoMuscular system + prefix: AISM + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/AISM_$1 +bioportal.allergydetector: + bioportal: + name: Allergy Detector II + prefix: ALLERGYDETECTOR + subjects: + - Dysfunction + uri_format: file://C:/Users/Nelson/workspace/JenaTutorial/src/br/com/allergydetector/resources/AllergyDetector.owl#$1 +bioportal.amino-acid: + bioportal: + name: Amino Acid Ontology + prefix: AMINO-ACID + subjects: + - Other + uri_format: http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#$1 +bioportal.amphx: + bioportal: + name: The Amphioxus Development and Anatomy Ontology + prefix: AMPHX + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/AMPHX_$1 +bioportal.ao: + bioportal: + name: Asthma Ontology + prefix: AO + subjects: + - Health + uri_format: http://childhealthservicemodels.eu/asthma#$1 +bioportal.apacomputer: + bioportal: + name: Computer Cluster + prefix: APACOMPUTER + subjects: + - Vocabularies + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apadisorders: + bioportal: + name: Disorders cluster + prefix: APADISORDERS + subjects: + - Vocabularies + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apaeducluster: + bioportal: + name: Educational Cluster + prefix: APAEDUCLUSTER + subjects: + - Vocabularies + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apaneurocluster: + bioportal: + name: APA Neuro Cluster + prefix: APANEUROCLUSTER + subjects: + - Vocabularies + uri_format: http://www.semanticweb.org/ontologies/2015/0/apaneurocluster.owl#$1 +bioportal.apaocuemploy: + bioportal: + name: APA Occupational and Employment cluster + prefix: APAOCUEMPLOY + subjects: + - Vocabularies + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apaonto: + bioportal: + name: Psychology Ontology + prefix: APAONTO + subjects: + - Biomedical Resources + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apastatistical: + bioportal: + name: APA Statistical Cluster + prefix: APASTATISTICAL + subjects: + - Vocabularies + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apatandt: + bioportal: + name: APA Tests and Testing cluster + prefix: APATANDT + subjects: + - Vocabularies + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apatreatment: + bioportal: + name: APA Treatment Cluster + prefix: APATREATMENT + subjects: + - Vocabularies + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.apo: + bioportal: + name: Ascomycete Phenotype Ontology + prefix: APO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/APO_$1 +bioportal.apollo-sv: + bioportal: + name: Apollo Structured Vocabulary + prefix: APOLLO-SV + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1 +bioportal.arcrc: + bioportal: + name: Arctic Report Card + prefix: ARCRC + subjects: [] + uri_format: http://purl.dataone.org/odo/ARCRC_$1 +bioportal.aro: + bioportal: + name: Antibiotic Resistance Ontology + prefix: ARO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/ARO_$1 +bioportal.asdpto: + bioportal: + name: Autism Spectrum Disorder Phenotype Ontology + prefix: ASDPTO + subjects: + - Phenotype + - Neurological Disorder + - Human + uri_format: http://cbmi.med.harvard.edu/asdphenotype#$1 +bioportal.aspect: + bioportal: + name: 'ASPECT: wind energy vAriableS, ParametErs and ConsTants' + prefix: ASPECT + subjects: + - Vocabularies + uri_format: http://purl.org/aspect$1 +bioportal.ato: + bioportal: + name: Amphibian Taxonomy Ontology + prefix: ATO + subjects: + - Taxonomic Classification + uri_format: http://purl.obolibrary.org/obo/ATO_$1 +bioportal.atol: + bioportal: + name: Animal Trait Ontology for Livestock + prefix: ATOL + subjects: [] + uri_format: http://opendata.inra.fr/ATOL/ATOL_$1 +bioportal.aura: + bioportal: + name: KB_Bio_101 + prefix: AURA + subjects: [] + uri_format: http://www.projecthalo.com/aura#$1 +bioportal.bao: + bioportal: + name: BioAssay Ontology + prefix: BAO + subjects: + - Molecule + - Biological Process + - Other + - Subcellular + - Chemical + - Cell + - Protein + - Vocabularies + - Physicochemical + uri_format: http://www.bioassayontology.org/bao#$1 +bioportal.bao-gpcr: + bioportal: + name: G Protein-Coupled Receptor BioAssays Ontology + prefix: BAO-GPCR + subjects: + - Molecule + - Biological Process + - Other + - Subcellular + - Chemical + - Protein + - Vocabularies + - Physicochemical + uri_format: http://www.bioassayontology.org/bao#$1 +bioportal.bcgo: + bioportal: + name: Breast Cancer Grading Ontology + prefix: BCGO + subjects: + - Biological Process + uri_format: http://www.owl-ontologies.com/Ontology1239104585.owl#$1 +bioportal.bci-o: + bioportal: + name: Brain-Computer Interaction (BCI) Ontology + prefix: BCI-O + subjects: + - Imaging + - Experimental Conditions + - Health + - Biomedical Resources + - Neurologic Disease + - Neurological Disorder + - Human + - Vocabularies + - Upper Level Ontology + uri_format: https://w3id.org/BCI-ontology#$1 +bioportal.bco: + bioportal: + name: Biological Collections Ontology + prefix: BCO + subjects: + - All Organisms + uri_format: http://purl.obolibrary.org/obo/bco_$1 +bioportal.bcs7: + bioportal: + name: Breast Cancer Staging - 7th Edition + prefix: BCS7 + subjects: [] + uri_format: http://idea.tw.rpi.edu/projects/heals/ontologies/cancer_staging_terms.owl#$1 +bioportal.bcs8: + bioportal: + name: Breast Cancer Staging - 8th Edition + prefix: BCS8 + subjects: [] + uri_format: http://idea.rpi.edu/ontologies/cancer_staging_terms.owl#$1 +bioportal.bcteo: + bioportal: + name: Bone and Cartilage Tissue Engineering Ontology + prefix: BCTEO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/ID_$1 +bioportal.bctt: + bioportal: + name: Behaviour Change Technique Taxonomy + prefix: BCTT + subjects: [] + uri_format: http://purl.bioontology.org/ontology/BCTT#$1 +bioportal.bdo: + bioportal: + name: Bone Dysplasia Ontology + prefix: BDO + subjects: + - Health + - Human + uri_format: http://purl.org/obo/owl/HP#$1 +bioportal.be: + bioportal: + name: Bioentities + prefix: BE + subjects: [] + uri_format: http://purl.obolibrary.org/obo/BE_$1 +bioportal.bflc: + bioportal: + name: LC BIBFRAME 2.0 Vocabulary Extension + prefix: BFLC + subjects: [] + uri_format: http://id.loc.gov/ontologies/bflc$1 +bioportal.bfo: + bioportal: + name: Basic Formal Ontology + prefix: BFO + subjects: + - Upper Level Ontology + uri_format: http://purl.obolibrary.org/obo/BFO_$1 +bioportal.bhn: + bioportal: + name: Biologie Hors Nomenclature + prefix: BHN + subjects: + - Health + - Vocabularies + uri_format: http://chu-rouen.fr/cismef/BHN#$1 +bioportal.bho: + bioportal: + name: Bleeding History Phenotype Ontology + prefix: BHO + subjects: + - Phenotype + uri_format: http://www.semanticweb.org/ontologies/2010/10/BPO.owl#$1 +bioportal.bibliotek-o: + bioportal: + name: The Biblioteko Ontology + prefix: BIBLIOTEK-O + subjects: [] + uri_format: http://bibliotek-o.org/1.1/ontology$1 +bioportal.bifo: + bioportal: + name: Biofilm Ontology + prefix: BIFO + subjects: + - Biomedical Resources + - Biological Process + uri_format: http://www.semanticweb.org/bowenliu/ontologies/2020/4/untitled-ontology-8#$1 +bioportal.bim: + bioportal: + name: Biomedical Image Ontology + prefix: BIM + subjects: + - Imaging + uri_format: http://cbakerlab.unbsj.ca:8080/ontologies/BIM.owl#$1 +bioportal.bin: + bioportal: + name: Body in Numbers project terminology + prefix: BIN + subjects: + - Taxonomic Classification + - Vocabularies + uri_format: http://purl.bioontology.org/ontology/BIN/BIN_$1 +bioportal.biolink: + bioportal: + name: Biolink Model + prefix: BIOLINK + subjects: + - All Organisms + - Biological Process + - Phenotype + - Chemical + - Cell + - Gene Product + uri_format: https://w3id.org/biolink/vocab$1 +bioportal.biomo: + bioportal: + name: Biological Observation Matrix Ontology + prefix: BIOMO + subjects: + - Other + uri_format: http://semanticscience.org/resource/SIO_$1 +bioportal.biomodels: + bioportal: + name: BioModels Ontology + prefix: BIOMODELS + subjects: + - All Organisms + - Biomedical Resources + - Biological Process + uri_format: http://purl.org/obo/owlapi/fma#$1 +bioportal.bipom: + bioportal: + name: Biological interlocked Process Ontology for metabolism + prefix: BIPOM + subjects: + - All Organisms + uri_format: http://purl.obolibrary.org/obo/BiPOm#$1 +bioportal.bipon: + bioportal: + name: Bacterial interlocked Process ONtology + prefix: BIPON + subjects: + - Biological Process + uri_format: http://www.semanticweb.org/BiPON/BiPON_$1 +bioportal.birnlex: + bioportal: + name: Biomedical Informatics Research Network Project Lexicon + prefix: BIRNLEX + subjects: + - Imaging + - Anatomy + uri_format: http://bioontology.org/projects/ontologies/birnlex#$1 +bioportal.bko: + bioportal: + name: Bricks ontology + prefix: BKO + subjects: + - Other + uri_format: http://sbgnbricks.org/BKO$1 +bioportal.bmt: + bioportal: + name: Biomedical Topics + prefix: BMT + subjects: [] + uri_format: http://edamontology.org/topic_$1 +bioportal.bno: + bioportal: + name: Bionutrition Ontology + prefix: BNO + subjects: + - Health + - Biomedical Resources + - Human + uri_format: http://www.owl-ontologies.com/Ontology1361987617.owl#$1 +bioportal.bof: + bioportal: + name: Biodiversity Ontology + prefix: BOF + subjects: [] + uri_format: http://www.owl-ontologies.com/BiodiversityOntologyFull.owl#$1 +bioportal.bp: + bioportal: + name: BioPAX Ontology of Biological Pathways + prefix: BP + subjects: + - Biological Process + uri_format: http://www.biopax.org/release/biopax-level3.owl#$1 +bioportal.bp-metadata: + bioportal: + name: BioPortal Metadata Ontology + prefix: BP-METADATA + subjects: + - Other + uri_format: http://protege.stanford.edu/ontologies/ChAO/changes.rdfs#$1 +bioportal.brct: + bioportal: + name: Brain Region & Cell Type terminology + prefix: BRCT + subjects: [] + uri_format: http://www.semanticweb.org/ontologies/2009/9/Ontology1255357986125.owl#$1 +bioportal.bridg: + bioportal: + name: Biomedical Research Integrated Domain Group Model + prefix: BRIDG + subjects: + - Health + uri_format: http://www.bridgmodel.org/owl#$1 +bioportal.bro: + bioportal: + name: Biomedical Resource Ontology + prefix: BRO + subjects: + - Biomedical Resources + uri_format: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#$1 +bioportal.bro_acronym: + bioportal: + name: Bro_Name + prefix: BRO_ACRONYM + subjects: [] + uri_format: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#$1 +bioportal.brso: + bioportal: + name: Biological Resource Schema Ontology + prefix: BRSO + subjects: + - All Organisms + uri_format: http://purl.jp/bio/10/brso$1 +bioportal.bsao: + bioportal: + name: Botryllus schlosseri anatomy and development ontology + prefix: BSAO + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/BSA_$1 +bioportal.bspo: + bioportal: + name: Spatial Ontology + prefix: BSPO + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/BSPO_$1 +bioportal.bt: + bioportal: + name: BioTop Ontology + prefix: BT + subjects: + - Upper Level Ontology + uri_format: http://purl.org/biotop/biotop.owl#$1 +bioportal.bto: + bioportal: + name: BRENDA Tissue and Enzyme Source Ontology + prefix: BTO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/BTO_$1 +bioportal.bto_ontology: + bioportal: + name: Brain Tumour Ontology + prefix: BTO_ONTOLOGY + subjects: + - Health + - Biomedical Resources + uri_format: http://www.semanticweb.org/samsung/ontologies/2012/10/untitled-ontology-9#$1 +bioportal.cabro: + bioportal: + name: Computer Assisted Brain Injury Rehabilitation Ontology + prefix: CABRO + subjects: + - Health + - Dysfunction + - Biomedical Resources + - Neurologic Disease + - Neurological Disorder + - Human + uri_format: http://www.semanticweb.org/dimitrios/ontologies/2013/2/untitled-ontology-2#$1 +bioportal.canco: + bioportal: + name: Cancer Chemoprevention Ontology + prefix: CANCO + subjects: + - Experimental Conditions + - Molecule + - Health + - Biomedical Resources + uri_format: http://chem.deri.ie/granatum#$1 +bioportal.canont: + bioportal: + name: 'Upper-Level Cancer Ontology ' + prefix: CANONT + subjects: [] + uri_format: http://purl.obolibrary.org/obo/ID_$1 +bioportal.cao: + bioportal: + name: Clusters of Orthologous Groups (COG) Analysis Ontology + prefix: CAO + subjects: + - Gene Product + uri_format: http://purl.obolibrary.org/obo/CAO_$1 +bioportal.carelex: + bioportal: + name: Content Archive Resource Exchange Lexicon + prefix: CARELEX + subjects: + - Vocabularies + uri_format: http://www.CareLex.org/2012/carelex.owl#$1 +bioportal.caro: + bioportal: + name: Common Anatomy Reference Ontology + prefix: CARO + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/CARO_$1 +bioportal.carre: + bioportal: + name: CARRE Risk Factor ontology + prefix: CARRE + subjects: + - Health + uri_format: file:/Users/allanthird/Work/CARRE/CARREOntology/carre-sensors.xml#$1 +bioportal.case-base-onto: + bioportal: + name: Case-base ontology for gastric dystemperament in Persian medicine + prefix: CASE-BASE-ONTO + subjects: + - Other + uri_format: http://www.semanticweb.org/hsh/ontologies/2019/7/CBRDystempOnto#$1 +bioportal.cbo: + bioportal: + name: Cell Behavior Ontology + prefix: CBO + subjects: + - All Organisms + - Biological Process + - Cell + uri_format: http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_1_2.owl#$1 +bioportal.ccf: + bioportal: + name: HuBMAP Common Coordinate Framework + prefix: CCF + subjects: + - Biomedical Resources + - Human + - Cell + uri_format: https://purl.org/ccf/ASCTB-TEMP_$1 +bioportal.cco: + bioportal: + name: Cell Cycle Ontology + prefix: CCO + subjects: + - Yeast + - Biological Process + - Arabidopsis + - Human + - Protein + uri_format: http://purl.obolibrary.org/obo/UniProt_$1 +bioportal.ccont: + bioportal: + name: Cell Culture Ontology + prefix: CCONT + subjects: + - Experimental Conditions + - Biological Process + - Vocabularies + uri_format: http://www.ebi.ac.uk/efo/EFO_$1 +bioportal.cctoo: + bioportal: + name: 'Cancer Care: Treatment Outcome Ontology' + prefix: CCTOO + subjects: + - Health + - Biomedical Resources + - Human + uri_format: http://purl.obolibrary.org/obo/CCTO_$1 +bioportal.cdao: + bioportal: + name: Comparative Data Analysis Ontology + prefix: CDAO + subjects: + - Experimental Conditions + uri_format: http://purl.obolibrary.org/obo/CDAO_$1 +bioportal.cdno: + bioportal: + name: Compositional Dietary Nutrition Ontology + prefix: CDNO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/CDNO_$1 +bioportal.cdo: + bioportal: + name: Chinese Diabetes Mellitus Ontology + prefix: CDO + subjects: + - Health + - Human + uri_format: http://purl.bioontology.org/ontology/CDO$1 +bioportal.cdpeo: + bioportal: + name: Chronic Disease Patient Education Ontology + prefix: CDPEO + subjects: + - Health + uri_format: http://www.semanticweb.org/ontologies/chronic-diease-patient-education-ontology#$1 +bioportal.cedarvs: + bioportal: + name: CEDAR Value Sets + prefix: CEDARVS + subjects: + - Other + uri_format: http://www.semanticweb.org/jgraybeal/ontologies/2015/7/cedarvaluesets#$1 +bioportal.ceph: + bioportal: + name: Cephalopod Ontology + prefix: CEPH + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/CEPH_$1 +bioportal.chd: + bioportal: + name: Congenital Heart Defects Ontology + prefix: CHD + subjects: + - Human + uri_format: http://homes.esat.kuleuven.be/~bioiuser/chdwiki/index.php$1 +bioportal.chear: + bioportal: + name: Children's Health Exposure Analysis Resource + prefix: CHEAR + subjects: + - Health + - Human + uri_format: http://hadatac.org/ont/chear#$1 +bioportal.chebi: + bioportal: + name: Chemical Entities of Biological Interest Ontology + prefix: CHEBI + subjects: + - Chemical + uri_format: http://purl.obolibrary.org/obo/CHEBI_$1 +bioportal.chembio: + bioportal: + name: 'Systems Chemical Biology and Chemogenomics Ontology ' + prefix: CHEMBIO + subjects: + - Molecule + - Biomedical Resources + - Biological Process + - Chemical + - Protein + uri_format: http://chem2bio2rdf.org/chem2bio2rdf.owl#$1 +bioportal.cheminf: + bioportal: + name: Chemical Information Ontology + prefix: CHEMINF + subjects: + - Chemical + uri_format: http://semanticscience.org/resource/CHEMINF_$1 +bioportal.chiro: + bioportal: + name: CHEBI Integrated Role Ontology + prefix: CHIRO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MP_$1 +bioportal.chmo: + bioportal: + name: Chemical Methods Ontology + prefix: CHMO + subjects: + - Chemical + uri_format: http://purl.obolibrary.org/obo/CHMO_$1 +bioportal.cido: + bioportal: + name: Coronavirus Infectious Disease Ontology + prefix: CIDO + subjects: + - All Organisms + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/CIDO_$1 +bioportal.cidoc-crm: + bioportal: + name: CIDOC Conceptual Reference Model + prefix: CIDOC-CRM + subjects: [] + uri_format: http://www.cidoc-crm.org/cidoc-crm/E78_$1 +bioportal.ciinteado: + bioportal: + name: Ciona intestinalis Anatomy and Development Ontology + prefix: CIINTEADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/CiinteA_$1 +bioportal.cio: + bioportal: + name: Confidence Information Ontology + prefix: CIO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/CIO_$1 +bioportal.cisaviado: + bioportal: + name: 'Ciona savignyi Anatomy and Development Ontology ' + prefix: CISAVIADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/CisaviA_$1 +bioportal.ckdo: + bioportal: + name: Chronic Kidney Disease Ontology + prefix: CKDO + subjects: [] + uri_format: http://clininf.eu/ckdo#$1 +bioportal.clao: + bioportal: + name: Collembola Anatomy Ontology + prefix: CLAO + subjects: + - Anatomy + - Animal Gross Anatomy + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/CLAO_$1 +bioportal.clo: + bioportal: + name: Cell Line Ontology + prefix: CLO + subjects: + - Experimental Conditions + - All Organisms + - Taxonomic Classification + - Biomedical Resources + - Biological Process + - Phenotype + - Anatomy + - Cell + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/CLO_$1 +bioportal.clyh: + bioportal: + name: Clytia hemisphaerica Development and Anatomy Ontology + prefix: CLYH + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/CLYH_$1 +bioportal.cmdo: + bioportal: + name: Clinical MetaData Ontology + prefix: CMDO + subjects: [] + uri_format: http://purl.bioontology.org/ontology/CMDO$1 +bioportal.cmo: + bioportal: + name: Clinical Measurement Ontology + prefix: CMO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/CMO_$1 +bioportal.cmpo: + bioportal: + name: Cellular microscopy phenotype ontology + prefix: CMPO + subjects: + - 'Cellular anatomy ' + - Phenotype + - Cell + uri_format: http://www.ebi.ac.uk/cmpo/CMPO_$1 +bioportal.cmr-qa: + bioportal: + name: Cardiovascular Magnetic Resonance Quality Assessment Ontology + prefix: CMR-QA + subjects: + - Imaging + - Health + - Vocabularies + uri_format: http://www.semanticweb.org/ukbiobank/ocmr_isg/CMR-QA#$1 +bioportal.cn: + bioportal: + name: computer network + prefix: CN + subjects: [] + uri_format: http://mmisw.org/ont/Technology/ComputerNetworks$1 +bioportal.cno: + bioportal: + name: Computational Neuroscience Ontology + prefix: CNO + subjects: + - Vocabularies + uri_format: http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#$1 +bioportal.cno_acronym: + bioportal: + name: CNO_NAME + prefix: CNO_ACRONYM + subjects: [] + uri_format: http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#$1 +bioportal.co-wheat: + bioportal: + name: 'Wheat Trait Ontology ' + prefix: CO-WHEAT + subjects: + - Phenotype + - Plant + uri_format: http://purl.obolibrary.org/obo/CO_$1 +bioportal.cob: + bioportal: + name: Core Ontology for Biology and Biomedicine + prefix: COB + subjects: + - Upper Level Ontology + uri_format: http://purl.obolibrary.org/obo/COB_$1 +bioportal.codo: + bioportal: + name: An Ontology for Collection and Analysis of COviD-19 Data + prefix: CODO + subjects: + - Health + - Human + - Vocabularies + uri_format: http://www.isibang.ac.in/ns/codo#$1 +bioportal.cogat: + bioportal: + name: Cognitive Atlas Ontology + prefix: COGAT + subjects: + - Phenotype + - Human + - Vocabularies + uri_format: file:/srv/ncbo/repository/COGAT/8/cogat.owl#$1 +bioportal.cogpo: + bioportal: + name: Cognitive Paradigm Ontology + prefix: COGPO + subjects: + - Imaging + - Experimental Conditions + - Human + uri_format: http://www.cogpo.org/ontologies/CogPOver1.owl#$1 +bioportal.cohsi2study: + bioportal: + name: cohsi2study + prefix: COHSI2STUDY + subjects: + - Vocabularies + uri_format: https://www.lumc.nl/fairontologies/aeterms/ae$1 +bioportal.cokpme: + bioportal: + name: 'COKPME - COVID19 Ontology for analyzing the Karnataka Private Medical Establishments Data ' + prefix: COKPME + subjects: + - Health + - Biomedical Resources + uri_format: http://www.iiitdwd.ac.in/ACB/COKPME#$1 +bioportal.comodi: + bioportal: + name: COMODI + prefix: COMODI + subjects: + - Development + - Vocabularies + uri_format: http://purl.uni-rostock.de/comodi/comodi#$1 +bioportal.contsonto: + bioportal: + name: Continuity of care + prefix: CONTSONTO + subjects: + - Health + uri_format: https://contsys.org/concept/healthcare_$1 +bioportal.copdo: + bioportal: + name: COPD Ontology + prefix: COPDO + subjects: + - Health + - Human + uri_format: http://webprotege.stanford.edu$1 +bioportal.costart: + bioportal: + name: Coding Symbols for a Thesaurus of Adverse Reaction Terms + prefix: COSTART + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/CST$1 +bioportal.covid-19: + bioportal: + name: COVID-19 Ontology + prefix: COVID-19 + subjects: + - Immunology + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.covid-19-ont-pm: + bioportal: + name: COVID-19OntologyInPatternMedicine + prefix: COVID-19-ONT-PM + subjects: + - Biomedical Resources + uri_format: http://www.semanticweb.org/hanfei/ontologies/2020/9/untitled-ontology-1306#$1 +bioportal.covid19: + bioportal: + name: COVID-19 Surveillance Ontology + prefix: COVID19 + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/clininf/covid19#$1 +bioportal.covid19-ibo: + bioportal: + name: Covid19 Impact on Banking Ontology + prefix: COVID19-IBO + subjects: + - Other + uri_format: http://www.semanticweb.org/archana/ontologies/2021/5/untitled-ontology-6#$1 +bioportal.covidcrfrapid: + bioportal: + name: WHO COVID-19 Rapid Version CRF semantic data model + prefix: COVIDCRFRAPID + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/NCIT_$1 +bioportal.cpro: + bioportal: + name: Computer-Based Patient Record Ontology + prefix: CPRO + subjects: + - Health + uri_format: http://purl.org/cpr$1 +bioportal.cpt: + bioportal: + name: CPT - Current Procedural Terminology + prefix: CPT + subjects: + - Other + uri_format: http://purl.bioontology.org/ontology/CPT$1 +bioportal.cptac: + bioportal: + name: CPTAC Proteomics Pipeline Infrastructure Ontology + prefix: CPTAC + subjects: + - Genomic and Proteomic + uri_format: http://proteomeontology.org/cpo.owl#$1 +bioportal.crisp: + bioportal: + name: Computer Retrieval of Information on Scientific Projects Thesaurus + prefix: CRISP + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/CSP$1 +bioportal.cro: + bioportal: + name: Contributor Role Ontology + prefix: CRO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/CRO_$1 +bioportal.cryoem: + bioportal: + name: Cryo Electron Microscopy + prefix: CRYOEM + subjects: + - Imaging + uri_format: http://scipion.i2pc.es/ontology/CRYOEM_$1 +bioportal.cseo: + bioportal: + name: Cigarette Smoke Exposure Ontology + prefix: CSEO + subjects: + - Health + uri_format: http://scai.fraunhofer.de/CSEO#$1 +bioportal.cso: + bioportal: + name: Clinical Study Ontology + prefix: CSO + subjects: [] + uri_format: http://webprotege.stanford.edu$1 +bioportal.csso: + bioportal: + name: Clinical Signs and Symptoms Ontology + prefix: CSSO + subjects: + - Health + uri_format: http://purl.jp/bio/11/csso/CSSO_$1 +bioportal.cstd: + bioportal: + name: Clinical smell and taste disorders + prefix: CSTD + subjects: + - Phenotype + uri_format: http://www.semanticweb.org/hsiehjulien/ontologies/2016/3/untitled-ontology-4#$1 +bioportal.ctcae: + bioportal: + name: Common Terminology Criteria for Adverse Events + prefix: CTCAE + subjects: [] + uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae5.owl#$1 +bioportal.cteno: + bioportal: + name: Ctenophore Ontology + prefix: CTENO + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/CTENO_$1 +bioportal.cto: + bioportal: + name: Clinical Trials Ontology + prefix: CTO + subjects: [] + uri_format: https://bio.scai.fraunhofer.de/ontology/CTO_$1 +bioportal.cto-ndd: + bioportal: + name: Clinical Trials Ontology - Neurodegenerative Diseases + prefix: CTO-NDD + subjects: + - Health + - Biomedical Resources + - Neurological Disorder + uri_format: http://www.semanticweb.org/ontologies/2012/0/Ontology1325521724189.owl#$1 +bioportal.ctont: + bioportal: + name: Epoch Clinical Trial Ontology + prefix: CTONT + subjects: + - Experimental Conditions + uri_format: http://epoch.stanford.edu/ClinicalTrialOntology.owl#$1 +bioportal.ctx: + bioportal: + name: Cerebrotendinous Xanthomatosis Ontology + prefix: CTX + subjects: + - Phenotype + uri_format: http://www.owl-ontologies.com/OntologyXCT.owl#$1 +bioportal.cu-vo: + bioportal: + name: Venom Ontology + prefix: CU-VO + subjects: + - Molecule + - Genomic and Proteomic + - Chemical + - Protein + uri_format: http://www.semanticweb.org/jdr2160/ontologies/2015/5/venom_ontology#$1 +bioportal.cvao: + bioportal: + name: STO + prefix: CVAO + subjects: [] + uri_format: http://www.semanticweb.org/ontologies/STO.owl#$1 +bioportal.cvdo: + bioportal: + name: Cardiovascular Disease Ontology + prefix: CVDO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/CVDO_$1 +bioportal.cwd: + bioportal: + name: Consumer Wearable Device + prefix: CWD + subjects: + - Health + uri_format: http://www.semanticweb.org/jbagwell/ontologies/2017/9/untitled-ontology-6#$1 +bioportal.cyto: + bioportal: + name: CYTOKINE + prefix: CYTO + subjects: + - Protein + uri_format: http://www.semanticweb.org/demetrios/ontologies/2014/5$1 +bioportal.datacite: + bioportal: + name: SPAR DataCite Ontology + prefix: DATACITE + subjects: + - Other + uri_format: http://purl.org/spar/datacite$1 +bioportal.datacite-vocab: + bioportal: + name: DATACITE V4.4 + prefix: DATACITE-VOCAB + subjects: [] + uri_format: http://purl.org/datacite/v4.4$1 +bioportal.dc: + bioportal: + name: Dublin Core + prefix: DC + subjects: + - Other + uri_format: http://purl.org/dc/terms$1 +bioportal.dcat: + bioportal: + name: Data Catalog Vocabulary + prefix: DCAT + subjects: + - Other + uri_format: http://www.w3.org/ns/dcat#$1 +bioportal.dcat-fdc: + bioportal: + name: Data Catalog Vocabulary (DCAT) + prefix: DCAT-FDC + subjects: [] + uri_format: http://www.w3.org/ns/prov#$1 +bioportal.dccdfv: + bioportal: + name: Dublin Core Collection Description Frequency Vocabulary + prefix: DCCDFV + subjects: + - Other + uri_format: http://purl.org/cld/freq$1 +bioportal.dcm: + bioportal: + name: DICOM Controlled Terminology + prefix: DCM + subjects: + - Imaging + uri_format: http://dicom.nema.org/resources/ontology/DCM$1 +bioportal.dcmitype: + bioportal: + name: DCMI Type Vocabulary + prefix: DCMITYPE + subjects: + - Other + uri_format: http://purl.org/dc/dcmitype$1 +bioportal.dco: + bioportal: + name: Dispedia Core Ontology + prefix: DCO + subjects: + - Health + - Other + - Human + - Vocabularies + uri_format: http://www.dispedia.de/o$1 +bioportal.dct: + bioportal: + name: DC Terms + prefix: DCT + subjects: + - Other + uri_format: http://purl.org/dc/terms$1 +bioportal.ddanat: + bioportal: + name: Dictyostelium Discoideum Anatomy Ontology + prefix: DDANAT + subjects: + - Gross Anatomy + - Anatomy + - Microbial Anatomy + uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 +bioportal.ddi: + bioportal: + name: Ontology for Drug Discovery Investigations + prefix: DDI + subjects: [] + uri_format: http://purl.obolibrary.org/obo/IAO_$1 +bioportal.ddiem: + bioportal: + name: Drug Database for Inborn Errors of Metabolism (DDIEM) Ontology + prefix: DDIEM + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/DDIEM_$1 +bioportal.ddpheno: + bioportal: + name: Dictyostelium Discoideum Phenotype Ontology + prefix: DDPHENO + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1 +bioportal.deb: + bioportal: + name: Devices, Experimental scaffolds and Biomaterials Ontology + prefix: DEB + subjects: + - Biomedical Resources + uri_format: http://www.semanticweb.org/osnathakimi/ontologies/deb#$1 +bioportal.dermlex: + bioportal: + name: Dermatology Lexicon + prefix: DERMLEX + subjects: + - Health + uri_format: http://www.owl-ontologies.com/unnamed.owl#$1 +bioportal.dermo: + bioportal: + name: Human Dermatological Disease Ontology + prefix: DERMO + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/DERMO_$1 +bioportal.dfo: + bioportal: + name: Databank Family Ontology + prefix: DFO + subjects: + - Biomedical Resources + uri_format: https://w3id.org/dfo/Death_$1 +bioportal.diab: + bioportal: + name: BioMedBridges Diabetes Ontology + prefix: DIAB + subjects: [] + uri_format: http://purl.obolibrary.org/obo/HP_$1 +bioportal.diagont: + bioportal: + name: Diagnostic Ontology + prefix: DIAGONT + subjects: [] + uri_format: http://www.owl-ontologies.com/RCTOntology.owl#$1 +bioportal.dideo: + bioportal: + name: Drug Interaction and Evidence Ontology + prefix: DIDEO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/DIDEO_$1 +bioportal.dikb: + bioportal: + name: Drug Interaction Knowledge Base Ontology + prefix: DIKB + subjects: + - Vocabularies + uri_format: http://purl.org/net/drug-interaction-knowledge-base/DIKB_evidence_ontology.owl#$1 +bioportal.dilon: + bioportal: + name: Dietary lifestyle ontology + prefix: DILON + subjects: + - Health + - Human + uri_format: http://www.co-ode.org/ontologies/ont.owl#$1 +bioportal.dinto: + bioportal: + name: The Drug-Drug Interactions Ontology + prefix: DINTO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/dinto_$1 +bioportal.disdriv: + bioportal: + name: Disease Drivers Ontology + prefix: DISDRIV + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/DISDRIV_$1 +bioportal.dloro: + bioportal: + name: Dependency Layered Ontology for Radiation Oncology + prefix: DLORO + subjects: + - Human + - Vocabularies + uri_format: http://www.semanticweb.org/alan/ontologies/2013/8/untitled-ontology-9#$1 +bioportal.doccc: + bioportal: + name: Diagnosis Ontology of Clinical Care Classification + prefix: DOCCC + subjects: + - Health + uri_format: http://www.semanticweb.org/hll/ontologies/2013/8/untitled-ontology-2#$1 +bioportal.doid: + bioportal: + name: Human Disease Ontology + prefix: DOID + subjects: + - Health + - Biomedical Resources + - Neurologic Disease + - Neurological Disorder + - Human + uri_format: http://purl.obolibrary.org/obo/DOID_$1 +bioportal.doremus-keys: + bioportal: + name: Doremus List of Keys + prefix: DOREMUS-KEYS + subjects: [] + uri_format: http://data.doremus.org/vocabulary/key$1 +bioportal.dpo: + bioportal: + name: Drosophila Phenotype Ontology + prefix: DPO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.dranpto: + bioportal: + name: Dementia-Related Agitation Non-Pharmacological Treatment Ontology + prefix: DRANPTO + subjects: + - Taxonomic Classification + - Health + - Vocabularies + uri_format: http://www.semanticweb.org/zhenyuzhang/ontologies/2019/8/nonpharmacological-intervention-for-agitation-in-dementia-ontology$1 +bioportal.dreamdnpto: + bioportal: + name: Dementia-Related Emotional And Mood Disturbance Non-Pharmacological Treatment Ontology + prefix: DREAMDNPTO + subjects: + - Taxonomic Classification + - Health + - Vocabularies + uri_format: http://www.semanticweb.org/zhenyuzhang/ontologies/2021/DREAMDNPTO#$1 +bioportal.dron: + bioportal: + name: The Drug Ontology + prefix: DRON + subjects: + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/DRON_$1 +bioportal.drpsnpto: + bioportal: + name: Dementia-Related Psychotic Symptoms Non-Pharmacological Treatment Ontology + prefix: DRPSNPTO + subjects: + - Taxonomic Classification + - Health + - Vocabularies + uri_format: http://www.semanticweb.org/zhenyuzhang/ontologies/2020/DRPSNPTO$1 +bioportal.dseo: + bioportal: + name: Data Science Education Ontology + prefix: DSEO + subjects: + - Biomedical Resources + - Other + uri_format: http://bigdatau.org/dseo#$1 +bioportal.dto: + bioportal: + name: Drug Target Ontology + prefix: DTO + subjects: + - Molecule + - Other + - Human + - Chemical + - Protein + - Gene Product + uri_format: http://www.drugtargetontology.org/dto/DTO_$1 +bioportal.duo: + bioportal: + name: The Data Use Ontology + prefix: DUO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/DUO_$1 +bioportal.e-ppo: + bioportal: + name: Enhanced Personal Profile Ontology + prefix: E-PPO + subjects: + - Human + uri_format: http://www.semanticweb.org/patienceusip/ontologies/2020/7/untitled-ontology-7#$1 +bioportal.ebp: + bioportal: + name: EmpowerBP + prefix: EBP + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/tswheeler/ontologies/2016/3/EmpowerBP#$1 +bioportal.ecao: + bioportal: + name: The Echinoderm Anatomy and Development Ontology + prefix: ECAO + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/ECAO_$1 +bioportal.ecg: + bioportal: + name: Electrocardiography Ontology + prefix: ECG + subjects: + - Biomedical Resources + uri_format: http://www.cvrgrid.org/files/ECGOntologyv1.owl#$1 +bioportal.eco: + bioportal: + name: Evidence and Conclusion Ontology + prefix: ECO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/ECO_$1 +bioportal.ecocore: + bioportal: + name: An ontology of core ecological entities + prefix: ECOCORE + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.ecp: + bioportal: + name: Electronic Care Plan + prefix: ECP + subjects: + - Taxonomic Classification + - Health + - Vocabularies + uri_format: http://iris.med.duth.gr/research/ecp/ontology/eCP.owl#$1 +bioportal.ecso: + bioportal: + name: The Ecosystem Ontology + prefix: ECSO + subjects: + - Other + uri_format: http://purl.dataone.org/odo/ECSO_$1 +bioportal.ecto: + bioportal: + name: Environmental conditions, treatments and exposures ontology + prefix: ECTO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/ECTO_$1 +bioportal.edam: + bioportal: + name: EDAM - Bioscientific data analysis ontology + prefix: EDAM + subjects: + - All Organisms + - Biomedical Resources + - Genomic and Proteomic + - Other + - Vocabularies + uri_format: http://edamontology.org/data_$1 +bioportal.edam-bioimaging: + bioportal: + name: EDAM Bioimaging Ontology + prefix: EDAM-BIOIMAGING + subjects: + - Imaging + - All Organisms + - Other + uri_format: http://edamontology.org/topic_$1 +bioportal.edda: + bioportal: + name: EDDA Study Designs Taxonomy + prefix: EDDA + subjects: + - Experimental Conditions + - Vocabularies + uri_format: http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1 +bioportal.edda_pt: + bioportal: + name: EDDA Publication Types Taxonomy + prefix: EDDA_PT + subjects: + - Experimental Conditions + - Vocabularies + uri_format: http://ontologies.dbmi.pitt.edu/edda/PublicationType.owl#$1 +bioportal.efo: + bioportal: + name: Experimental Factor Ontology + prefix: EFO + subjects: + - Experimental Conditions + - Biological Process + uri_format: http://www.ebi.ac.uk/efo/EFO_$1 +bioportal.ego: + bioportal: + name: Epigenome Ontology + prefix: EGO + subjects: + - Molecule + - Health + - Genomic and Proteomic + uri_format: http://purl.obolibrary.org/obo/EGO_$1 +bioportal.ehda: + bioportal: + name: Human Developmental Anatomy Ontology, timed version + prefix: EHDA + subjects: + - Gross Anatomy + - Human Developmental Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/EHDA_$1 +bioportal.ehdaa: + bioportal: + name: Human Developmental Anatomy Ontology, abstract version 1 + prefix: EHDAA + subjects: + - Gross Anatomy + - Human Developmental Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 +bioportal.eld: + bioportal: + name: EthiopianListOfDiseases + prefix: ELD + subjects: + - Vocabularies + uri_format: https://github.com/VODANA$1 +bioportal.elig: + bioportal: + name: Eligibility Feature Hierarchy + prefix: ELIG + subjects: [] + uri_format: http://www.semanticweb.org/ontologies/2012/8/Ontology1348158066194.owl#$1 +bioportal.elter_cl: + bioportal: + name: eLTER Controlled Lists + prefix: ELTER_CL + subjects: + - Other + uri_format: http://vocabs.lter-europe.net/eLTER_/CL$1 +bioportal.emap: + bioportal: + name: Mouse Gross Anatomy and Development Ontology + prefix: EMAP + subjects: + - Mouse Anatomy + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/EMAP_$1 +bioportal.emapa: + bioportal: + name: Mouse gross anatomy and development, timed + prefix: EMAPA + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/EMAPA_$1 +bioportal.emif-ad: + bioportal: + name: EMIF-AD ontology + prefix: EMIF-AD + subjects: + - Health + - Neurologic Disease + uri_format: http://www.semanticweb.org/emif/ontologies/2015/AD$1 +bioportal.emo: + bioportal: + name: Enzyme Mechanism Ontology + prefix: EMO + subjects: + - Protein + uri_format: http://www.semanticweb.org/ontologies/2011/1/14/EMO.owl/EMO_$1 +bioportal.enm: + bioportal: + name: eNanoMapper + prefix: ENM + subjects: + - Health + - Chemical + uri_format: http://purl.enanomapper.org/onto/ENM_$1 +bioportal.entity: + bioportal: + name: ISO-15926-2_2003_entityMembership + prefix: ENTITY + subjects: + - Other + uri_format: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003#$1 +bioportal.envo: + bioportal: + name: Environment Ontology + prefix: ENVO + subjects: + - Experimental Conditions + - Other + - Physicochemical + uri_format: http://purl.obolibrary.org/obo/ENVO_$1 +bioportal.envs_variables: + bioportal: + name: ENVS variables + prefix: ENVS_VARIABLES + subjects: [] + uri_format: http://purl.org/m4m-dk-2/variables$1 +bioportal.envthes: + bioportal: + name: Thesaurus for long-term ecological research, monitoring, experiments + prefix: ENVTHES + subjects: + - Other + uri_format: http://vocabs.lter-europe.net/EnvThes$1 +bioportal.eo: + bioportal: + name: Ethnicity Ontoloy + prefix: EO + subjects: + - Other + uri_format: http://www.semanticweb.org/ethnicityOntology#$1 +bioportal.eo1: + bioportal: + name: Example Ontology + prefix: EO1 + subjects: [] + uri_format: http://www.fairdatacollective.com/template-vocabulary$1 +bioportal.eol: + bioportal: + name: Environment Ontology for Livestock + prefix: EOL + subjects: [] + uri_format: http://purl.org/obo/owlEOL_$1 +bioportal.ep: + bioportal: + name: Cardiac Electrophysiology Ontology + prefix: EP + subjects: + - Experimental Conditions + uri_format: http://www.cvrgrid.org/ontologies/Electrophysiology#$1 +bioportal.epie: + bioportal: + name: Epigenetic Entity + prefix: EPIE + subjects: + - Other + uri_format: https://pat.nichd.nih.gov/patepigeneticentity$1 +bioportal.epilont: + bioportal: + name: Epilepsy Ontology + prefix: EPILONT + subjects: + - Health + - Biomedical Resources + - Neurologic Disease + - Neurological Disorder + - Human + - Development + - Vocabularies + uri_format: http://www.semanticweb.org/ontologies/2009/3/EpilepsyOntology.owl#$1 +bioportal.epio: + bioportal: + name: EpilepsyOntology + prefix: EPIO + subjects: + - Neurological Disorder + uri_format: http://purl.obolibrary.org/obo/DOID_$1 +bioportal.epip: + bioportal: + name: Epigenetic Process + prefix: EPIP + subjects: + - Biological Process + uri_format: https://pat.nichd.nih.gov/patepigeneticprocess$1 +bioportal.episem: + bioportal: + name: Epilepsy Semiology + prefix: EPISEM + subjects: + - Neurological Disorder + uri_format: http://www.semanticweb.org/danielhier/ontologies/2019/3/untitled-ontology-57$1 +bioportal.epo: + bioportal: + name: Early Pregnancy Ontology + prefix: EPO + subjects: + - Imaging + uri_format: http://www.semanticweb.org/ontologies/epo.owl#$1 +bioportal.epso: + bioportal: + name: Epilepsy and Seizure Ontology + prefix: EPSO + subjects: + - Neurologic Disease + - Neurological Disorder + uri_format: http://www.case.edu/EpilepsyOntology.owl#$1 +bioportal.ero: + bioportal: + name: Eagle-I Research Resource Ontology + prefix: ERO + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/ERO_$1 +bioportal.esfo: + bioportal: + name: Enzyme Structure Function Ontology + prefix: ESFO + subjects: + - Protein + uri_format: http://www.semanticweb.org/shoshana/ontologies/2014/8/untitled-ontology-8#$1 +bioportal.esso: + bioportal: + name: Epilepsy Syndrome Seizure Ontology + prefix: ESSO + subjects: + - Neurologic Disease + uri_format: http://www.semanticweb.org/rjyy/ontologies/2015/5/ESSO#$1 +bioportal.etanc: + bioportal: + name: ETHIOPIANC + prefix: ETANC + subjects: + - Vocabularies + uri_format: https://github.com/VODANA/Controlled-vocabulary/ethanc$1 +bioportal.ethanc: + bioportal: + name: ETHANC + prefix: ETHANC + subjects: + - Vocabularies + uri_format: https://github.com/VODANA/Controlled-vocabulary/ethanc$1 +bioportal.ethopd: + bioportal: + name: Ethiopian OPD + prefix: ETHOPD + subjects: + - Vocabularies + uri_format: https://github.com/VODANA/Controlled-vocabulary/ethanc$1 +bioportal.eupath: + bioportal: + name: VEuPathDB Ontology + prefix: EUPATH + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 +bioportal.evi: + bioportal: + name: Evidence Graph Ontology + prefix: EVI + subjects: + - Experimental Conditions + - Biomedical Resources + - Biological Process + - Other + uri_format: https://w3id.org/EVI#$1 +bioportal.exact: + bioportal: + name: An ontology for experimental actions + prefix: EXACT + subjects: [] + uri_format: http://www.owl-ontologies.com/Ontology1184060740.owl#$1 +bioportal.exmo: + bioportal: + name: Exercise Medicine Ontology + prefix: EXMO + subjects: + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/exm.owl/EXM_$1 +bioportal.exo: + bioportal: + name: Exposure Ontology + prefix: EXO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/ExO_$1 +bioportal.exon: + bioportal: + name: Experimental Ontology + prefix: EXON + subjects: [] + uri_format: urn:absolute:Experiment01#$1 +bioportal.extract: + bioportal: + name: EXTeRnAl Conditions Taxonomy (EXTRACT) + prefix: EXTRACT + subjects: [] + uri_format: http://purl.org/extract$1 +bioportal.faldo: + bioportal: + name: 'Feature Annotation Location Description Ontology ' + prefix: FALDO + subjects: + - Other + - Protein + - Vocabularies + uri_format: http://biohackathon.org/resource/faldo#$1 +bioportal.fall: + bioportal: + name: MyOntoServiceFull_FallDetection + prefix: FALL + subjects: [] + uri_format: http://www.semanticweb.org/abed/ontologies/2015/2/untitled-ontology-346#$1 +bioportal.fao: + bioportal: + name: Fungal Gross Anatomy Ontology + prefix: FAO + subjects: + - Gross Anatomy + - Anatomy + - Microbial Anatomy + uri_format: http://purl.obolibrary.org/obo/FAO_$1 +bioportal.fast-event: + bioportal: + name: FAST (Faceted Application of Subject Terminology) Event + prefix: FAST-EVENT + subjects: [] + uri_format: http://schema.org$1 +bioportal.fast-event-skos: + bioportal: + name: FAST (Faceted Application of Subject Terminology) Event Facet + prefix: FAST-EVENT-SKOS + subjects: [] + uri_format: http://data.bnf.fr/ark:/12148$1 +bioportal.fast-formgenre: + bioportal: + name: FAST (Faceted Application of Subject Terminology) FormGenre facet + prefix: FAST-FORMGENRE + subjects: [] + uri_format: http://id.loc.gov/authorities/subjects$1 +bioportal.fast-genreform: + bioportal: + name: FAST (Faceted Access of Subject Terminology) GenreForm + prefix: FAST-GENREFORM + subjects: + - Other + uri_format: http://id.loc.gov/authorities/subjects$1 +bioportal.fast-title: + bioportal: + name: FAST (Faceted Application of Subject Terminology) Title Facet + prefix: FAST-TITLE + subjects: [] + uri_format: http://data.bnf.fr/ark:/12148$1 +bioportal.fb-bt: + bioportal: + name: Drosophila Gross Anatomy Ontology + prefix: FB-BT + subjects: + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/FBbt_$1 +bioportal.fb-cv: + bioportal: + name: FlyBase Controlled Vocabulary + prefix: FB-CV + subjects: + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/FBcv_$1 +bioportal.fb-dv: + bioportal: + name: Drosophila Development Ontology + prefix: FB-DV + subjects: + - Development + - Animal Development + uri_format: http://purl.obolibrary.org/obo/FBdv_$1 +bioportal.fb-sp: + bioportal: + name: Fly Taxonomy + prefix: FB-SP + subjects: + - Taxonomic Classification + uri_format: http://purl.obolibrary.org/obo/FBsp_$1 +bioportal.fbbi: + bioportal: + name: Biological Imaging Methods Ontology + prefix: FBbi + subjects: + - Imaging + - Experimental Conditions + uri_format: http://purl.obolibrary.org/obo/FBbi_$1 +bioportal.fcc1: + bioportal: + name: Fernald Community Cohort N + prefix: FCC1 + subjects: + - Health + uri_format: http://www.semanticweb.org/diwaleva/ontologies/2019/9/fcc-ontology#$1 +bioportal.fdc-gdmt: + bioportal: + name: Ontology for Generic Dataset Metadata Template + prefix: FDC-GDMT + subjects: + - Vocabularies + uri_format: http://vocab.fairdatacollective.org/gdmt$1 +bioportal.fdsajfahsjk: + bioportal: + name: OWL_XML_Tool5 + prefix: FDSAJFAHSJK + subjects: [] + uri_format: http://example.com/owl/families/import/familyImport17$1 +bioportal.fdt-o: + bioportal: + name: FAIR Data Train Ontology + prefix: FDT-O + subjects: + - Vocabularies + uri_format: https://w3id.org/fdp/fdt-o#$1 +bioportal.fenics: + bioportal: + name: Functional Epilepsy Nomenclature for Ion Channels + prefix: FENICS + subjects: + - Biological Process + - Neurological Disorder + - Protein + - Gene Product + uri_format: http://webprotege.stanford.edu$1 +bioportal.fg: + bioportal: + name: FAIR Genomes + prefix: FG + subjects: + - Health + - Biomedical Resources + - Genomic and Proteomic + - Human + uri_format: https://w3id.org/fair-genomes/ontology$1 +bioportal.fgnhns: + bioportal: + name: FoodGroupNHNS + prefix: FGNHNS + subjects: [] + uri_format: http://purl.obolibrary.org/obo/NIBIOHN_$1 +bioportal.fhho: + bioportal: + name: Family Health History Ontology + prefix: FHHO + subjects: + - Health + uri_format: http://www.owl-ontologies.com/Ontology1172270693.owl#$1 +bioportal.fideo: + bioportal: + name: Food Interactions with Drugs Evidence Ontology + prefix: FIDEO + subjects: + - Human + uri_format: http://purl.obolibrary.org/obo/FIDEO_$1 +bioportal.fire: + bioportal: + name: Fire Ontology + prefix: FIRE + subjects: [] + uri_format: http://cerrado.linkeddata.es/ecology/fire#$1 +bioportal.fish-ast: + bioportal: + name: FISH Archaeological Sciences Thesaurus + prefix: FISH-AST + subjects: [] + uri_format: http://purl.org/heritagedata/schemes/560/concepts$1 +bioportal.fisho: + bioportal: + name: Fish Ontology + prefix: FISHO + subjects: + - Fish Anatomy + uri_format: http://bioportal.bioontology.org/ontologies/FISHO#$1 +bioportal.fix: + bioportal: + name: Physico-Chemical Methods and Properties + prefix: FIX + subjects: [] + uri_format: http://purl.obolibrary.org/obo/FIX_$1 +bioportal.flopo: + bioportal: + name: Flora Phenotype Ontology + prefix: FLOPO + subjects: + - Phenotype + - Plant + uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 +bioportal.flu: + bioportal: + name: Influenza Ontology + prefix: FLU + subjects: [] + uri_format: http://purl.obolibrary.org/obo/FLU_$1 +bioportal.flyglycodb: + bioportal: + name: FlyGlycoDB + prefix: FLYGLYCODB + subjects: + - Gene Product + uri_format: http://www.flyglycodb.org/ontologies/2015$1 +bioportal.fmpm: + bioportal: + name: Food Matrix for Predictive Microbiology + prefix: FMPM + subjects: + - Biomedical Resources + - Vocabularies + uri_format: urn:absolute:FMPM#$1 +bioportal.fo: + bioportal: + name: Fern Ontology + prefix: FO + subjects: + - Plant Anatomy + uri_format: http://purl.jp/bio/01/fo#$1 +bioportal.foaf: + bioportal: + name: Friend of a Friend Vocabulary + prefix: FOAF + subjects: + - Other + uri_format: http://xmlns.com/foaf/0.1$1 +bioportal.fobi: + bioportal: + name: FOBI (Food-Biomarker Ontology) + prefix: FOBI + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/FOBI_$1 +bioportal.foodon: + bioportal: + name: The FoodOn Food Ontology + prefix: FOODON + subjects: + - All Organisms + - Health + - Biomedical Resources + - Plant + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/FOODON_$1 +bioportal.fovt: + bioportal: + name: FuTRES Ontology of Vertebrate Traits + prefix: FOVT + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/FOVT_$1 +bioportal.fplx: + bioportal: + name: FamPlex + prefix: FPLX + subjects: + - Protein + uri_format: http://purl.obolibrary.org/obo/FPLX_$1 +bioportal.frmo: + bioportal: + name: 'Fall Risk Management Ontology ' + prefix: FRMO + subjects: + - Other + uri_format: http://www.semanticweb.org/ftuha/ontologies/2021/5/FRMO-01untitled-ontology-175$1 +bioportal.ftc: + bioportal: + name: Functional Therapeutic Chemical Classification System + prefix: FTC + subjects: + - Chemical + uri_format: http://www.ebi.ac.uk/chembl/ftc/FTC_$1 +bioportal.fypo: + bioportal: + name: Fission Yeast Phenotype Ontology + prefix: FYPO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/FYPO_$1 +bioportal.g-prov: + bioportal: + name: Guideline Provenance + prefix: G-PROV + subjects: [] + uri_format: http://www.w3.org/ns/prov#$1 +bioportal.galen: + bioportal: + name: Galen Ontology + prefix: GALEN + subjects: + - Other + uri_format: http://www.co-ode.org/ontologies/galen#$1 +bioportal.gaz: + bioportal: + name: Gazetteer + prefix: GAZ + subjects: [] + uri_format: http://purl.obolibrary.org/obo/GAZ_$1 +bioportal.gbm: + bioportal: + name: Glioblastoma + prefix: GBM + subjects: + - Health + - Anatomy + - Human + uri_format: http://www.semanticweb.org/ontologies/2010/10/BPO.owl#$1 +bioportal.gbol: + bioportal: + name: GBOL + prefix: GBOL + subjects: + - All Organisms + uri_format: http://gbol.life/0.1$1 +bioportal.gco: + bioportal: + name: Genome Component Ontology + prefix: GCO + subjects: + - Biomedical Resources + - Genomic and Proteomic + uri_format: http://rdf.biosemantics.org/ontologies/genomecomponents#$1 +bioportal.gdco: + bioportal: + name: Data Collection Ontology + prefix: GDCO + subjects: + - Development + uri_format: http://purl.org/dco/v1#$1 +bioportal.gecko: + bioportal: + name: Genomics Cohorts Knowledge Ontology + prefix: GECKO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/GECKO_$1 +bioportal.gene-cds: + bioportal: + name: Genomic Clinical Decision Support Ontology + prefix: GENE-CDS + subjects: + - Health + - Genomic and Proteomic + - Human + uri_format: http://www.genomic-cds.org/ont/genomic-cds.owl#$1 +bioportal.geno: + bioportal: + name: Genotype Ontology + prefix: GENO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/GENO_$1 +bioportal.geo: + bioportal: + name: Geographical Entity Ontology + prefix: GEO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/GEO_$1 +bioportal.geosparql: + bioportal: + name: GeoSPARQL + prefix: GEOSPARQL + subjects: + - Other + uri_format: http://www.opengis.net/ont/geosparql#$1 +bioportal.geospecies: + bioportal: + name: GeoSpecies Ontology + prefix: GEOSPECIES + subjects: + - Other + uri_format: http://rdf.geospecies.org/ont/geospecies#$1 +bioportal.gexo: + bioportal: + name: Gene Expression Ontology + prefix: GEXO + subjects: + - Biological Process + uri_format: http://identifiers.org/intact$1 +bioportal.gffo: + bioportal: + name: Genetic Feature Format Ontology + prefix: GFFO + subjects: + - Genomic and Proteomic + - Protein + - Gene Product + - Vocabularies + uri_format: https://raw.githubusercontent.com/mpievolbio-scicomp/GenomeFeatureFormatOntology/main/gffo#$1 +bioportal.gfo: + bioportal: + name: General Formal Ontology + prefix: GFO + subjects: + - All Organisms + - Upper Level Ontology + uri_format: http://www.onto-med.de/ontologies/gfo.owl#$1 +bioportal.gfo-bio: + bioportal: + name: General Formal Ontology for Biology + prefix: GFO-BIO + subjects: + - Mouse Anatomy + - All Organisms + - 'Cellular anatomy ' + - Molecule + - Gross Anatomy + - Biological Process + - Subcellular + - Phenotype + - Human Developmental Anatomy + - Plant Anatomy + - Anatomy + - Plant + - Human + - Subcellular anatomy + - Chemical + - Cell + - Development + - Protein + - Animal Gross Anatomy + - Gene Product + - Plant Development + - Animal Development + uri_format: http://onto.eva.mpg.de/ontologies/gfo-bio.owl#$1 +bioportal.gfvo: + bioportal: + name: Genomic Feature and Variation Ontology + prefix: GFVO + subjects: + - Biomedical Resources + - Genomic and Proteomic + - Biological Process + - Human + - Gene Product + uri_format: https://www.codamono.com/biointerchange/gfvo#$1 +bioportal.glyco: + bioportal: + name: Glycomics Ontology + prefix: GLYCO + subjects: + - Molecule + - Biomedical Resources + - Other + - Chemical + - Protein + uri_format: http://glycomics.ccrc.uga.edu/ontologies/GlycO#$1 +bioportal.glycocoo: + bioportal: + name: GlycoConjugate Ontology + prefix: GLYCOCOO + subjects: + - Other + uri_format: http://purl.jp/bio/12/glyco/glycan#$1 +bioportal.glycordf: + bioportal: + name: GlycoRDF + prefix: GLYCORDF + subjects: [] + uri_format: http://purl.jp/bio/12/glyco/glycan#$1 +bioportal.gml: + bioportal: + name: Ontology for Geography Markup Language (GML3.0) + prefix: GML + subjects: + - Other + uri_format: http://loki.cae.drexel.edu/~wbs/ontology/2004/09/ogc-gml#$1 +bioportal.gmm: + bioportal: + name: GoMapMan + prefix: GMM + subjects: + - Biological Process + - Arabidopsis + - Plant + uri_format: http://purl.obolibrary.org/obo/GMM_$1 +bioportal.gmo: + bioportal: + name: Growth Medium Ontology + prefix: GMO + subjects: + - Other + uri_format: http://purl.jp/bio/10/gmo/GMO_$1 +bioportal.gno: + bioportal: + name: Glycan Naming Ontology + prefix: GNO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/GNO_$1 +bioportal.go: + bioportal: + name: Gene Ontology + prefix: GO + subjects: + - Genomic and Proteomic + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.go-ext: + bioportal: + name: Gene Ontology Extension + prefix: GO-EXT + subjects: [] + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.gpml: + bioportal: + name: Graphical Pathway Markup Language + prefix: GPML + subjects: + - Biological Process + - Vocabularies + uri_format: http://vocabularies.wikipathways.org/gpml#$1 +bioportal.gro: + bioportal: + name: Gene Regulation Ontology + prefix: GRO + subjects: + - Genomic and Proteomic + uri_format: http://www.bootstrep.eu/ontology/GRO#$1 +bioportal.gro-cpd: + bioportal: + name: Cereal Plant Development Ontology + prefix: GRO-CPD + subjects: + - Plant + - Development + - Plant Development + uri_format: http://purl.obolibrary.org/obo/GRO_$1 +bioportal.gro-cpga: + bioportal: + name: Cereal Plant Gross Anatomy Ontology + prefix: GRO-CPGA + subjects: [] + uri_format: http://purl.obolibrary.org/obo/PO_$1 +bioportal.gsso: + bioportal: + name: Gender, Sex, and Sexual Orientation Ontology + prefix: GSSO + subjects: + - Other + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/GSSO_$1 +bioportal.gvo: + bioportal: + name: Genome Variation Ontology + prefix: GVO + subjects: + - Genomic and Proteomic + uri_format: http://genome-variation.org/resource/gvo#$1 +bioportal.haauraado: + bioportal: + name: Halocynthia aurantium Anatomy and Development Ontology + prefix: HAAURAADO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/HaauraA_$1 +bioportal.hamidehsgh: + bioportal: + name: Inherited Retinal Dystrophy + prefix: HAMIDEHSGH + subjects: + - Human + uri_format: http://www.semanticweb.org/hamide/ontologies/2019/3/IRD_$1 +bioportal.hancestro: + bioportal: + name: Human Ancestry Ontology + prefix: HANCESTRO + subjects: + - Experimental Conditions + - Human + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/HANCESTRO_$1 +bioportal.hao: + bioportal: + name: Hymenoptera Anatomy Ontology + prefix: HAO + subjects: + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/HAO_$1 +bioportal.haroreado: + bioportal: + name: Halocynthia roretzi Anatomy and Development Ontology + prefix: HAROREADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/HaroreA_$1 +bioportal.hasco: + bioportal: + name: Human-Aware Science Ontology + prefix: HASCO + subjects: + - Upper Level Ontology + uri_format: http://hadatac.org/ont/hasco$1 +bioportal.hcdr: + bioportal: + name: Homelessness and Clinical Data Recording + prefix: HCDR + subjects: + - Other + uri_format: http://www.semanticweb.org/m14067/ontologies/2020/0/untitled-ontology-5#$1 +bioportal.hcodonont: + bioportal: + name: HGeneCodonOntology + prefix: HCODONONT + subjects: + - Biomedical Resources + uri_format: http://bioportal/bioontology.org/ontologies/HIVO0004#$1 +bioportal.hcpcs: + bioportal: + name: Healthcare Common Procedure Coding System + prefix: HCPCS + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/HCPCS$1 +bioportal.hdmponto: + bioportal: + name: HierarchicalDMProcessOnto + prefix: HDMPONTO + subjects: + - Taxonomic Classification + uri_format: http://www.semanticweb.org/mantx/ontologies/Process.owl#$1 +bioportal.hecon: + bioportal: + name: 'HECON: Health Condition Evolution Ontology' + prefix: HECON + subjects: + - Health + - Other + uri_format: http://kmi.open.ac.uk/conrad/HECON#$1 +bioportal.heio: + bioportal: + name: Regional Healthcare System Interoperability and Information Exchange Measurement Ontology + prefix: HEIO + subjects: + - Other + uri_format: http://whistl.uwaterloo.ca/heio.owl#$1 +bioportal.hfo: + bioportal: + name: Heart Failure Ontology + prefix: HFO + subjects: + - Ethology + - Health + - Phenotype + - Human + - Vocabularies + uri_format: http://bmi.utah.edu/ontologies/hfontology$1 +bioportal.hgnc: + bioportal: + name: HUGO Gene Nomenclature + prefix: HGNC + subjects: + - Health + uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Hugo.owl#$1 +bioportal.hgnc-nr: + bioportal: + name: HGNC New Releases Ontology + prefix: HGNC-NR + subjects: + - Genomic and Proteomic + uri_format: http://identifiers.org/hgnc$1 +bioportal.hhear: + bioportal: + name: Human Health Exposure Analysis Resource + prefix: HHEAR + subjects: + - Health + uri_format: http://purl.org/twc/HHEAR_$1 +bioportal.hino: + bioportal: + name: Human Interaction Network Ontology + prefix: HINO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/HINO_$1 +bioportal.hivcrs: + bioportal: + name: HIVCompoundRels + prefix: HIVCRS + subjects: [] + uri_format: http://www.semanticweb.org/hanfei/ontologies/2017/2/untitled-ontology-287#$1 +bioportal.hivmt: + bioportal: + name: HIVMutation + prefix: HIVMT + subjects: + - Biomedical Resources + uri_format: http://bioportal/bioontology.org/ontologies/HIVO0004#$1 +bioportal.hivo004: + bioportal: + name: HIVOntologymain.owl + prefix: HIVO004 + subjects: + - Immunology + - Taxonomic Classification + - Molecule + - Health + - Dysfunction + - Biomedical Resources + - Biological Process + - Subcellular + - Protein + uri_format: http://bioportal/bioontology.org/ontologies/HIVO0004#$1 +bioportal.hl7: + bioportal: + name: Health Level Seven Reference Implementation Model, Version 3 + prefix: HL7 + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/HL7$1 +bioportal.hmislab0115: + bioportal: + name: HMIS LAB 011 5 + prefix: HMISLAB0115 + subjects: [] + uri_format: http://www.fairdatacollective.com/template-vocabulary$1 +bioportal.hns: + bioportal: + name: HNS_Ontolgoy + prefix: HNS + subjects: + - Health + - Neurologic Disease + - Human + uri_format: http://www.humannervousystem.org/KAnOE/2014/dave86#$1 +bioportal.ho: + bioportal: + name: Histological Ontology + prefix: HO + subjects: + - Biomedical Resources + uri_format: http://www.univalle.edu.co/ontologies/organ#$1 +bioportal.hoip: + bioportal: + name: Homeostasis imbalance process ontology + prefix: HOIP + subjects: + - Dysfunction + - Biological Process + uri_format: http://purl.bioontology.org/ontology/HOIP/HOIP_$1 +bioportal.hom: + bioportal: + name: Ontology of Homology and Related Concepts in Biology + prefix: HOM + subjects: + - All Organisms + - Molecule + - Other + - Anatomy + - Development + uri_format: http://purl.obolibrary.org/obo/HOM_$1 +bioportal.home: + bioportal: + name: Health Ontology for Minority Equity + prefix: HOME + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/navyarenjith/ontologies/2021/3/untitled-ontology-5#$1 +bioportal.hoom: + bioportal: + name: HPO - ORDO Ontological Module + prefix: HOOM + subjects: + - Health + - Biomedical Resources + - Phenotype + - Human + uri_format: http://www.semanticweb.org/ontology/HOOM#$1 +bioportal.hord: + bioportal: + name: Holistic Ontology of Rare Diseases + prefix: HORD + subjects: + - Health + uri_format: https://cdn.rawgit.com/laiasubirats/rarediseasesontology/master/ICD10_1.0.owl#$1 +bioportal.hp: + bioportal: + name: Human Phenotype Ontology + prefix: HP + subjects: + - Health + - Phenotype + - Human + uri_format: http://purl.obolibrary.org/obo/HP_$1 +bioportal.hp_o: + bioportal: + name: Hypersensitivity pneumonitis ontology + prefix: HP_O + subjects: + - Other + uri_format: http://www.semanticweb.org/dellvostro3750/ontologies/2018/2/untitled-ontology-10#$1 +bioportal.hpio: + bioportal: + name: Host Pathogen Interactions Ontology + prefix: HPIO + subjects: + - Health + uri_format: http://www.semanticweb.org/ontologies/2010/5/22/Ontology1277229984000.owl#$1 +bioportal.hrdo: + bioportal: + name: Disease core ontology applied to Rare Diseases + prefix: HRDO + subjects: + - Health + - Human + uri_format: http://www.limics.org/hrdo/rdfns#$1 +bioportal.hsapdv: + bioportal: + name: Human Developmental Stages Ontology + prefix: HSAPDV + subjects: [] + uri_format: http://purl.obolibrary.org/obo/HsapDv_$1 +bioportal.hso: + bioportal: + name: Health Surveillance Ontology + prefix: HSO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/HSO_$1 +bioportal.htn: + bioportal: + name: Hypertension Ontology + prefix: HTN + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/HTN_$1 +bioportal.hto: + bioportal: + name: Horridge Test Ontology + prefix: HTO + subjects: [] + uri_format: http://protege.stanford.edu/ontologies/hto/846c3f2b_$1 +bioportal.hupson: + bioportal: + name: Human Physiology Simulation Ontology + prefix: HUPSON + subjects: + - Health + uri_format: http://scai.fraunhofer.de/HuPSON#$1 +bioportal.i-adopt: + bioportal: + name: I-ADOPT Framework Ontology + prefix: I-ADOPT + subjects: + - Other + uri_format: https://w3id.org/iadopt/ont$1 +bioportal.i2sv: + bioportal: + name: Integration and Implementation Sciences Vocabulary + prefix: I2SV + subjects: + - Other + - Vocabularies + uri_format: https://i2insights.org/index/integration-and-implementation-sciences-vocabulary#$1 +bioportal.iaml-mop: + bioportal: + name: IAML Medium of Performance Vocabulary + prefix: IAML-MOP + subjects: + - Other + uri_format: http://data.doremus.org/vocabulary/iaml/mop$1 +bioportal.iao: + bioportal: + name: Information Artifact Ontology + prefix: IAO + subjects: + - Imaging + - Biomedical Resources + - Other + uri_format: http://purl.obolibrary.org/obo/IAO_$1 +bioportal.ibd: + bioportal: + name: Indian Biodiversity Ontology + prefix: IBD + subjects: [] + uri_format: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1 +bioportal.ibio: + bioportal: + name: IndianBiodiversity + prefix: IBIO + subjects: [] + uri_format: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1 +bioportal.ibo: + bioportal: + name: Imaging Biomarker Ontology + prefix: IBO + subjects: + - Imaging + - Health + - Biological Process + - Phenotype + - Human + uri_format: http://www.semanticweb.org/eamdouni/ontologies/2015/5/IBO#$1 +bioportal.icd10: + bioportal: + name: International Classification of Diseases, Version 10 + prefix: ICD10 + subjects: [] + uri_format: http://purl.bioontology.org/ontology/ICD10$1 +bioportal.icd10cm: + bioportal: + name: International Classification of Diseases, Version 10 - Clinical Modification + prefix: ICD10CM + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/ICD10CM$1 +bioportal.icd10pcs: + bioportal: + name: International Classification of Diseases, Version 10 - Procedure Coding System + prefix: ICD10PCS + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/ICD10PCS$1 +bioportal.icd11-bodysystem: + bioportal: + name: Body System Terms from ICD11 + prefix: ICD11-BODYSYSTEM + subjects: + - Anatomy + uri_format: http://who.int/bodysystem.owl#$1 +bioportal.icd9cm: + bioportal: + name: International Classification of Diseases, Version 9 - Clinical Modification + prefix: ICD9CM + subjects: [] + uri_format: http://purl.bioontology.org/ontology/ICD9CM$1 +bioportal.icdo: + bioportal: + name: International Classification of Diseases Ontology + prefix: ICDO + subjects: + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/ICDO_$1 +bioportal.iceci: + bioportal: + name: International Classification of External Causes of Injuries + prefix: ICECI + subjects: [] + uri_format: http://who.int/iceci#$1 +bioportal.iceo: + bioportal: + name: Integrative and Conjugative Element Ontology + prefix: ICEO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/ICEO_$1 +bioportal.icf: + bioportal: + name: International Classification of Functioning, Disability and Health + prefix: ICF + subjects: + - Health + - Human + - Vocabularies + uri_format: http://who.int/icf#$1 +bioportal.icnp: + bioportal: + name: International Classification for Nursing Practice + prefix: ICNP + subjects: + - Taxonomic Classification + uri_format: http://www.icn.ch/icnp#$1 +bioportal.ico: + bioportal: + name: Informed Consent Ontology + prefix: ICO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/ICO_$1 +bioportal.icpc2p: + bioportal: + name: International Classification of Primary Care - 2 PLUS + prefix: ICPC2P + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/ICPC2P$1 +bioportal.icps: + bioportal: + name: International Classification for Patient Safety + prefix: ICPS + subjects: + - Health + uri_format: http://www.ICPS/ontologies/ActionsToReduceRisk#$1 +bioportal.icw: + bioportal: + name: International Classification of Wellness + prefix: ICW + subjects: + - Taxonomic Classification + - Health + uri_format: http://webprotege.stanford.edu$1 +bioportal.id-amr: + bioportal: + name: Infectious Diseases and Antimicrobial Resistance + prefix: ID-AMR + subjects: + - Health + uri_format: http://purl.org/zonmw/id-amr$1 +bioportal.idem: + bioportal: + name: 'IDEM: wInD Energy Models Taxonomy' + prefix: IDEM + subjects: [] + uri_format: http://purl.org/idem$1 +bioportal.idg_gl: + bioportal: + name: IDG gene list + prefix: IDG_GL + subjects: + - Other + uri_format: http://druggablegenome.net$1 +bioportal.ido: + bioportal: + name: Infectious Disease Ontology + prefix: IDO + subjects: + - All Organisms + - Health + uri_format: http://purl.obolibrary.org/obo/IDO_$1 +bioportal.ido-covid-19: + bioportal: + name: The COVID-19 Infectious Disease Ontology + prefix: IDO-COVID-19 + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/IDO_$1 +bioportal.idobru: + bioportal: + name: Brucellosis Ontology + prefix: IDOBRU + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/IDO_$1 +bioportal.idoden: + bioportal: + name: Dengue Fever Ontology + prefix: IDODEN + subjects: + - Health + - Other + - Human + uri_format: http://purl.bioontology.org/ontology/IDODEN_$1 +bioportal.idomal: + bioportal: + name: Malaria Ontology + prefix: IDOMAL + subjects: [] + uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1 +bioportal.idqa: + bioportal: + name: Image and Data Quality Assessment Ontology + prefix: IDQA + subjects: + - Imaging + uri_format: http://purl.obolibrary.org/obo/ID_$1 +bioportal.ifar: + bioportal: + name: Fanconi Anemia Ontology + prefix: IFAR + subjects: + - Other + uri_format: http://www.semanticweb.org/ontologies/2012/11/abnormalities.owl#$1 +bioportal.illnessinjury: + bioportal: + name: Illness and Injury + prefix: ILLNESSINJURY + subjects: + - Taxonomic Classification + - Health + - Human + uri_format: http://www.owl-ontologies.com/unnamed.owl#$1 +bioportal.imgt-ontology: + bioportal: + name: Immunogenetics Ontology + prefix: IMGT-ONTOLOGY + subjects: + - Immunology + uri_format: http://www.imgt.org/download/IMGT-ONTOLOGY/IMGT-ONTOLOGY-v1-0-3.owl#$1 +bioportal.inbancido: + bioportal: + name: 'Assessment of Indian Economy During Covid-19 ' + prefix: INBANCIDO + subjects: [] + uri_format: http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#$1 +bioportal.inbiodiv: + bioportal: + name: An Ontology for Indian Biodiversity Knowledge Management + prefix: INBIODIV + subjects: [] + uri_format: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1 +bioportal.incentive: + bioportal: + name: INCENTIVE Community Controlled Vocabulary + prefix: INCENTIVE + subjects: [] + uri_format: http://purl.org/incentive$1 +bioportal.incentive-vars: + bioportal: + name: INCENTIVE Variables + prefix: INCENTIVE-VARS + subjects: [] + uri_format: http://purl.org/incentive$1 +bioportal.infrarisk: + bioportal: + name: InfraRisk Ontology + prefix: INFRARISK + subjects: + - Other + uri_format: https://www.infrarisk-fp7.eu/vocabs/#$1 +bioportal.ino: + bioportal: + name: Interaction Network Ontology + prefix: INO + subjects: + - All Organisms + - Biological Process + uri_format: http://purl.obolibrary.org/obo/INO_$1 +bioportal.insecth: + bioportal: + name: insectH + prefix: INSECTH + subjects: + - Anatomy + uri_format: http://neuromorpho.org/ontologies/insectH.owl#$1 +bioportal.insname: + bioportal: + name: VODANAINSNAMES + prefix: INSNAME + subjects: + - Other + uri_format: https://www.vodan-totafrica.info/vocs/institutions$1 +bioportal.into: + bioportal: + name: Indian Terrorism Ontology + prefix: INTO + subjects: [] + uri_format: http://www.semanticweb.org/Terrorism#$1 +bioportal.inverseroles: + bioportal: + name: ISO-15926-2_2003_inverseRoles + prefix: INVERSEROLES + subjects: + - Other + uri_format: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003#$1 +bioportal.iobc: + bioportal: + name: Interlinking Ontology for Biological Concepts + prefix: IOBC + subjects: [] + uri_format: http://purl.jp/bio/4/id$1 +bioportal.ird: + bioportal: + name: Inherited Retinal Dystrophies + prefix: IRD + subjects: [] + uri_format: http://www.semanticweb.org/msh/ontologies/2019/9/untitled-ontology-3#$1 +bioportal.irdg: + bioportal: + name: 'Data harmonization ontology for cross border malaria surveillance ' + prefix: IRDG + subjects: + - Health + uri_format: http://www.semanticweb.org/IRDGuyamazon#$1 +bioportal.iso-15926-2_2003: + bioportal: + name: ISO-15926-2_2003_oil + prefix: ISO-15926-2_2003 + subjects: + - Upper Level Ontology + uri_format: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003#$1 +bioportal.iso-annotations: + bioportal: + name: ISO-15926-2_2003_annotations + prefix: ISO-ANNOTATIONS + subjects: + - Other + uri_format: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003#$1 +bioportal.iso-food: + bioportal: + name: A formal representation of the knowledge within the domain of Isotopes for Food Science + prefix: ISO-FOOD + subjects: + - Chemical + uri_format: http://www.semanticweb.org/tome/ontologies/2018/3/ISO-FOOD#$1 +bioportal.iso19108to: + bioportal: + name: ISO 19108 Temporal Objects + prefix: ISO19108TO + subjects: + - Other + uri_format: http://def.isotc211.org/iso19108/2006/TemporalObjects#$1 +bioportal.iso19110: + bioportal: + name: ISO 19110 Methodology for Feature Cataloguing + prefix: ISO19110 + subjects: + - Other + uri_format: http://def.isotc211.org/iso19110/2005/MethodologyForFeatureCataloguing#$1 +bioportal.iso19115: + bioportal: + name: ISO 19115 + prefix: ISO19115 + subjects: + - Other + uri_format: http://loki.cae.drexel.edu/~wbs/ontology/2004/09/iso-19115#$1 +bioportal.iso19115cc: + bioportal: + name: ISO 19115 Common Classes + prefix: ISO19115CC + subjects: + - Other + uri_format: http://def.isotc211.org/iso19115/-1/2014/CommonClasses#$1 +bioportal.iso19115ci: + bioportal: + name: ISO 19115 Citation Information + prefix: ISO19115CI + subjects: + - Other + uri_format: http://def.isotc211.org/iso19115/-1/2014/CitationAndResponsiblePartyInformation#$1 +bioportal.iso19115con: + bioportal: + name: ISO 19115 Constraints Information + prefix: ISO19115CON + subjects: + - Other + uri_format: http://def.isotc211.org/iso19115/-1/2014/ConstraintInformation#$1 +bioportal.iso19115di: + bioportal: + name: ISO 19115 Distribution Information + prefix: ISO19115DI + subjects: + - Other + uri_format: http://def.isotc211.org/iso19115/-1/2014/DistributionInformation#$1 +bioportal.iso19115dtc: + bioportal: + name: ISO 19115 Date Type Code + prefix: ISO19115DTC + subjects: + - Other + uri_format: http://def.isotc211.org/iso19115/-1/2014/CitationAndResponsiblePartyInformation/code/CI_/DateTypeCode$1 +bioportal.iso19115ex: + bioportal: + name: ISO 19115 Extent Information + prefix: ISO19115EX + subjects: + - Other + uri_format: http://def.isotc211.org/iso19115/-1/2014/ExtentInformation#$1 +bioportal.iso19115id: + bioportal: + name: ISO 19115 Identification Information + prefix: ISO19115ID + subjects: + - Other + uri_format: http://def.isotc211.org/iso19115/2003/IdentificationInformation#$1 +bioportal.iso19115mi: + bioportal: + name: ISO 19115 Metadata Information + prefix: ISO19115MI + subjects: [] + uri_format: http://def.isotc211.org/iso19115/-1/2014/CitationAndResponsiblePartyInformation#$1 +bioportal.iso19115pr: + bioportal: + name: ISO 19115 Codelists + prefix: ISO19115PR + subjects: + - Other + uri_format: http://www.geosciml.org/vocabularies/iso-19115-codelists.owl#$1 +bioportal.iso19115roles: + bioportal: + name: ISO 19115 Role Codes + prefix: ISO19115ROLES + subjects: [] + uri_format: http://def.isotc211.org/iso19115/-1/2014/CitationAndResponsiblePartyInformation/code/CI_/RoleCode$1 +bioportal.iso19115srs: + bioportal: + name: ISO 19115 Reference Systems + prefix: ISO19115SRS + subjects: + - Other + uri_format: http://www.w3.org/2004/02/skos/core#$1 +bioportal.iso19115tcc: + bioportal: + name: ISO 19115 Topic Categories + prefix: ISO19115TCC + subjects: + - Other + uri_format: http://def.seegrid.csiro.au/isotc211/iso19115/2003/code/TopicCategory$1 +bioportal.iso639-2: + bioportal: + name: 'ISO 639-2: Codes for the Representation of Names of Languages' + prefix: ISO639-2 + subjects: + - Other + uri_format: http://www.fao.org/aims/aos/languagecode.owl#$1 +bioportal.issva: + bioportal: + name: International Society for the Study of Vascular Anomalies (ISSVA) Ontology + prefix: ISSVA + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/ISSVA/ISSVA_$1 +bioportal.itemas: + bioportal: + name: Medical Technology Innovation in healthcare centers + prefix: ITEMAS + subjects: + - Other + uri_format: http://www.semanticweb.org/avl/ontologies/2017/7/ITEMAS_v1.2#$1 +bioportal.ito: + bioportal: + name: Intelligence Task Ontology + prefix: ITO + subjects: + - Other + uri_format: https://identifiers.org/ito:ITO_$1 +bioportal.ixno: + bioportal: + name: Interaction Ontology + prefix: IXNO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.jerm: + bioportal: + name: Just Enough Results Model Ontology + prefix: JERM + subjects: + - Experimental Conditions + - Biomedical Resources + - Biological Process + - Other + uri_format: http://jermontology.org/ontology/JERMOntology#$1 +bioportal.kenyaanc: + bioportal: + name: kenyaancfile + prefix: KENYAANC + subjects: [] + uri_format: http://www.w3.org/2004/02/skos/core#$1 +bioportal.kisao: + bioportal: + name: Kinetic Simulation Algorithm Ontology + prefix: KISAO + subjects: + - Other + uri_format: http://www.biomodels.net/kisao/KISAO#$1 +bioportal.koro: + bioportal: + name: Knowledge Object Reference Ontology + prefix: KORO + subjects: + - Biomedical Resources + uri_format: http://www.knowledgegrid.org/koro#$1 +bioportal.ktao: + bioportal: + name: Kidney Tissue Atlas Ontology + prefix: KTAO + subjects: + - 'Cellular anatomy ' + - Molecule + - Health + - Dysfunction + - Biomedical Resources + - Genomic and Proteomic + - Biological Process + - Subcellular + - Phenotype + - Human Developmental Anatomy + - Anatomy + - Human + - Subcellular anatomy + - Cell + - Development + - Gene Product + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.labo: + bioportal: + name: clinical LABoratory Ontology + prefix: LABO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/LABO_$1 +bioportal.land-surface: + bioportal: + name: Land Surface classifiers + prefix: LAND-SURFACE + subjects: + - Vocabularies + uri_format: http://anzsoil.org/def/au/asls/land-surface$1 +bioportal.landform: + bioportal: + name: Landform classifiers + prefix: LANDFORM + subjects: + - Vocabularies + uri_format: http://anzsoil.org/def/au/asls/landform$1 +bioportal.lbo: + bioportal: + name: Livestock Breed Ontology + prefix: LBO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/LBO_$1 +bioportal.lc-media: + bioportal: + name: Library of Congress Media Types Scheme + prefix: LC-MEDIA + subjects: [] + uri_format: http://id.loc.gov/vocabulary/mediaTypes$1 +bioportal.lda: + bioportal: + name: Ontology of Language Disorder in Autism + prefix: LDA + subjects: + - Health + uri_format: http://www.semanticweb.org/ontologies/2008/10/languageacquisition_autism.owl#$1 +bioportal.legalapa: + bioportal: + name: legalapa + prefix: LEGALAPA + subjects: [] + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.legalapatest2: + bioportal: + name: apalegal + prefix: LEGALAPATEST2 + subjects: [] + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +bioportal.lepao: + bioportal: + name: Lepidoptera Anatomy Ontology + prefix: LEPAO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/LEPAO_$1 +bioportal.lhn: + bioportal: + name: Loggerhead Nesting Ontology + prefix: LHN + subjects: [] + uri_format: http://purl.obolibrary.org/obo/B8467_$1 +bioportal.lico: + bioportal: + name: Liver Case Ontology (LiCO) + prefix: LICO + subjects: + - Health + uri_format: http://vavlab.ee.boun.edu.tr/carera/khaos/lico.owl#$1 +bioportal.lifo: + bioportal: + name: Life Ontology + prefix: LIFO + subjects: + - All Organisms + uri_format: http://purl.obolibrary.org/obo/LifO_$1 +bioportal.lion: + bioportal: + name: LipidOntology + prefix: LION + subjects: + - Molecule + - Physicochemical + uri_format: http://purl.obolibrary.org/obo/LION_$1 +bioportal.lipro: + bioportal: + name: Lipid Ontology + prefix: LIPRO + subjects: [] + uri_format: http://semanticscience.org/sadi/ontology/leo.owl#$1 +bioportal.loinc: + bioportal: + name: Logical Observation Identifier Names and Codes + prefix: LOINC + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/LNC$1 +bioportal.longcovid: + bioportal: + name: Long Covid Phenotype Ontology + prefix: LONGCOVID + subjects: + - Health + - Phenotype + uri_format: http://www.semanticweb.org/orchid/ontologies/2021/Long-Covid-Phenotype-Ontology#$1 +bioportal.lpt: + bioportal: + name: Livestock Product Trait Ontology + prefix: LPT + subjects: [] + uri_format: http://purl.obolibrary.org/obo/LPT_$1 +bioportal.lungmap-human: + bioportal: + name: Anatomic Ontology for Human Lung Maturation + prefix: LUNGMAP-HUMAN + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/LMHA_$1 +bioportal.lungmap_h_cell: + bioportal: + name: Cell Ontology for Human Lung Maturation + prefix: LUNGMAP_H_CELL + subjects: + - Cell + uri_format: http://purl.obolibrary.org/obo/LMHA_$1 +bioportal.lungmap_m_cell: + bioportal: + name: Cell Ontology for Mouse Lung Maturation + prefix: LUNGMAP_M_CELL + subjects: + - Cell + uri_format: http://purl.obolibrary.org/obo/LMMA_$1 +bioportal.m4m-20-subjects: + bioportal: + name: M4M.20 FAIRWare Subjects + prefix: M4M-20-SUBJECTS + subjects: [] + uri_format: http://purl.org/m4m20/subjects$1 +bioportal.m4m-20-variables: + bioportal: + name: M4M.20 FAIRWare Variables + prefix: M4M-20-VARIABLES + subjects: [] + uri_format: http://purl.org/m4m20/variables$1 +bioportal.m4m-21-subjects: + bioportal: + name: M4M.21 FAIRWare Subjects + prefix: M4M-21-SUBJECTS + subjects: [] + uri_format: http://purl.org/m4m21/subjects$1 +bioportal.m4m-21-variables: + bioportal: + name: M4M.21 FAIRWare Variables + prefix: M4M-21-VARIABLES + subjects: [] + uri_format: http://purl.org/m4m21/variables$1 +bioportal.m4m19-subs: + bioportal: + name: M4M19 Subjects + prefix: M4M19-SUBS + subjects: [] + uri_format: http://purl.org/m4m19/subjects$1 +bioportal.m4m19-vars: + bioportal: + name: M4M19 Variables + prefix: M4M19-VARS + subjects: [] + uri_format: http://purl.org/m4m19/variables$1 +bioportal.ma: + bioportal: + name: Mouse Adult Gross Anatomy Ontology + prefix: MA + subjects: + - Mouse Anatomy + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/MA_$1 +bioportal.mads-rdf: + bioportal: + name: Metadata Authority Description Schema in RDF + prefix: MADS-RDF + subjects: + - Other + uri_format: http://www.loc.gov/mads/rdf/v1#$1 +bioportal.mamo: + bioportal: + name: Mathematical Modelling Ontology + prefix: MAMO + subjects: + - Other + uri_format: http://identifiers.org/mamo/MAMO_$1 +bioportal.marc-languages: + bioportal: + name: MARC List for Languages + prefix: MARC-LANGUAGES + subjects: [] + uri_format: http://id.loc.gov/vocabulary/languages$1 +bioportal.mat: + bioportal: + name: Minimal Anatomical Terminology + prefix: MAT + subjects: + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/MAT_$1 +bioportal.matr: + bioportal: + name: Material + prefix: MATR + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matr.owl#$1 +bioportal.matrcompound: + bioportal: + name: Material Compound + prefix: MATRCOMPOUND + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matrCompound.owl#$1 +bioportal.matrelement: + bioportal: + name: Material Element + prefix: MATRELEMENT + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matrElement.owl#$1 +bioportal.matrrock: + bioportal: + name: Material Rock + prefix: MATRROCK + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matrRock.owl#$1 +bioportal.matrrockigneous: + bioportal: + name: Material Rock Igneouus + prefix: MATRROCKIGNEOUS + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matrRockIgneous.owl#$1 +bioportal.maxo: + bioportal: + name: Medical Action Ontology + prefix: MAXO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MAXO_$1 +bioportal.mcbcc: + bioportal: + name: Breast Tissue Cell Lines Ontology + prefix: MCBCC + subjects: + - Cell + uri_format: http://purl.obolibrary.org/obo/MCBCC_0000275#$1 +bioportal.mccl: + bioportal: + name: Cell Line Ontology [by Mahadevan] + prefix: MCCL + subjects: + - Health + - Anatomy + - Cell + - Protein + uri_format: http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1 +bioportal.mccv: + bioportal: + name: Microbial Culture Collection Vocabulary + prefix: MCCV + subjects: + - Other + uri_format: http://purl.jp/bio/10/mccv#$1 +bioportal.mchvodanaterms: + bioportal: + name: MCHVODANATERMS + prefix: MCHVODANATERMS + subjects: [] + uri_format: https://github.com/mariambasajja$1 +bioportal.mco: + bioportal: + name: Microbial Conditions Ontology + prefix: MCO + subjects: + - Experimental Conditions + uri_format: http://purl.obolibrary.org/obo/MCO_$1 +bioportal.mddb: + bioportal: + name: Master Drug Data Base Clinical Drugs + prefix: MDDB + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/MDDB$1 +bioportal.medeon: + bioportal: + name: Medical Error Ontology + prefix: MEDEON + subjects: + - Health + uri_format: http://www.semanticweb.org/chen/ontologies/2015/8/untitled-ontology-72#$1 +bioportal.medlineplus: + bioportal: + name: MedlinePlus Health Topics + prefix: MEDLINEPLUS + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/MEDLINEPLUS$1 +bioportal.medo: + bioportal: + name: Mouse Experimental Design Ontology + prefix: MEDO + subjects: [] + uri_format: http://www.ebi.ac.uk/efo/medo/MEDO_$1 +bioportal.mego: + bioportal: + name: Mobile Genetic Element Ontology + prefix: MEGO + subjects: + - Biological Process + - Gene Product + uri_format: http://purl.obolibrary.org/obo/phi_$1 +bioportal.melo: + bioportal: + name: Melanoma Ontology + prefix: MELO + subjects: + - Health + - Biomedical Resources + - Human + uri_format: http://purl.obolibrary.org/obo/FMA_$1 +bioportal.meo: + bioportal: + name: Metagenome and Microbes Environmental Ontology + prefix: MEO + subjects: + - Other + uri_format: http://purl.jp/bio/11/meo/MEO_$1 +bioportal.mepo: + bioportal: + name: Mapping of Epilepsy Ontologies + prefix: MEPO + subjects: + - Health + - Biomedical Resources + - Biological Process + - Neurologic Disease + - Neurological Disorder + - Human + - Development + - Protein + - Gene Product + - Vocabularies + uri_format: http://www.semanticweb.org/rjyy/ontologies/2015/5/ESSO#$1 +bioportal.mera: + bioportal: + name: Medical Educational Resource Aggregator + prefix: MERA + subjects: + - Vocabularies + uri_format: https://carre.kmi.open.ac.uk/ontology/educational.owl#$1 +bioportal.mesh: + bioportal: + name: Medical Subject Headings + prefix: MESH + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/MESH$1 +bioportal.mf: + bioportal: + name: Mental Functioning Ontology + prefix: MF + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MF_$1 +bioportal.mfo: + bioportal: + name: Medaka Fish Anatomy and Development Ontology + prefix: MFO + subjects: + - Fish Anatomy + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/MFO_$1 +bioportal.mfoem: + bioportal: + name: Emotion Ontology + prefix: MFOEM + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/MFOEM_$1 +bioportal.mfomd: + bioportal: + name: MFO Mental Disease Ontology + prefix: MFOMD + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/MFOMD_$1 +bioportal.mhc: + bioportal: + name: Major Histocompatibility Complex Ontology + prefix: MHC + subjects: + - Genomic and Proteomic + uri_format: http://purl.org/stemnet/MHC#$1 +bioportal.mhcro: + bioportal: + name: MHC Restriction Ontology + prefix: MHCRO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MRO_$1 +bioportal.mhmo: + bioportal: + name: Mental Health Management Ontology + prefix: MHMO + subjects: + - Health + uri_format: http://mental-ontology.com/mental_health_bfo.owl#$1 +bioportal.mi: + bioportal: + name: Molecular Interactions + prefix: MI + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MI_$1 +bioportal.miapa: + bioportal: + name: MIAPA Ontology + prefix: MIAPA + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MIAPA_$1 +bioportal.mido: + bioportal: + name: Medical Imaging and Diagnostic Ontology + prefix: MIDO + subjects: + - Imaging + - Health + - Biomedical Resources + - Biological Process + - Anatomy + - Human + uri_format: http://radlex.org/RID$1 +bioportal.mim: + bioportal: + name: Molecular Interaction Map + prefix: MIM + subjects: + - Biological Process + - Vocabularies + uri_format: http://purl.bioontology.org/ontology/MIM#$1 +bioportal.mineral: + bioportal: + name: Material Mineral + prefix: MINERAL + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matrMineral.owl#$1 +bioportal.mini-fast-1: + bioportal: + name: mini fast test + prefix: MINI-FAST-1 + subjects: [] + uri_format: http://id.loc.gov/authorities/subjects$1 +bioportal.mirnao: + bioportal: + name: MicroRNA Ontology + prefix: MIRNAO + subjects: + - Other + uri_format: http://anobase.vectorbase.org/mirnao/mirnao.owl#$1 +bioportal.miro: + bioportal: + name: Mosquito Insecticide Resistance + prefix: MIRO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/MIRO_$1 +bioportal.mixs: + bioportal: + name: Minimal Information about any Sequence Ontology + prefix: MIXS + subjects: + - Experimental Conditions + - All Organisms + - Molecule + - Other + - Vocabularies + uri_format: https://w3id.org/mixs/vocab$1 +bioportal.mixscv: + bioportal: + name: Minimal Information about any Sequence (MIxS) Controlled Vocabularies + prefix: MIXSCV + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MVC_$1 +bioportal.mltx: + bioportal: + name: Machine Learning Methodology Taxonomy Mapping + prefix: MLTX + subjects: + - Vocabularies + uri_format: http://webprotege.stanford.edu$1 +bioportal.mmo: + bioportal: + name: Measurement Method Ontology + prefix: MMO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/MMO_$1 +bioportal.mmusdv: + bioportal: + name: Mouse Developmental Stages + prefix: MMUSDV + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MmusDv_$1 +bioportal.mnr: + bioportal: + name: 'Material Natural Resource ' + prefix: MNR + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matrNaturalResource.owl#$1 +bioportal.mnv: + bioportal: + name: VODANA Migrants + prefix: MNV + subjects: + - Vocabularies + uri_format: https://www.vodan-totafrica.info/vocs/vodan-migrant-content$1 +bioportal.mo: + bioportal: + name: Microarray and Gene Expression Data Ontology + prefix: MO + subjects: + - Experimental Conditions + uri_format: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#$1 +bioportal.moc: + bioportal: + name: Material Organic Compound + prefix: MOC + subjects: + - Upper Level Ontology + uri_format: http://sweet.jpl.nasa.gov/2.3/matrOrganicCompound.owl#$1 +bioportal.modsci: + bioportal: + name: Modern Science Ontology + prefix: MODSCI + subjects: + - Upper Level Ontology + uri_format: https://w3id.org/skgo/modsci#$1 +bioportal.mondo: + bioportal: + name: Mondo Disease Ontology + prefix: MONDO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MONDO_$1 +bioportal.mono: + bioportal: + name: Monogenean Ontology + prefix: MONO + subjects: [] + uri_format: http://www.owl-ontologies.com/MO.owl#$1 +bioportal.moocciado: + bioportal: + name: Molgula occidentalis Anatomy and Development Ontology + prefix: MOOCCIADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/MoocciA_$1 +bioportal.mooccuado: + bioportal: + name: Molgula occulta Anatomy and Development Ontology + prefix: MOOCCUADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/MooccuA_$1 +bioportal.mooculado: + bioportal: + name: Molgula oculata Anatomy and Development Ontology + prefix: MOOCULADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/MooculA_$1 +bioportal.mop: + bioportal: + name: Molecular Process Ontology + prefix: MOP + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MOP_$1 +bioportal.mosaic: + bioportal: + name: The MOSAiC Ontology + prefix: MOSAIC + subjects: [] + uri_format: https://purl.dataone.org/odo/MOSAIC_$1 +bioportal.mp: + bioportal: + name: Mammalian Phenotype Ontology + prefix: MP + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/MP_$1 +bioportal.mpath: + bioportal: + name: Mouse Pathology Ontology + prefix: MPATH + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/MPATH_$1 +bioportal.mpio: + bioportal: + name: Minimum PDDI Information Ontology + prefix: MPIO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/MPIO_$1 +bioportal.mpo: + bioportal: + name: Microbial Phenotype Ontology + prefix: MPO + subjects: + - Phenotype + - Microbial Anatomy + uri_format: http://purl.jp/bio/10/mpo#$1 +bioportal.mro: + bioportal: + name: Defen + prefix: MRO + subjects: [] + uri_format: http://www.semanticweb.org/projectlab/ontologies/2016/8/untitled-ontology-23#$1 +bioportal.mso: + bioportal: + name: Multiple sclerosis ontology + prefix: MSO + subjects: + - Neurologic Disease + uri_format: http://scai.fraunhofer.de/MSOntology#$1 +bioportal.mstde: + bioportal: + name: Minimal Standard Terminology of Digestive Endoscopy + prefix: MSTDE + subjects: [] + uri_format: http://purl.bioontology.org/ontology/MSTDE$1 +bioportal.mstde-fre: + bioportal: + name: Minimal Standard Terminology of Digestive Endoscopy, French + prefix: MSTDE-FRE + subjects: [] + uri_format: http://purl.bioontology.org/ontology/MSTDE-FRE$1 +bioportal.msv: + bioportal: + name: Metagenome Sample Vocabulary + prefix: MSV + subjects: + - Other + uri_format: http://purl.jp/bio/11/msv/MSV_$1 +bioportal.mwla: + bioportal: + name: Medical Web Lifestyle Aggregator + prefix: MWLA + subjects: + - Vocabularies + uri_format: http://carre.kmi.open.ac.uk/ontology/lifestyle.owl#$1 +bioportal.nando: + bioportal: + name: Nanbyo Disease Ontology + prefix: NANDO + subjects: + - Health + - Biomedical Resources + - Human + uri_format: http://nanbyodata.jp/ontology/NANDO_$1 +bioportal.natpro: + bioportal: + name: Natural Products Ontology + prefix: NATPRO + subjects: [] + uri_format: http://www.owl-ontologies.com/NPOntology.owl#$1 +bioportal.nbo: + bioportal: + name: Neuro Behavior Ontology + prefix: NBO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/NBO_$1 +bioportal.ncbitaxon: + bioportal: + name: National Center for Biotechnology Information (NCBI) Organismal Classification + prefix: NCBITAXON + subjects: + - Taxonomic Classification + uri_format: http://purl.bioontology.org/ontology/NCBITAXON$1 +bioportal.nccnehr: + bioportal: + name: NCCN EHR Oncology Categories + prefix: NCCNEHR + subjects: + - Health + - Biomedical Resources + uri_format: http://www.semanticweb.org/lamb/ontologies/NCCN-EHR#$1 +bioportal.ncco: + bioportal: + name: Nursing Care Coordination Ontology + prefix: NCCO + subjects: + - Health + uri_format: http://www.semanticweb.org/vanessa/ontologies/2012/7/untitled-ontology-33#$1 +bioportal.ncit: + bioportal: + name: National Cancer Institute Thesaurus + prefix: NCIT + subjects: [] + uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1 +bioportal.ncro: + bioportal: + name: Non-coding RNA Ontology + prefix: NCRO + subjects: [] + uri_format: http://purl.obolibrary.org/NCRO_$1 +bioportal.nddo: + bioportal: + name: Neurodegenerative Disease Data Ontology + prefix: NDDO + subjects: + - Neurologic Disease + - Neurological Disorder + uri_format: http://www.purl.org/NDDO/NDDO_$1 +bioportal.neicbeer: + bioportal: + name: The NeIC PaRI beer vocabulary + prefix: NEICBEER + subjects: + - Other + uri_format: http://ontology.deic.dk/cv/beer-ontology$1 +bioportal.nemo: + bioportal: + name: Neural ElectroMagnetic Ontology + prefix: NEMO + subjects: + - Imaging + - Experimental Conditions + - Biological Process + - Anatomy + - Human + uri_format: http://purl.bioontology.org/NEMO/ontology/NEMO.owl#$1 +bioportal.neo: + bioportal: + name: Neurologic Examination Ontology + prefix: NEO + subjects: + - Taxonomic Classification + - Health + - Neurologic Disease + - Neurological Disorder + uri_format: http://www.semanticweb.org/danielhier/ontologies/2019/3/untitled-ontology-57#$1 +bioportal.neomark3: + bioportal: + name: Neomark Oral Cancer Ontology, version 3 + prefix: NEOMARK3 + subjects: + - Health + uri_format: http://www.neomark.eu/ontologies$1 +bioportal.neomark4: + bioportal: + name: Neomark Oral Cancer Ontology, version 4 + prefix: NEOMARK4 + subjects: + - Health + - Genomic and Proteomic + - Anatomy + - Human + uri_format: http://neomark.owl#$1 +bioportal.nero: + bioportal: + name: 'Named Entity Recognition Ontology ' + prefix: NERO + subjects: + - Biomedical Resources + uri_format: http://www.cs.man.ac.uk/~stevensr/ontology/ner.owl#$1 +bioportal.neudigs: + bioportal: + name: Neuroscience Domain Insight Graph + prefix: NEUDIGS + subjects: + - 'Cellular anatomy ' + - Anatomy + - Cell + uri_format: http://bmkeg.isi.edu/neuDIGs#$1 +bioportal.neumore: + bioportal: + name: Neural Motor Recovery Ontology + prefix: NEUMORE + subjects: [] + uri_format: http://neumore.cis.usouthal.edu/ontologies/NeuMORE-v0.1.owl#$1 +bioportal.ngbo: + bioportal: + name: Next Generation Biobanking Ontology + prefix: NGBO + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/ngbo.owl/NGBO_$1 +bioportal.ngsonto: + bioportal: + name: NGS ontology + prefix: NGSONTO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/NGS_$1 +bioportal.nidm-results: + bioportal: + name: NIDM-Results + prefix: NIDM-RESULTS + subjects: + - Imaging + - Other + uri_format: http://purl.org/nidash/nidm#$1 +bioportal.nifcell: + bioportal: + name: Neuroscience Information Framework (NIF) Cell Ontology + prefix: NIFCELL + subjects: [] + uri_format: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl#$1 +bioportal.nifdys: + bioportal: + name: Neuroscience Information Framework (NIF) Dysfunction Ontlogy + prefix: NIFDYS + subjects: [] + uri_format: http://purl.obolibrary.org/obo/PATO_$1 +bioportal.nifstd: + bioportal: + name: Neuroscience Information Framework (NIF) Standard Ontology + prefix: NIFSTD + subjects: + - All Organisms + - 'Cellular anatomy ' + - Molecule + - Dysfunction + - Biological Process + - Other + - Subcellular + - Neurologic Disease + - Neurological Disorder + - Anatomy + - Subcellular anatomy + - Cell + uri_format: http://uri.neuinfo.org/nif/nifstd/nifext_$1 +bioportal.nifsubcell: + bioportal: + name: Neuroscience Information Framework (NIF) Subcellular Ontology + prefix: NIFSUBCELL + subjects: [] + uri_format: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#$1 +bioportal.nigo: + bioportal: + name: Neural-Immune Gene Ontology + prefix: NIGO + subjects: + - Biological Process + - Other + - Human + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.nihss: + bioportal: + name: National Institutes of Health Stroke Scale Ontology + prefix: NIHSS + subjects: + - Neurologic Disease + uri_format: https://mre.zcu.cz/ontology/nihss.owl#$1 +bioportal.nio: + bioportal: + name: Neuropsychological Integrative Ontology + prefix: NIO + subjects: + - Neurologic Disease + uri_format: http://www.semanticweb.org/alba/ontologies/2020/10/NIO#$1 +bioportal.nist_gel: + bioportal: + name: NIST Genome Editing Lexicon + prefix: NIST_GEL + subjects: + - Molecule + - Genomic and Proteomic + - Gene Product + uri_format: http://webprotege.stanford.edu$1 +bioportal.nlmvs: + bioportal: + name: NIH NLM Value Sets + prefix: NLMVS + subjects: [] + uri_format: http://purl.bioontology.org/ontology/SNOMEDCT$1 +bioportal.nln: + bioportal: + name: NLighten Ontology + prefix: NLN + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/IAO_$1 +bioportal.nmdco: + bioportal: + name: NMDC Ontology + prefix: NMDCO + subjects: + - Other + - Plant + uri_format: http://purl.obolibrary.org/obo/ENVO_$1 +bioportal.nmobr: + bioportal: + name: NeuroMorpho.Org brain region ontologies + prefix: NMOBR + subjects: + - Mouse Anatomy + - 'Cellular anatomy ' + - Gross Anatomy + - Phenotype + - Development + uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1 +bioportal.nmosp: + bioportal: + name: NeuroMorpho.Org species ontology + prefix: NMOSP + subjects: + - All Organisms + uri_format: http://neuromorpho.org/ontologies/NMOSp.owl#$1 +bioportal.nmr: + bioportal: + name: NMR-Controlled Vocabulary + prefix: NMR + subjects: + - Molecule + - Biomedical Resources + - Other + - Subcellular + - Chemical + - Protein + - Vocabularies + - Physicochemical + uri_format: http://nmrML.org/nmrCV#$1 +bioportal.nomen: + bioportal: + name: NOMEN - A nomenclatural ontology for biological names + prefix: NOMEN + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/NOMEN_$1 +bioportal.nonrcto: + bioportal: + name: Non-Randomized Controlled Trials Ontology + prefix: NONRCTO + subjects: [] + uri_format: http://www.owl-ontologies.com/RCTOntology.owl#$1 +bioportal.npi: + bioportal: + name: Non-Pharmacological Interventions (NPIs) + prefix: NPI + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/NPI#$1 +bioportal.npokb: + bioportal: + name: Neuron Phenotype Ontology + prefix: NPOKB + subjects: + - 'Cellular anatomy ' + - Phenotype + - Cell + uri_format: http://purl.obolibrary.org/obo/UBERON_$1 +bioportal.nxdx: + bioportal: + name: Test NXDX + prefix: NXDX + subjects: + - Neurologic Disease + uri_format: http://www.semanticweb.org/ontologies/Prostate_cancer#$1 +bioportal.oa: + bioportal: + name: Web Annotation Ontology + prefix: OA + subjects: + - Upper Level Ontology + uri_format: http://www.w3.org/ns/oa#$1 +bioportal.oae: + bioportal: + name: Ontology of Adverse Events + prefix: OAE + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/OAE_$1 +bioportal.oarcs: + bioportal: + name: Ontology of Arthropod Circulatory Systems + prefix: OARCS + subjects: + - Anatomy + uri_format: http://purl.obolibrary.org/obo/OARCS_$1 +bioportal.oba: + bioportal: + name: Ontology of Biological Attributes + prefix: OBA + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/OBA_$1 +bioportal.obcs: + bioportal: + name: Ontology of Biological and Clinical Statistics + prefix: OBCS + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/OBCS_$1 +bioportal.obi: + bioportal: + name: Ontology for Biomedical Investigations + prefix: OBI + subjects: + - Experimental Conditions + uri_format: http://purl.obolibrary.org/obo/OBI_$1 +bioportal.obi_bcgo: + bioportal: + name: Beta Cell Genomics Ontology + prefix: OBI_BCGO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/BCGO_$1 +bioportal.obi_iee: + bioportal: + name: 'The Ontology for Biomedical Investigation based Inner Ear Electrophysiology ' + prefix: OBI_IEE + subjects: [] + uri_format: http://purl.obolibrary.org/obo/OBI_$1 +bioportal.obib: + bioportal: + name: Ontology for Biobanking + prefix: OBIB + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/OBIB_$1 +bioportal.obiws: + bioportal: + name: Bioinformatics Web Service Ontology + prefix: OBIWS + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/OBIws_$1 +bioportal.oboe: + bioportal: + name: The Extensible Observation Ontology + prefix: OBOE + subjects: [] + uri_format: http://ecoinformatics.org/oboe/oboe.1.2/oboe-standards.owl#$1 +bioportal.oboe-sbc: + bioportal: + name: Santa Barbara Coastal Observation Ontology + prefix: OBOE-SBC + subjects: + - Other + uri_format: https://code.ecoinformatics.org/code/semtools/trunk/dev/oboe/oboe-sbc.owl#$1 +bioportal.oborel: + bioportal: + name: Relations Ontology + prefix: OBOREL + subjects: [] + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.obs: + bioportal: + name: OntoBioStat + prefix: OBS + subjects: [] + uri_format: http://www.semanticweb.org/Thibaut/ontologies/2021/3/OntoBioStat#$1 +bioportal.oce: + bioportal: + name: Ontology of Chemical Elements + prefix: OCE + subjects: + - Physicochemical + uri_format: http://purl.obolibrary.org/obo/OCE_$1 +bioportal.ochv: + bioportal: + name: Ontology of Consumer Health Vocabulary + prefix: OCHV + subjects: + - Vocabularies + uri_format: http://sbmi.uth.tmc.edu/ontology/ochv#$1 +bioportal.ocimido: + bioportal: + name: Ocular Immune-Mediated Inflammatory Diseases Ontology + prefix: OCIMIDO + subjects: + - Phenotype + uri_format: https://github.com/sap218/ocimido/blob/master/ontology/ocimido.owl#$1 +bioportal.ocmr: + bioportal: + name: Ontology of Chinese Medicine for Rheumatism + prefix: OCMR + subjects: + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/CHEBI_$1 +bioportal.ocre: + bioportal: + name: Ontology of Clinical Research + prefix: OCRE + subjects: + - Biomedical Resources + uri_format: http://purl.org/net/OCRe/OCRe.owl#$1 +bioportal.ocvdae: + bioportal: + name: Ontology of Cardiovascular Drug Adverse Events + prefix: OCVDAE + subjects: [] + uri_format: http://purl.obolibrary.org/obo/OAE_$1 +bioportal.odae: + bioportal: + name: Ontology of Drug Adverse Events + prefix: ODAE + subjects: + - Health + uri_format: http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#$1 +bioportal.odnae: + bioportal: + name: Ontology of Drug Neuropathy Adverse Events + prefix: ODNAE + subjects: + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/ODNAE_$1 +bioportal.of: + bioportal: + name: OntoFood + prefix: OF + subjects: + - Health + - Biological Process + uri_format: http://www.owl-ontologies.com/Ontology1435740495.owl#$1 +bioportal.ofsmr: + bioportal: + name: Open Predictive Microbiology Ontology + prefix: OFSMR + subjects: + - Biomedical Resources + - Vocabularies + uri_format: urn:absolute:OFSMR#$1 +bioportal.ogdi: + bioportal: + name: Ontology for Genetic Disease Investigations + prefix: OGDI + subjects: + - Experimental Conditions + uri_format: http://purl.obolibrary.org/obo/ODGI.owl#$1 +bioportal.ogg: + bioportal: + name: Ontology of Genes and Genomes + prefix: OGG + subjects: + - Genomic and Proteomic + - Human + - Gene Product + uri_format: http://purl.obolibrary.org/obo/OGG_$1 +bioportal.ogg-mm: + bioportal: + name: Ontology of Genes and Genomes - Mouse + prefix: OGG-MM + subjects: + - Molecule + - Biomedical Resources + - Genomic and Proteomic + uri_format: http://purl.obolibrary.org/obo/OGG_$1 +bioportal.ogi: + bioportal: + name: Ontology for Genetic Interval + prefix: OGI + subjects: + - Genomic and Proteomic + uri_format: http://purl.obolibrary.org/obo/OGI_$1 +bioportal.ogmd: + bioportal: + name: Ontology of Glucose Metabolism Disorder + prefix: OGMD + subjects: + - Human + uri_format: http://purl.obolibrary.org/obo/OGMD_$1 +bioportal.ogms: + bioportal: + name: Ontology for General Medical Science + prefix: OGMS + subjects: [] + uri_format: http://purl.obolibrary.org/obo/OGMS_$1 +bioportal.ogr: + bioportal: + name: Ontology of Geographical Region + prefix: OGR + subjects: + - Vocabularies + uri_format: http://www.owl-ontologies.com/GeographicalRegion.owl#$1 +bioportal.ogroup: + bioportal: + name: Orthologous Group Ontology + prefix: OGROUP + subjects: + - Gene Product + uri_format: http://protozoadb.biowebdb.org/22/ogroup#$1 +bioportal.ogsf: + bioportal: + name: Ontology for Genetic Susceptibility Factor + prefix: OGSF + subjects: + - Health + - Genomic and Proteomic + - Human + uri_format: http://purl.obolibrary.org/obo/OGSF_$1 +bioportal.ohd: + bioportal: + name: The Oral Health and Disease Ontology + prefix: OHD + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/OHD_$1 +bioportal.ohmi: + bioportal: + name: Ontology of Host-Microbe Interactions + prefix: OHMI + subjects: + - Experimental Conditions + - Immunology + - Biological Process + - Phenotype + - Microbial Anatomy + uri_format: http://purl.obolibrary.org/obo/OHMI_$1 +bioportal.ohpi: + bioportal: + name: Ontology of Host-Pathogen Interactions + prefix: OHPI + subjects: + - Immunology + - Molecule + - Health + - Biological Process + - Cell + uri_format: http://purl.obolibrary.org/obo/OHPI_$1 +bioportal.olam: + bioportal: + name: Ontology of Laboratory Animal Medicine + prefix: OLAM + subjects: + - All Organisms + uri_format: http://purl.obolibrary.org/obo/OLAM_$1 +bioportal.olatdv: + bioportal: + name: Medaka Developmental Stages + prefix: OLATDV + subjects: [] + uri_format: http://purl.obolibrary.org/obo/OlatDv_$1 +bioportal.om: + bioportal: + name: Ontology of units of Measure + prefix: OM + subjects: + - Other + - Plant + uri_format: http://www.ontology-of-units-of-measure.org/resource/om-2$1 +bioportal.omit: + bioportal: + name: Ontology for MicroRNA Target + prefix: OMIT + subjects: + - Molecule + - Biological Process + - Human + - Cell + - Protein + - Gene Product + uri_format: http://purl.obolibrary.org/obo/OMIT_$1 +bioportal.omo: + bioportal: + name: OBO Metadata Ontology + prefix: OMO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/IAO_$1 +bioportal.omp: + bioportal: + name: Ontology of Microbial Phenotypes + prefix: OMP + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/OMP_$1 +bioportal.omrse: + bioportal: + name: Ontology of Medically Related Social Entities + prefix: OMRSE + subjects: [] + uri_format: http://purl.obolibrary.org/obo/OMRSE_$1 +bioportal.omv: + bioportal: + name: Ontology Metadata Vocabulary + prefix: OMV + subjects: + - Vocabularies + uri_format: http://omv.ontoware.org/2005/05/ontology#$1 +bioportal.one: + bioportal: + name: Ontology for Nutritional Epidemiology + prefix: ONE + subjects: + - Health + - Biomedical Resources + - Human + uri_format: http://purl.obolibrary.org/obo/OBI_$1 +bioportal.onl-dp: + bioportal: + name: Dataset processing + prefix: ONL-DP + subjects: + - Imaging + uri_format: http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl#$1 +bioportal.onl-mr-da: + bioportal: + name: Magnetic Resonance Dataset Acquisition Ontology + prefix: ONL-MR-DA + subjects: + - Imaging + uri_format: http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl#$1 +bioportal.onl-msa: + bioportal: + name: Mental State Assessment + prefix: ONL-MSA + subjects: + - Health + - Neurological Disorder + - Human + uri_format: http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-mental-state-assessment.owl#$1 +bioportal.onl-tasks: + bioportal: + name: Cognitive Reserves Assessment Tasks + prefix: ONL-TASKS + subjects: + - Health + - Neurological Disorder + - Human + uri_format: http://www.semanticweb.org/bakaev/ontologies/2020/3/untitled-ontology-25#$1 +bioportal.onlira: + bioportal: + name: Ontology of Liver for Radiology + prefix: ONLIRA + subjects: [] + uri_format: http://vavlab.ee.boun.edu.tr/carera/onlira.owl#$1 +bioportal.ons: + bioportal: + name: Ontology for Nutritional Studies + prefix: ONS + subjects: + - Experimental Conditions + - Health + - Biomedical Resources + - Human + uri_format: http://purl.obolibrary.org/obo/ONS_$1 +bioportal.onstr: + bioportal: + name: Ontology for Newborn Screening Follow-up and Translational Research + prefix: ONSTR + subjects: + - Health + - Dysfunction + - Biological Process + - Phenotype + - Human + - Development + uri_format: http://onstr.googlecode.com/svn/tags/currentRelease/2014-09-03/ONSTR.owl#$1 +bioportal.ontoad: + bioportal: + name: Bilingual Ontology of Alzheimer's Disease and Related Diseases + prefix: ONTOAD + subjects: + - Health + - Dysfunction + - Neurologic Disease + - Neurological Disorder + - Human + uri_format: http://doe-generated-ontology.com/OntoAD#$1 +bioportal.ontoavida: + bioportal: + name: 'OntoAvida: ontology for Avida digital evolution platform' + prefix: ONTOAVIDA + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/ONTOAVIDA_$1 +bioportal.ontodm-algorithm: + bioportal: + name: OntoDM-core/algorithms + prefix: ONTODM-ALGORITHM + subjects: + - Other + uri_format: http://www.ontodm.com/OntoDM-core/OntoDM_$1 +bioportal.ontodm-core: + bioportal: + name: Ontology of Core Data Mining Entities + prefix: ONTODM-CORE + subjects: [] + uri_format: http://www.ontodm.com/OntoDM-core/OntoDM_$1 +bioportal.ontodm-kdd: + bioportal: + name: Ontology of Data Mining Investigations + prefix: ONTODM-KDD + subjects: [] + uri_format: http://kt.ijs.si/panovp/OntoDM-KDD.owl#$1 +bioportal.ontodt: + bioportal: + name: Ontology of Datatypes + prefix: ONTODT + subjects: [] + uri_format: http://www.ontodm.com/OntoDT#$1 +bioportal.ontokbcf: + bioportal: + name: Ontological Knowledge Base Model for Cystic Fibrosis + prefix: ONTOKBCF + subjects: + - Health + - Biomedical Resources + - Phenotype + - Gene Product + uri_format: http://www.owl-ontologies.com/assert.owl#$1 +bioportal.ontolurgences: + bioportal: + name: Emergency care ontology + prefix: ONTOLURGENCES + subjects: + - Health + uri_format: http://www.limics.fr/ontologies/ontolurgences#$1 +bioportal.ontoma: + bioportal: + name: Ontology of Alternative Medicine, French + prefix: ONTOMA + subjects: [] + uri_format: http://www.semanticweb.org/associatedmedicine/lavima/2011/10/Ontology1.owl#$1 +bioportal.ontoneo: + bioportal: + name: Obstetric and Neonatal Ontology + prefix: ONTONEO + subjects: + - Health + - Biomedical Resources + - Human + uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1 +bioportal.ontoparon: + bioportal: + name: Ontology of Amyotrophic Lateral Sclerosis, all modules + prefix: ONTOPARON + subjects: + - Neurologic Disease + uri_format: http://www.limics.fr/ontologies/ontoparonsoc#$1 +bioportal.ontoparon_social: + bioportal: + name: Ontology of amyotrophic lateral sclerosis, social module + prefix: ONTOPARON_SOCIAL + subjects: + - Neurological Disorder + uri_format: http://www.limics.fr/ontologies/ontoparonsoc#$1 +bioportal.ontopbm: + bioportal: + name: Ontology for Process-Based Modeling of Dynamical Systems (OntoPBM) + prefix: ONTOPBM + subjects: + - Other + uri_format: http://w3id.org/ontopbm#$1 +bioportal.ontopneumo: + bioportal: + name: Ontology of Pneumology + prefix: ONTOPNEUMO + subjects: + - Health + - Human + uri_format: http://doe-generated-ontology.com/OntoPneumo#$1 +bioportal.ontopsychia: + bioportal: + name: OntoPsychia, social module + prefix: ONTOPSYCHIA + subjects: + - Human + uri_format: http://www.limics.fr/ontologies/ontopsychiasoc#$1 +bioportal.ontoreplicov: + bioportal: + name: OntoRepliCov + prefix: ONTOREPLICOV + subjects: + - Biological Process + uri_format: http://www.semanticweb.org/wissame.laddada/ontologies/2020/9/SARS_CoV_2#$1 +bioportal.ontosim: + bioportal: + name: The Ontology of Information System on Mortality + prefix: ONTOSIM + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/DIASUS/OntoSIM#$1 +bioportal.ontosinasc: + bioportal: + name: Ontology of Information System on Live Births + prefix: ONTOSINASC + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/DIASUS/OntoSINASC#$1 +bioportal.ontotox: + bioportal: + name: Chemotherapy Toxicities Ontology + prefix: ONTOTOX + subjects: + - Biomedical Resources + uri_format: http://OntoTox.owl#$1 +bioportal.ontotoxnuc: + bioportal: + name: Ontology of Nuclear Toxicity + prefix: ONTOTOXNUC + subjects: + - Taxonomic Classification + - Chemical + uri_format: http://www.cea.fr/ontotoxnuc#$1 +bioportal.ontovip: + bioportal: + name: Medical image simulation + prefix: OntoVIP + subjects: + - Imaging + uri_format: http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl#$1 +bioportal.ooevv: + bioportal: + name: Ontology of Experimental Variables and Values + prefix: OOEVV + subjects: + - Vocabularies + uri_format: http://bmkeg.isi.edu/ooevv$1 +bioportal.oostt: + bioportal: + name: Ontology of Organizational Structures of Trauma centers and Trauma systems + prefix: OOSTT + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/OOSTT_$1 +bioportal.opb: + bioportal: + name: Ontology of Physics for Biology + prefix: OPB + subjects: + - Biomedical Resources + - Biological Process + - Phenotype + - Chemical + - Physicochemical + uri_format: http://bhi.washington.edu/OPB#$1 +bioportal.opde: + bioportal: + name: OPD-Ethiopia + prefix: OPDE + subjects: [] + uri_format: http://www.mudhc.edu.et/template-vocabulary#$1 +bioportal.opdront: + bioportal: + name: OPD Register Ontology + prefix: OPDRONT + subjects: [] + uri_format: http://www.fairdatacollective.com/template-vocabulary$1 +bioportal.opdt: + bioportal: + name: opd_test + prefix: OPDT + subjects: [] + uri_format: http://www.fairdatacollective.com/template-vocabulary$1 +bioportal.opdzimbabwe: + bioportal: + name: OPDZimbabwe + prefix: OPDZIMBABWE + subjects: + - Vocabularies + uri_format: http://www.vocab.vodana.org/vocabularies/opd$1 +bioportal.ope: + bioportal: + name: Ontology of Physical Exercises + prefix: OPE + subjects: + - Health + - Other + - Anatomy + - Human + uri_format: http://www.semanticweb.org/ontologies/2013/2/OPE.owl#$1 +bioportal.opl: + bioportal: + name: Ontology for Parasite LifeCycle + prefix: OPL + subjects: + - Phenotype + - Development + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/OPL_$1 +bioportal.opmi: + bioportal: + name: Ontology of Precision Medicine and Investigation + prefix: OPMI + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/OPMI_$1 +bioportal.optimal: + bioportal: + name: 'OPTImAL: An ontology for patient adherence modeling in physical activity domain' + prefix: OPTIMAL + subjects: + - Taxonomic Classification + - Health + uri_format: http://webprotege.stanford.edu/project/B1YA5aP4fTfTaBBx7flwQP#$1 +bioportal.orcs: + bioportal: + name: Ontology for Representing CDM Semantics + prefix: ORCS + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/ORCS_$1 +bioportal.ornaseq: + bioportal: + name: Ontology of RNA Sequencing + prefix: ORNASEQ + subjects: + - Experimental Conditions + uri_format: http://purl.obolibrary.org/obo/ORNASEQ_$1 +bioportal.orth: + bioportal: + name: Orthology Ontology + prefix: ORTH + subjects: + - All Organisms + - Genomic and Proteomic + uri_format: http://purl.org/net/orth#$1 +bioportal.osm: + bioportal: + name: Ontologia de Saúde Mental + prefix: OSM + subjects: [] + uri_format: https://saudeconectada.org/saude_mental.owl#$1 +bioportal.ovae: + bioportal: + name: Ontology of Vaccine Adverse Events + prefix: OVAE + subjects: + - Immunology + - Health + - Phenotype + - Human + uri_format: http://purl.obolibrary.org/obo/OVAE_$1 +bioportal.paco: + bioportal: + name: Physical Activity Ontology + prefix: PACO + subjects: + - Health + - Other + - Human + uri_format: http://www.semanticweb.org/hyk038/ontologies/2018/7/untitled-ontology-17#$1 +bioportal.pae: + bioportal: + name: Plant Anatomy + prefix: PAE + subjects: + - Plant Anatomy + - Plant + uri_format: http://purl.obolibrary.org/obo/PO_$1 +bioportal.panda: + bioportal: + name: Probabilistic Knowledge Assembly Ontology + prefix: PANDA + subjects: [] + uri_format: http://purl.bioontology.org/net/brunel/panda#$1 +bioportal.panet: + bioportal: + name: PaN Experimental technique + prefix: PANET + subjects: + - Other + uri_format: http://purl.org/pan-science/PaNET$1 +bioportal.partumdo: + bioportal: + name: postpartum depression ontology + prefix: PARTUMDO + subjects: + - Phenotype + - Neurologic Disease + - Neurological Disorder + - Human + - Vocabularies + uri_format: http://www.semanticweb.org/rbmor/ontologies/2021/1/1/untitled-ontology-133#$1 +bioportal.patct: + bioportal: + name: Placental Cell Type + prefix: PATCT + subjects: + - Cell + uri_format: https://pat.nichd.nih.gov/placentalcelltype$1 +bioportal.patel: + bioportal: + name: Archana Patel + prefix: PATEL + subjects: + - Other + uri_format: http://www.semanticweb.org/ambrish/ontologies/2020/10/untitled-ontology-24#$1 +bioportal.patgv: + bioportal: + name: Placental Genetic Variance + prefix: PATGV + subjects: + - Genomic and Proteomic + uri_format: https://pat.nichd.nih.gov/patgeneticvariance$1 +bioportal.pathlex: + bioportal: + name: Anatomic Pathology Lexicon + prefix: PATHLEX + subjects: + - Taxonomic Classification + - Health + - Anatomy + - Vocabularies + uri_format: http://www.semanticweb.org/david/ontologies/2013/0/pathLex.owl#$1 +bioportal.patit: + bioportal: + name: Placental Investigative Technique + prefix: PATIT + subjects: + - Other + uri_format: https://pat.nichd.nih.gov/patinvestigativetechniques$1 +bioportal.patmhc: + bioportal: + name: Placental Maternal Health Conditions + prefix: PATMHC + subjects: + - Health + uri_format: http://pat.nichd.nih.gov/maternalconditions$1 +bioportal.pato: + bioportal: + name: Phenotypic Quality Ontology + prefix: PATO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/PATO_$1 +bioportal.pav: + bioportal: + name: PAV Provenance, Authoring and Versioning + prefix: PAV + subjects: + - Other + - Vocabularies + uri_format: http://xmlns.com/foaf/0.1$1 +bioportal.pcalion: + bioportal: + name: Prostate Cancer Lifestyle Ontology + prefix: PCALION + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/ontologies/Prostate_cancer#$1 +bioportal.pcao: + bioportal: + name: Prostate Cancer Ontology + prefix: PCAO + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/ontologies/2018/1/ProstateCancer.owl#$1 +bioportal.pcl: + bioportal: + name: Provisional Cell Ontology + prefix: PCL + subjects: + - Cell + uri_format: https://identifiers.org/ncbigene$1 +bioportal.pcmo: + bioportal: + name: 'Pediatric Consultation and Monitoring Ontology ' + prefix: PCMO + subjects: + - Health + uri_format: http://www.semanticweb.org/com/ontologies/2015/4/untitled-ontology-44#$1 +bioportal.pco: + bioportal: + name: Population and Community Ontology + prefix: PCO + subjects: + - All Organisms + - Other + uri_format: http://purl.obolibrary.org/obo/PCO_$1 +bioportal.pdo: + bioportal: + name: Pathogenic Disease Ontology + prefix: PDO + subjects: + - Health + uri_format: http://purl.jp/bio/11/pdo/PDO_$1 +bioportal.pdo_cas: + bioportal: + name: Plant Diversity Ontology + prefix: PDO_CAS + subjects: + - Plant + uri_format: http://www.stkos-ontology/domain/plantbiodiversity#$1 +bioportal.pdon: + bioportal: + name: Parkinson's Disease Ontology + prefix: PDON + subjects: [] + uri_format: http://www.semanticweb.org/ontologies/2011/1/Ontology1296772722296.owl#$1 +bioportal.pdq: + bioportal: + name: Physician Data Query + prefix: PDQ + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/PDQ$1 +bioportal.pdro: + bioportal: + name: The Prescription of Drugs Ontology + prefix: PDRO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/OBI_$1 +bioportal.pdumdv: + bioportal: + name: Platynereis Developmental Stages + prefix: PDUMDV + subjects: [] + uri_format: http://purl.obolibrary.org/obo/PdumDv_$1 +bioportal.pe: + bioportal: + name: Pulmonary Embolism Ontology + prefix: PE + subjects: + - Health + - Biomedical Resources + - Human + - Vocabularies + uri_format: http://bmi.utah.edu/ontologies/peontology$1 +bioportal.pe-o: + bioportal: + name: Pre-eclampsia Ontology + prefix: PE-O + subjects: + - Health + - Human + uri_format: http://www.pepathway.org/peo/1.2#$1 +bioportal.peao: + bioportal: + name: Plant Experimental Assay Ontology + prefix: PEAO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/PO_$1 +bioportal.peco: + bioportal: + name: Plant Experimental Conditions Ontology + prefix: PECO + subjects: + - Experimental Conditions + - Phenotype + - Plant + uri_format: http://purl.obolibrary.org/obo/PECO_$1 +bioportal.pedterm: + bioportal: + name: Pediatric Terminology + prefix: PEDTERM + subjects: + - Health + - Human + uri_format: http://www.owl-ontologies.com/Ontology1358660052.owl#$1 +bioportal.peo: + bioportal: + name: Parasite Experiment Ontology + prefix: PEO + subjects: [] + uri_format: http://knoesis.wright.edu/ParasiteExperiment.owl#$1 +bioportal.pgxo: + bioportal: + name: PGxO + prefix: PGXO + subjects: + - Biomedical Resources + uri_format: http://pgxo.loria.fr$1 +bioportal.phage: + bioportal: + name: Phylogenetics Ontology + prefix: PHAGE + subjects: + - Upper Level Ontology + uri_format: http://purl.obolibrary.org/obo/GO_$1 +bioportal.phenx: + bioportal: + name: PhenX Phenotypic Terms + prefix: PHENX + subjects: + - Phenotype + uri_format: http://purl.bioontology.org/ontology/phenX$1 +bioportal.phfumiado: + bioportal: + name: Phallusia fumigata Anatomy and Development Ontology + prefix: PHFUMIADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/PhfumiA_$1 +bioportal.phipo: + bioportal: + name: Pathogen Host Interaction Phenotype Ontology + prefix: PHIPO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/PHIPO_$1 +bioportal.phmammado: + bioportal: + name: Phallusia mammillata Anatomy and Development Ontology + prefix: PHMAMMADO + subjects: + - Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/PhmammA_$1 +bioportal.phylont: + bioportal: + name: Phylogenetic Ontology + prefix: PHYLONT + subjects: + - Other + uri_format: http://www.co-ode.org/ontologies/ont.owl#$1 +bioportal.piero: + bioportal: + name: Enzyme Reaction Ontology for annotating Partial Information of chemical transformation + prefix: PIERO + subjects: [] + uri_format: http://reactionontology.org/piero$1 +bioportal.pino: + bioportal: + name: Pregnancy Information Needs Ontology + prefix: PINO + subjects: + - Health + uri_format: http://www.semanticweb.org/luyu/ontologies/2021/3/pregnancy_information_needs_ontology#$1 +bioportal.plana: + bioportal: + name: Planarian Anatomy and Developmental Stage Ontolgoy + prefix: PLANA + subjects: + - Anatomy + - Development + - Animal Gross Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/PLANA_$1 +bioportal.planp: + bioportal: + name: Planarian Phenotype Ontology + prefix: PLANP + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/PLANP_$1 +bioportal.plantso: + bioportal: + name: Plant Stress Ontology + prefix: PLANTSO + subjects: + - Plant + uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1 +bioportal.plio: + bioportal: + name: Protein-ligand interaction ontology + prefix: PLIO + subjects: [] + uri_format: http://www.semanticweb.org/ontologies/2010/3/Ontology1271664172453.owl#$1 +bioportal.pma: + bioportal: + name: Portfolio Management Application + prefix: PMA + subjects: + - Health + - Human + uri_format: http://www.bioontology.org/pma.owl#$1 +bioportal.pmapp-pmo: + bioportal: + name: PMO Precision Medicine Ontology + prefix: PMAPP-PMO + subjects: + - Biomedical Resources + uri_format: http://www.phoc.org.cn/pmo/class/PMO_$1 +bioportal.pmd: + bioportal: + name: Persian Medicine Diseases Ontology + prefix: PMD + subjects: + - Health + - Human + uri_format: http://www.onto-med.de/ontologies/gfo-persian-medicine-diseases.owl#$1 +bioportal.pmdo: + bioportal: + name: Parkinson and Movement Disorder Ontology + prefix: PMDO + subjects: + - Phenotype + - Neurologic Disease + - Neurological Disorder + - Human + uri_format: http://www.case.edu/PMDO#$1 +bioportal.pmo: + bioportal: + name: Performed Music Ontology + prefix: PMO + subjects: + - Upper Level Ontology + uri_format: http://performedmusicontology.org/ontology$1 +bioportal.pmo-speed: + bioportal: + name: PMO Playing Speed Vocabulary + prefix: PMO-SPEED + subjects: [] + uri_format: http://performedmusicontology.org/ontologies/vocabularies/playing_/speed$1 +bioportal.pmr: + bioportal: + name: Physical Medicine and Rehabilitation + prefix: PMR + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/PMR.owl#$1 +bioportal.pnado: + bioportal: + name: Pneumonia Diagnosis Ontology + prefix: PNADO + subjects: + - Health + - Human + uri_format: http://purl.obolibrary.org/obo/PNADO_$1 +bioportal.po: + bioportal: + name: Plant Ontology + prefix: PO + subjects: + - Plant Anatomy + - Plant + - Plant Development + uri_format: http://purl.obolibrary.org/obo/PO_$1 +bioportal.poro: + bioportal: + name: Porifera Ontology + prefix: PORO + subjects: + - Phenotype + - Anatomy + uri_format: http://purl.obolibrary.org/obo/PORO_$1 +bioportal.pp: + bioportal: + name: Pipeline Patterns Ontology + prefix: PP + subjects: + - Upper Level Ontology + uri_format: https://bitbucket.org/PlantExpAssay/ontology/raw/v0.1/PipelinePatterns.owl#$1 +bioportal.ppo: + bioportal: + name: Plant Phenology Ontology + prefix: PPO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/PPO_$1 +bioportal.pr: + bioportal: + name: Protein Ontology + prefix: PR + subjects: + - All Organisms + - Protein + uri_format: http://purl.obolibrary.org/obo/PR_$1 +bioportal.pregonto: + bioportal: + name: Pregnancy Ontology + prefix: PREGONTO + subjects: + - Biological Process + uri_format: http://www.clininf.eu/pregnancy#$1 +bioportal.premedonto: + bioportal: + name: Precision Medicine Ontology + prefix: PREMEDONTO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/NCIT_$1 +bioportal.preo: + bioportal: + name: Presence Ontology + prefix: PREO + subjects: + - Health + - Biomedical Resources + - Human + uri_format: http://presence-ontology.org/ontology$1 +bioportal.procchemical: + bioportal: + name: Chemical Process + prefix: PROCCHEMICAL + subjects: [] + uri_format: http://sweet.jpl.nasa.gov/2.3/propChemical.owl#$1 +bioportal.proj: + bioportal: + name: Project ontology + prefix: PROJ + subjects: + - Other + uri_format: http://linked.data.gov.au/def/project#$1 +bioportal.propreo: + bioportal: + name: Proteomics Data and Process Provenance Ontology + prefix: PROPREO + subjects: [] + uri_format: http://lsdis.cs.uga.edu/projects/glycomics/propreo#$1 +bioportal.provo: + bioportal: + name: Provenance Ontology + prefix: PROVO + subjects: [] + uri_format: http://www.w3.org/ns/prov#$1 +bioportal.psdo: + bioportal: + name: Performance Summary Display Ontology + prefix: PSDO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/PSDO_$1 +bioportal.psds: + bioportal: + name: Plant Structure Development Stage + prefix: PSDS + subjects: + - Plant + - Development + - Plant Development + uri_format: http://purl.obolibrary.org/obo/PO_$1 +bioportal.pseudo: + bioportal: + name: Pseudogene + prefix: pseudo + subjects: [] + uri_format: http://purl.obolibrary.org/obo/PGO_$1 +bioportal.psimod: + bioportal: + name: Protein Modification Ontology + prefix: PSIMOD + subjects: [] + uri_format: http://purl.obolibrary.org/obo/MOD_$1 +bioportal.pso: + bioportal: + name: PatientSafetyOntology + prefix: PSO + subjects: + - Health + - Vocabularies + uri_format: http://www.semanticweb.org/schra/ontologies/2017/4/PRIME_NewOntology#$1 +bioportal.pso_2: + bioportal: + name: PatientSafetyOntologyRevisted + prefix: PSO_2 + subjects: + - Health + uri_format: http://ontorion.com/PSO#$1 +bioportal.pto: + bioportal: + name: Plant Trait Ontology + prefix: PTO + subjects: + - Phenotype + - Plant + uri_format: http://purl.obolibrary.org/obo/TO_$1 +bioportal.ptrans: + bioportal: + name: Pathogen Transmission Ontology + prefix: PTRANS + subjects: + - Health + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/TRANS_$1 +bioportal.pts: + bioportal: + name: Pathway Terminology System + prefix: PTS + subjects: [] + uri_format: http://scai.fraunhofer.de/PTS#$1 +bioportal.pvonto: + bioportal: + name: Pharmacovigilance Ontology + prefix: PVONTO + subjects: [] + uri_format: http://neumore.cis.usouthal.edu/ontologies/NeuMORE-v0.1.owl#$1 +bioportal.pw: + bioportal: + name: Pathway Ontology + prefix: PW + subjects: + - Biological Process + uri_format: http://purl.obolibrary.org/obo/PW_$1 +bioportal.qudt: + bioportal: + name: Quantities, Units, Dimensions, and Types Ontology + prefix: QUDT + subjects: + - Other + uri_format: http://qudt.org/schema/qudt$1 +bioportal.qudt2: + bioportal: + name: Quantities, Units, Dimensions and Types (QUDT) Schema - Version 2.0 + prefix: QUDT2 + subjects: + - Upper Level Ontology + uri_format: http://qudt.org/schema/qudt$1 +bioportal.radlex: + bioportal: + name: Radiology Lexicon + prefix: RADLEX + subjects: [] + uri_format: http://radlex.org/RID$1 +bioportal.radxtt-mvreasons: + bioportal: + name: RADx Tiger Team Missing Value Reasons + prefix: RADXTT-MVREASONS + subjects: + - Vocabularies + uri_format: https://radx.orgx/vocs/missing-value-reason$1 +bioportal.rao: + bioportal: + name: Rheumatoid Arthritis ontology + prefix: RAO + subjects: + - Health + - Biomedical Resources + - Human + - Vocabularies + uri_format: http://bmi.utah.edu/ontologies/peontology$1 +bioportal.rb: + bioportal: + name: RegenBase ontology + prefix: RB + subjects: + - Health + uri_format: http://regenbase.org/ontology#$1 +bioportal.rbo: + bioportal: + name: Radiation Biology Ontology + prefix: RBO + subjects: + - Biological Process + uri_format: http://purl.obolibrary.org/obo/RBO_$1 +bioportal.rctont: + bioportal: + name: Randomized Controlled Trials Ontology + prefix: RCTONT + subjects: + - Biomedical Resources + uri_format: http://www.owl-ontologies.com/RCTOntology.owl#$1 +bioportal.rda-content: + bioportal: + name: RDA Content type + prefix: RDA-CONTENT + subjects: + - Other + uri_format: http://rdaregistry.info/termList/RDAContentType$1 +bioportal.rda-issuance: + bioportal: + name: RDA Mode of Issuance + prefix: RDA-ISSUANCE + subjects: + - Vocabularies + uri_format: http://www.w3.org/2004/02/skos/core#$1 +bioportal.rdfs: + bioportal: + name: The RDF Schema vocabulary + prefix: RDFS + subjects: + - Vocabularies + uri_format: http://www.w3.org/2000/01/rdf-schema#$1 +bioportal.rdl: + bioportal: + name: RDL + prefix: RDL + subjects: + - Other + uri_format: http://rds.posccaesar.org/2008/02/OWL/ISO-15926-2_2003#$1 +bioportal.rdo: + bioportal: + name: Reusable Biodiversity Ontology + prefix: RDO + subjects: [] + uri_format: http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1 +bioportal.repo: + bioportal: + name: Reproductive Trait and Phenotype Ontology + prefix: REPO + subjects: + - Phenotype + uri_format: http://purl.bioontology.org/ontology/REPO.owl#$1 +bioportal.reproduce-me: + bioportal: + name: REPRODUCE-ME + prefix: REPRODUCE-ME + subjects: [] + uri_format: https://w3id.org/reproduceme#$1 +bioportal.reto: + bioportal: + name: Regulation of Transcription Ontology + prefix: RETO + subjects: + - Biological Process + uri_format: http://identifiers.org/uniprot$1 +bioportal.rex: + bioportal: + name: Physico-Chemical Process + prefix: REX + subjects: + - Physicochemical + uri_format: http://purl.obolibrary.org/obo/REX_$1 +bioportal.rexo: + bioportal: + name: Regulation of Gene Expression Ontolology + prefix: REXO + subjects: [] + uri_format: http://identifiers.org/intact$1 +bioportal.rnao: + bioportal: + name: RNA Ontology + prefix: RNAO + subjects: + - All Organisms + uri_format: http://purl.obolibrary.org/obo/RNAO_$1 +bioportal.rnprio: + bioportal: + name: Research Network and Patient Registry Inventory Ontology + prefix: RNPRIO + subjects: + - Biomedical Resources + uri_format: http://www.semanticweb.org/ontologies/2013/1/PCORI.owl#$1 +bioportal.rnrmu: + bioportal: + name: RNRMU + prefix: RNRMU + subjects: + - Development + uri_format: http://ontology.rsmu.ru/Subject79/Module4$1 +bioportal.ro: + bioportal: + name: Radiomics Ontology + prefix: RO + subjects: + - Imaging + - Biomedical Resources + uri_format: http://www.radiomics.org/RO$1 +bioportal.roleo: + bioportal: + name: Role Ontology + prefix: ROLEO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/RoleO_$1 +bioportal.roo: + bioportal: + name: Radiation Oncology Ontology + prefix: ROO + subjects: + - Imaging + - Health + - Human + - Development + - Vocabularies + uri_format: http://www.cancerdata.org/roo$1 +bioportal.ros: + bioportal: + name: Radiation Oncology Structures Ontology + prefix: ROS + subjects: + - Imaging + - Anatomy + - Human + uri_format: urn:absolute:RadiationOncologyStructuresOntology#$1 +bioportal.rpo: + bioportal: + name: Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology + prefix: RPO + subjects: + - Immunology + - Phenotype + - Human + uri_format: http://www.semanticweb.org/ontologies/2012/5/Ontology1338526551855.owl#$1 +bioportal.rs: + bioportal: + name: Rat Strain Ontology + prefix: RS + subjects: [] + uri_format: http://purl.obolibrary.org/obo/RS_$1 +bioportal.rsa: + bioportal: + name: Reference Sequence Annotation + prefix: RSA + subjects: + - Biomedical Resources + - Genomic and Proteomic + uri_format: http://rdf.biosemantics.org/ontologies/rsa#$1 +bioportal.rvo: + bioportal: + name: Research Variable Ontology + prefix: RVO + subjects: + - Other + uri_format: http://w3id.org/rv-ontology#$1 +bioportal.rxno: + bioportal: + name: Name Reaction Ontology + prefix: RXNO + subjects: + - Chemical + uri_format: http://purl.obolibrary.org/obo/RXNO_$1 +bioportal.sao: + bioportal: + name: Subcellular Anatomy Ontology + prefix: SAO + subjects: + - Anatomy + uri_format: http://ccdb.ucsd.edu/SAO/1.2#$1 +bioportal.sarsmutonto: + bioportal: + name: Ontology of SARS-CoV2 mutations + prefix: SARSMUTONTO + subjects: + - Genomic and Proteomic + - Gene Product + uri_format: file://C/Users/Jamal/Desktop/SARSMutOnto.owl#$1 +bioportal.sbo: + bioportal: + name: Systems Biology Ontology + prefix: SBO + subjects: + - Vocabularies + uri_format: http://purl.obolibrary.org/obo/SBO_$1 +bioportal.sbol: + bioportal: + name: Synthetic Biology Open Language Visual Ontology + prefix: SBOL + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/SBOL_$1 +bioportal.scdo: + bioportal: + name: Sickle Cell Disease Ontology + prefix: SCDO + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/SCDO_$1 +bioportal.schema: + bioportal: + name: Schema.org core and all extension vocabularies + prefix: SCHEMA + subjects: + - Vocabularies + uri_format: http://schema.org$1 +bioportal.scio: + bioportal: + name: Spinal Cord Injury Ontology + prefix: SCIO + subjects: + - Experimental Conditions + - Biomedical Resources + - Neurologic Disease + - Neurological Disorder + uri_format: http://psink.de/scio$1 +bioportal.sco: + bioportal: + name: Study Cohort Ontology + prefix: SCO + subjects: + - Health + - Biomedical Resources + uri_format: http://hadatac.org/ont/hasco$1 +bioportal.sd3: + bioportal: + name: Simulation Delivery and Documentation Deviations + prefix: SD3 + subjects: + - Other + uri_format: http://www.wiser.pitt.edu/ontologies/SimulationScenarioDeviations.owl#$1 +bioportal.sdo: + bioportal: + name: Sleep Domain Ontology + prefix: SDO + subjects: + - Health + - Phenotype + - Neurologic Disease + - Neurological Disorder + - Human + uri_format: http://mimi.case.edu/ontologies/2009/1/SDO.owl#$1 +bioportal.sedi: + bioportal: + name: Semantic DICOM Ontology + prefix: SEDI + subjects: [] + uri_format: http://semantic-dicom.org/dcm#$1 +bioportal.senso: + bioportal: + name: Sensitive Data Ontology + prefix: SENSO + subjects: + - Other + - Vocabularies + uri_format: http://purl.dataone.org/odo/SENSO_$1 +bioportal.sep: + bioportal: + name: Sample Processing and Separation Techniques Ontology + prefix: SEP + subjects: [] + uri_format: http://purl.obolibrary.org/obo/sep_$1 +bioportal.sepio: + bioportal: + name: Scientific Evidence and Provenance Information Ontology + prefix: SEPIO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/SEPIO_$1 +bioportal.shr: + bioportal: + name: Student Health Record Ontology + prefix: SHR + subjects: [] + uri_format: http://www.shojaee.com/shr/shr.owl#$1 +bioportal.sibo: + bioportal: + name: Social Inset Behavior Ontology + prefix: SIBO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/SIBO_$1 +bioportal.sio: + bioportal: + name: Semanticscience Integrated Ontology + prefix: SIO + subjects: + - Yeast + - All Organisms + - 'Cellular anatomy ' + - Taxonomic Classification + - Molecule + - Biomedical Resources + - Genomic and Proteomic + - Biological Process + - Subcellular + - Phenotype + - Subcellular anatomy + - Chemical + - Cell + - Protein + - Gene Product + - Vocabularies + - Physicochemical + uri_format: http://semanticscience.org/resource/SIO_$1 +bioportal.sitbac: + bioportal: + name: Situation-Based Access Control Ontology + prefix: SITBAC + subjects: + - Other + uri_format: http://www.semanticweb.org/ontologies/2008/1/Ontology1204037102846.owl#$1 +bioportal.sk: + bioportal: + name: Digital Forensic + prefix: SK + subjects: [] + uri_format: http://www.semanticweb.org/sandeepak/digitalforensic#$1 +bioportal.smash: + bioportal: + name: SMASH Ontology + prefix: SMASH + subjects: + - Health + uri_format: http://aimlab.cs.uoregon.edu/smash/ontologies/social-activity.owl#$1 +bioportal.smo: + bioportal: + name: Syrian Movies Ontology + prefix: SMO + subjects: [] + uri_format: http://www.semanticweb.org/iyaszawde/ontologies/2022/SyrianMoviesOntology#$1 +bioportal.snmi: + bioportal: + name: Systematized Nomenclature of Medicine, International Version + prefix: SNMI + subjects: [] + uri_format: http://purl.bioontology.org/ontology/SNMI$1 +bioportal.snpo: + bioportal: + name: Single-Nucleotide Polymorphism (SNP) Ontology + prefix: SNPO + subjects: + - Genomic and Proteomic + uri_format: http://www.loria.fr/~coulet/ontology/snpontology/version1.6/snpontology_full.owl#$1 +bioportal.so: + bioportal: + name: Sequence Types and Features Ontology + prefix: SO + subjects: + - Genomic and Proteomic + uri_format: http://purl.obolibrary.org/obo/SO_$1 +bioportal.socpres: + bioportal: + name: Social Prescribing Ontology + prefix: SOCPRES + subjects: + - Other + uri_format: http://www.semanticweb.org/social-prescribing#$1 +bioportal.soho: + bioportal: + name: Social Determinants of Health Ontology + prefix: SOHO + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/navyarenjith/ontologies/2022/1/untitled-ontology-50#$1 +bioportal.sopharm: + bioportal: + name: Suggested Ontology for Pharmacogenomics + prefix: SOPHARM + subjects: + - Genomic and Proteomic + uri_format: http://www.loria.fr/~coulet/sopharm/SOPHARM_$1 +bioportal.sos: + bioportal: + name: emergência + prefix: SOS + subjects: [] + uri_format: https://purl.org/samu#$1 +bioportal.soy: + bioportal: + name: Soy Ontology + prefix: SOY + subjects: + - Plant + uri_format: http://purl.obolibrary.org/obo/SOY_$1 +bioportal.sp: + bioportal: + name: SMART Protocols + prefix: SP + subjects: + - Biological Process + uri_format: http://prismstandard.org/namespaces/basic/2.0$1 +bioportal.spd: + bioportal: + name: Spider Anatomy Ontology + prefix: SPD + subjects: + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/SPD_$1 +bioportal.spo: + bioportal: + name: Skin Physiology Ontology + prefix: SPO + subjects: + - Biological Process + uri_format: http://www.semanticweb.org/ontologies/2008/8/SPO_lightweight_merged.owl#$1 +bioportal.spto: + bioportal: + name: Solanaceae Phenotype Ontology + prefix: SPTO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/SP_$1 +bioportal.sse: + bioportal: + name: Surgical Secondary Events + prefix: SSE + subjects: + - Health + uri_format: http://www.mskcc.org/ontologies/2013/03/sae.owl#$1 +bioportal.ssn: + bioportal: + name: Semantic Sensor Network Ontology + prefix: SSN + subjects: + - Other + uri_format: http://www.w3.org/ns/ssn$1 +bioportal.sso: + bioportal: + name: Syndromic Surveillance Ontology + prefix: SSO + subjects: + - Taxonomic Classification + - Biomedical Resources + uri_format: http://surveillance.mcgill.ca/sso/syndromes.owl#$1 +bioportal.stato: + bioportal: + name: Statistics Ontology + prefix: STATO + subjects: + - Experimental Conditions + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/STATO_$1 +bioportal.stmso: + bioportal: + name: symptomatic treatment of multiple sclerosis ontology + prefix: STMSO + subjects: + - All Organisms + uri_format: http://www.semanticweb.org/lenovo/ontologies/2021/1/STMSO#$1 +bioportal.sto-draft: + bioportal: + name: The Stroke Ontology + prefix: STO-DRAFT + subjects: [] + uri_format: http://www.semanticweb.org/ontologies/STO.owl#$1 +bioportal.sty: + bioportal: + name: Semantic Types Ontology + prefix: STY + subjects: [] + uri_format: http://purl.bioontology.org/ontology/STY$1 +bioportal.suicideo: + bioportal: + name: suicideonto + prefix: suicideo + subjects: + - Other + uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1 +bioportal.surgical: + bioportal: + name: Nurse Surgical + prefix: SURGICAL + subjects: + - Health + uri_format: http://www.co-ode.org/ontologies/ont.owl#$1 +bioportal.sweet: + bioportal: + name: Semantic Web for Earth and Environment Technology Ontology + prefix: SWEET + subjects: [] + uri_format: http://sweetontology.net/propIndex$1 +bioportal.swo: + bioportal: + name: Software Ontology + prefix: SWO + subjects: + - Experimental Conditions + - Biomedical Resources + uri_format: http://www.ebi.ac.uk/swo/SWO_$1 +bioportal.symp: + bioportal: + name: Symptom Ontology + prefix: SYMP + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/SYMP_$1 +bioportal.syn: + bioportal: + name: Sage Bionetworks Synapse Ontology + prefix: SYN + subjects: [] + uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1 +bioportal.tads: + bioportal: + name: Tick Gross Anatomy Ontology + prefix: TADS + subjects: + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/TADS_$1 +bioportal.tao: + bioportal: + name: Teleost Anatomy Ontology + prefix: TAO + subjects: + - Fish Anatomy + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/TAO_$1 +bioportal.taxrank: + bioportal: + name: Taxonomic Rank Vocabulary + prefix: TAXRANK + subjects: [] + uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1 +bioportal.tcdo: + bioportal: + name: Traditional Chinese Drug Ontology + prefix: TCDO + subjects: [] + uri_format: http://OntoTCM.org.cn/ontologies/TCDO_$1 +bioportal.tco: + bioportal: + name: Thyroid Cancer Ontology + prefix: TCO + subjects: + - Health + - Human + uri_format: http://www.semanticweb.org/hx-jta/ontologies/thyroid_cancer_ontology#$1 +bioportal.tdwgspec: + bioportal: + name: TDWG Specimen LSID Ontology + prefix: TDWGSPEC + subjects: + - Taxonomic Classification + uri_format: http://rs.tdwg.org/ontology/voc/Specimen#$1 +bioportal.teddy: + bioportal: + name: Terminology for the Description of Dynamics + prefix: TEDDY + subjects: + - Other + uri_format: http://identifiers.org/teddy/TEDDY_$1 +bioportal.tempo: + bioportal: + name: TempO + prefix: TEMPO + subjects: + - Other + uri_format: http://purl.org/tempo$1 +bioportal.teo: + bioportal: + name: Time Event Ontology + prefix: TEO + subjects: + - Other + uri_format: http://informatics.mayo.edu/TEO.owl#$1 +bioportal.tephram4mexample: + bioportal: + name: Tephra M4M Example + prefix: TEPHRAM4MEXAMPLE + subjects: + - Other + uri_format: https://example.com/tephra/vocs/m4m-tephra$1 +bioportal.test-m4m20-pav: + bioportal: + name: test-m4m20-subjects-pav + prefix: TEST-M4M20-PAV + subjects: [] + uri_format: http://purl.org/m4m20/subjects$1 +bioportal.test_a: + bioportal: + name: TEST_A + prefix: TEST_A + subjects: + - Other + uri_format: https://bioportal.databiology.com/test1.owl#$1 +bioportal.test_cbi: + bioportal: + name: test_cbi + prefix: TEST_CBI + subjects: + - Vocabularies + uri_format: http://webprotege.stanford.edu$1 +bioportal.testex: + bioportal: + name: test1 + prefix: TESTEX + subjects: + - Human + uri_format: https://bioportal.databiology.com/test1.owl#$1 +bioportal.tgma: + bioportal: + name: Mosquito Gross Anatomy Ontology + prefix: TGMA + subjects: + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/TGMA_$1 +bioportal.tim: + bioportal: + name: Terra Interoperability Model + prefix: TIM + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/OBI_$1 +bioportal.time: + bioportal: + name: OWL-Time + prefix: TIME + subjects: + - Other + uri_format: http://www.w3.org/2006/time#$1 +bioportal.timebank: + bioportal: + name: Timebank Ontology + prefix: TIMEBANK + subjects: + - Other + - Human + uri_format: https://w3id.org/timebank#$1 +bioportal.tm-const: + bioportal: + name: Traditional Medicine Constitution Value Set + prefix: TM-CONST + subjects: + - Human + uri_format: http://who.int/ictm/constitution#$1 +bioportal.tm-mer: + bioportal: + name: Traditional Medicine Meridian Value Sets + prefix: TM-MER + subjects: [] + uri_format: http://who.int/ictm/meridians#$1 +bioportal.tm-other-factors: + bioportal: + name: Traditional Medicine Other Factors Value Set + prefix: TM-OTHER-FACTORS + subjects: + - Human + uri_format: http://who.int/ictm/otherFactors#$1 +bioportal.tm-signs-and-sympts: + bioportal: + name: Traditional Medicine Signs and Symptoms Value Set + prefix: TM-SIGNS-AND-SYMPTS + subjects: [] + uri_format: http://who.int/ictm/signsAndSymptoms#$1 +bioportal.tma: + bioportal: + name: Tissue Microarray Ontology + prefix: TMA + subjects: + - Experimental Conditions + - Biomedical Resources + - Other + uri_format: http://bioontology.org/ontologies/tma-minimal#$1 +bioportal.tml: + bioportal: + name: trasformative machine learning metadata + prefix: TML + subjects: + - Other + - Vocabularies + uri_format: http://www.semanticweb.org/larisa/ontologies/2020/5/untitled-ontology-33#$1 +bioportal.tmo: + bioportal: + name: Translational Medicine Ontology + prefix: TMO + subjects: + - All Organisms + - Health + uri_format: http://www.w3.org/2001/sw/hcls/ns/transmed/TMO_$1 +bioportal.tok: + bioportal: + name: Terminological and Ontological Knowledge Resources Ontology + prefix: TOK + subjects: + - Taxonomic Classification + uri_format: http://cui.unige.ch/isi/onto/tok/TOK.owl#$1 +bioportal.top-menelas: + bioportal: + name: Menelas Project Top-Level Ontology + prefix: TOP-MENELAS + subjects: [] + uri_format: http://www.limics.fr/ontologies/menelastop#$1 +bioportal.trak: + bioportal: + name: Taxonomy for Rehabilitation of Knee Conditions + prefix: TRAK + subjects: + - Biomedical Resources + uri_format: http://purl.obolibrary.org/obo/TRAK_$1 +bioportal.trans: + bioportal: + name: Nurse Transitional + prefix: TRANS + subjects: + - Health + uri_format: http://www.cablesat.com.au/research/transitional.owl#$1 +bioportal.triage: + bioportal: + name: Nurse triage + prefix: TRIAGE + subjects: + - Health + uri_format: http://www.semanticweb.org/philshields/ontologies/2015/4/untitled-ontology-59#$1 +bioportal.tron: + bioportal: + name: Tribolium Ontology + prefix: TRON + subjects: + - Anatomy + - Development + uri_format: http://purl.obolibrary.org/obo/TrOn_$1 +bioportal.tto: + bioportal: + name: Teleost Taxonomy Ontology + prefix: TTO + subjects: + - Taxonomic Classification + uri_format: http://purl.obolibrary.org/obo/TTO_$1 +bioportal.txpo: + bioportal: + name: Toxic Process Ontology + prefix: TXPO + subjects: + - Dysfunction + - Biological Process + uri_format: http://purl.obolibrary.org/obo/TXPO_$1 +bioportal.typon: + bioportal: + name: Microbial Typing Ontology + prefix: TYPON + subjects: [] + uri_format: http://purl.phyloviz.net/ontology/typon#$1 +bioportal.uganda_diseases: + bioportal: + name: Uganda_diseases + prefix: UGANDA_DISEASES + subjects: + - Vocabularies + uri_format: https://www.vodan-totafrica.info/vocs$1 +bioportal.umms: + bioportal: + name: FirstOntologyForUMMS + prefix: UMMS + subjects: [] + uri_format: https://w3id.org/umms/ekg/onto01$1 +bioportal.unitsont: + bioportal: + name: Units Ontology + prefix: UNITSONT + subjects: + - Other + uri_format: http://mimi.case.edu/ontologies/2009/1/UnitsOntology#$1 +bioportal.uo: + bioportal: + name: Units of Measurement Ontology + prefix: UO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/UO_$1 +bioportal.upa: + bioportal: + name: Unipathway + prefix: UPA + subjects: [] + uri_format: http://purl.obolibrary.org/obo/UPa_$1 +bioportal.vandf: + bioportal: + name: Veterans Health Administration National Drug File + prefix: VANDF + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/VANDF$1 +bioportal.vario: + bioportal: + name: Variation Ontology + prefix: VARIO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/VariO_$1 +bioportal.vdot: + bioportal: + name: Viral Disease Ontology Trunk + prefix: VDOT + subjects: + - Immunology + - Health + - Protein + uri_format: http://www.ifomis.org/vdot/vdot_core.owl#$1 +bioportal.veo: + bioportal: + name: Visualized Emotion Ontology + prefix: VEO + subjects: + - Other + uri_format: http://sbmi.uth.tmc.edu/ontology/VEO#$1 +bioportal.vfb_drivers: + bioportal: + name: vfb_drivers + prefix: VFB_DRIVERS + subjects: [] + uri_format: http://flybase.org/reports$1 +bioportal.vhog: + bioportal: + name: Vertebrate Homologous Organ Group Ontology + prefix: VHOG + subjects: + - Mouse Anatomy + - Fish Anatomy + - Gross Anatomy + - Human Developmental Anatomy + - Anatomy + - Human + - Animal Gross Anatomy + - Animal Development + uri_format: http://purl.obolibrary.org/obo/VHOG_$1 +bioportal.vico: + bioportal: + name: Vaccination Informed Consent Ontology + prefix: VICO + subjects: + - Immunology + - Health + uri_format: http://purl.obolibrary.org/obo/VICO_$1 +bioportal.vido: + bioportal: + name: Virus Infectious Disease Ontology + prefix: VIDO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/VIDO_$1 +bioportal.vio: + bioportal: + name: Vaccine Investigation Ontology + prefix: VIO + subjects: [] + uri_format: http://purl.obolibrary.org/obo/VO_$1 +bioportal.vivo: + bioportal: + name: VIVO Ontology for Researcher Discovery + prefix: VIVO + subjects: + - Other + uri_format: http://vivoweb.org/ontology/core#$1 +bioportal.vivo-isf: + bioportal: + name: VIVO-Integrated Semantic Framework + prefix: VIVO-ISF + subjects: + - Other + uri_format: http://www.w3.org/2006/vcard/ns#$1 +bioportal.vo: + bioportal: + name: Vaccine Ontology + prefix: VO + subjects: + - All Organisms + - Immunology + - Health + uri_format: http://purl.obolibrary.org/obo/VO_$1 +bioportal.vodana-general: + bioportal: + name: VODANATERMS + prefix: VODANA-GENERAL + subjects: + - Vocabularies + uri_format: http://www.vodan-totafrica.info/vocs/vgt$1 +bioportal.vodana-mi: + bioportal: + name: VODANA-MIGRANTS-INTERVIEWS + prefix: VODANA-MI + subjects: + - Health + - Vocabularies + uri_format: https://www.vodan-totafrica.info/vocs/miv$1 +bioportal.vodana-migrants: + bioportal: + name: VODANA MIGRANTS VOCABULARY + prefix: VODANA-MIGRANTS + subjects: + - Health + - Vocabularies + uri_format: https://www.vodan-totafrica.info/vocs/vodan-migrant-content$1 +bioportal.vodana-mpa: + bioportal: + name: VODANA-MIGRANTS-PRESS ARTICLES + prefix: VODANA-MPA + subjects: + - Health + - Vocabularies + uri_format: https://www.vodan-totafrica.info/vocs/mnv$1 +bioportal.vodanacovid: + bioportal: + name: VODANA-COVIDTERMS + prefix: VODANACOVID + subjects: + - Health + uri_format: https://github.com/mariambasajja$1 +bioportal.vodanadiseases: + bioportal: + name: VODANADiseases + prefix: VODANADISEASES + subjects: + - Vocabularies + uri_format: http://vocab.vodan-totafrica.info/vodana-terms/vdiseases$1 +bioportal.vodanakenya: + bioportal: + name: VODANA KENYA + prefix: VODANAKENYA + subjects: + - Vocabularies + uri_format: http://www.vodan-totafrica.info/vodana-terms$1 +bioportal.vodanamflcode: + bioportal: + name: VODANAFACILITIESLIST + prefix: VODANAMFLCODE + subjects: + - Vocabularies + uri_format: http://vocab.vodana.org/vmfl$1 +bioportal.vodananigeria: + bioportal: + name: VODANANIGERIA + prefix: VODANANIGERIA + subjects: + - Health + uri_format: https://github.com/mariambasajja$1 +bioportal.vodanauganda: + bioportal: + name: VODANAUGANDA + prefix: VODANAUGANDA + subjects: [] + uri_format: https://github.com/mariambasajja/vocablary1$1 +bioportal.vsao: + bioportal: + name: Vertebrate Skeletal Anatomy Ontology + prefix: VSAO + subjects: + - Fish Anatomy + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/VSAO_$1 +bioportal.vso: + bioportal: + name: Vital Sign Ontology + prefix: VSO + subjects: + - Health + uri_format: http://purl.obolibrary.org/obo/VSO_$1 +bioportal.vt: + bioportal: + name: Vertebrate Trait Ontology + prefix: VT + subjects: [] + uri_format: http://purl.obolibrary.org/obo/VT_$1 +bioportal.vto: + bioportal: + name: Vertebrate Taxonomy Ontology + prefix: VTO + subjects: + - Taxonomic Classification + uri_format: http://purl.obolibrary.org/obo/VTO_$1 +bioportal.wb-bt: + bioportal: + name: C. elegans Gross Anatomy Vocabulary + prefix: WB-BT + subjects: + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/WBbt_$1 +bioportal.wb-ls: + bioportal: + name: C. elegans Development Vocabulary + prefix: WB-LS + subjects: + - Development + - Animal Development + uri_format: http://purl.obolibrary.org/obo/WBls_$1 +bioportal.wb-phenotype: + bioportal: + name: C. elegans Phenotype Vocabulary + prefix: WB-PHENOTYPE + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/WBPhenotype_$1 +bioportal.wc: + bioportal: + name: Whole-cell modeling ontology + prefix: WC + subjects: + - Molecule + - Other + - Cell + uri_format: http://purl.obolibrary.org/obo/WC_$1 +bioportal.wear: + bioportal: + name: 'WEAR: Wind Energy mAteRials Taxonomy' + prefix: WEAR + subjects: [] + uri_format: http://purl.org/wear$1 +bioportal.weave: + bioportal: + name: 'WEAVE: Wind Energy ActiVitiEs' + prefix: WEAVE + subjects: [] + uri_format: http://purl.org/weave$1 +bioportal.wetaxtopics: + bioportal: + name: 'NEAT: wiNd Energy tAxonomy of Topics' + prefix: WETAXTOPICS + subjects: + - Taxonomic Classification + uri_format: http://purl.org/neat$1 +bioportal.who-art: + bioportal: + name: World Health Organization (WHO) Adverse Reaction Terminology + prefix: WHO-ART + subjects: + - Health + uri_format: http://purl.bioontology.org/ontology/WHO$1 +bioportal.wikipathways: + bioportal: + name: WikiPathways + prefix: WIKIPATHWAYS + subjects: + - Biological Process + - Vocabularies + uri_format: http://vocabularies.wikipathways.org/wp#$1 +bioportal.wsio: + bioportal: + name: Web-Service Interaction Ontology + prefix: WSIO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/WSIO_$1 +bioportal.xao: + bioportal: + name: Xenopus Anatomy Ontology + prefix: XAO + subjects: + - Anatomy + - Development + uri_format: http://purl.obolibrary.org/obo/XAO_$1 +bioportal.xco: + bioportal: + name: Experimental Conditions Ontology + prefix: XCO + subjects: + - Experimental Conditions + - Phenotype + uri_format: http://purl.obolibrary.org/obo/XCO_$1 +bioportal.xeo: + bioportal: + name: XEML Environment Ontology + prefix: XEO + subjects: + - Other + uri_format: http://purl.obolibrary.org/obo/XEO_$1 +bioportal.xlmod: + bioportal: + name: mass spectrometry cross-linking and derivatization reagents + prefix: XLMOD + subjects: + - Genomic and Proteomic + uri_format: http://purl.obolibrary.org/obo/XLMOD_$1 +bioportal.xpo: + bioportal: + name: Xenopus Phenotype Ontology + prefix: XPO + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/XPO_$1 +bioportal.xref-funder-reg: + bioportal: + name: CrossRef Funder Registry + prefix: XREF-FUNDER-REG + subjects: + - Other + uri_format: http://dx.doi.org/10.13039$1 +bioportal.zea: + bioportal: + name: Maize Gross Anatomy Ontology + prefix: ZEA + subjects: + - Plant Anatomy + uri_format: http://purl.obolibrary.org/obo/ZEA_$1 +bioportal.zeco: + bioportal: + name: Zebrafish Experimental Conditions Ontology + prefix: ZECO + subjects: + - Experimental Conditions + uri_format: http://purl.obolibrary.org/obo/ZECO_$1 +bioportal.zfa: + bioportal: + name: Zebrafish Anatomy and Development Ontology + prefix: ZFA + subjects: + - Fish Anatomy + - Gross Anatomy + - Anatomy + - Animal Gross Anatomy + uri_format: http://purl.obolibrary.org/obo/ZFA_$1 +bioportal.zonmw-admin-md: + bioportal: + name: ZonMW Administrative Metadata Vocabulary + prefix: ZONMW-ADMIN-MD + subjects: [] + uri_format: http://www.fair-data-collective.com/zonmw/projectadmin$1 +bioportal.zonmw-content: + bioportal: + name: ZonMW COVID-19 + prefix: ZONMW-CONTENT + subjects: [] + uri_format: http://purl.org/zonmw/covid19$1 +bioportal.zonmw-generic: + bioportal: + name: ZonMw Generic Terms + prefix: ZONMW-GENERIC + subjects: + - Other + uri_format: http://purl.org/zonmw/generic$1 +bioportal.zp: + bioportal: + name: Zebrafish Phenotype Ontology + prefix: ZP + subjects: + - Phenotype + uri_format: http://purl.obolibrary.org/obo/ZP_$1 diff --git a/fuji_server/data/linked_vocabs/bioregistry.json b/fuji_server/data/linked_vocabs/bioregistry.json deleted file mode 100644 index 7530ace6..00000000 --- a/fuji_server/data/linked_vocabs/bioregistry.json +++ /dev/null @@ -1,61916 +0,0 @@ -{ - 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}, - "n2t": { - "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.", - "example": "B00162", - "homepage": "http://www.3dmet.dna.affrc.go.jp/", - "name": "3DMET database", - "namespaceEmbeddedInLui": false, - "pattern": "^B\\d{5}$", - "prefix": "3dmet", - "uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1" - }, - "name": "3D Metabolites", - "prefixcommons": { - "description": "3DMET is a database of three-dimensional structures of natural metabolites.", - "example": "B00162", - "homepage": "http://www.3dmet.dna.affrc.go.jp", - "keywords": [ - "chemical", - "metabolite", - "structure" - ], - "miriam": "3dmet", - "name": "Three-Dimensional Structure Database of Natural Metabolites", - "pattern": "^B\\d{5}$", - "prefix": "3dmet", - "pubmed_ids": [ - "23293959", - "29892514" - ] - }, - "wikidata": { - "database": "Q23948774", - "prefix": "P2796" - } - }, - "4dn.biosource": { - "cellosaurus": { - "category": "Biological sample resources", - 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BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", - "id": "2674", - "name": "Bacterial Diversity Metadatabase", - "prefix": "FAIRsharing.aSszvY", - "subjects": [ - "Biodiversity", - "Life Science", - "Microbiology" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.aSszvY", - "miriam": "bacdive", - "n2t": "bacdive" - }, - "miriam": { - "deprecated": false, - "description": "BacDive\u2014the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.", - "homepage": "https://bacdive.dsmz.de/", - "id": "00000676", - "name": "Bacterial Diversity Metadatabase", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "bacdive", - "sampleId": "131392", - "uri_format": "https://bacdive.dsmz.de/strain/$1" - }, - "n2t": { - "description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.", - "example": "131392", - "homepage": "https://bacdive.dsmz.de/", - "name": "Bacterial Diversity Metadatabase", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "bacdive", - "uri_format": "https://bacdive.dsmz.de/strain/$1" - } - }, - "bacmap.biog": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "BACMAP.BIOG", - "uri_format": "http://identifiers.org/bacmap.biog/$1" - }, - "mappings": { - "biocontext": "BACMAP.BIOG", - "miriam": "bacmap.biog", - "n2t": "bacmap.biog" - }, - "miriam": { - "deprecated": false, - "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.", - "homepage": "http://bacmap.wishartlab.com/", - "id": "00000361", - "name": "BacMap Biography", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "bacmap.biog", - "sampleId": "1050", - "uri_format": "http://bacmap.wishartlab.com/organisms/$1" - }, - "n2t": { - "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.", - "example": "1050", - "homepage": "http://bacmap.wishartlab.com/", - "name": "BacMap Biography at University of Alberta", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "bacmap.biog", - "uri_format": "http://bacmap.wishartlab.com/organisms/$1" - } - }, - "bacmap.map": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "BACMAP.MAP", - "uri_format": "http://identifiers.org/bacmap.map/$1" - }, - "mappings": { - "biocontext": "BACMAP.MAP", - "miriam": "bacmap.map", - "n2t": "bacmap.map" - }, - "miriam": { - "deprecated": false, - "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.", - "homepage": "http://bacmap.wishartlab.com/", - "id": "00000416", - "name": "BacMap Map", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", - "prefix": "bacmap.map", - "sampleId": "AP011135", - "uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html" - }, - "n2t": { - "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.", - "example": "AP011135", - "homepage": "http://bacmap.wishartlab.com/", - "name": "BacMap Genome Map at University of Alberta", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", - "prefix": "bacmap.map", - "uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html" - } - }, - "bactibase": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.", - "example": "BAC045", - "fairsharing": { - "abbreviation": "BACTIBASE", - "description": "BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.", - "id": "1928", - "name": "Bactibase: database dedicated to bacteriocins", - "prefix": "FAIRsharing.5f5mfm", - "subjects": [ - "Life Science" - ] - }, - "homepage": "http://bactibase.hammamilab.org", - "mappings": { - "fairsharing": "FAIRsharing.5f5mfm", - "prefixcommons": "bactibase" - }, - "name": "Bactibase", - "prefixcommons": { - "description": "BACTIBASE contains calculated or predicted physicochemical properties of 177 bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.", - "example": "BAC152", - "homepage": "http://bactibase.pfba-lab-tun.org/main.php", - "keywords": [ - "protein" - ], - "name": "Bactibase: database dedicated to bacteriocins", - "pattern": "^BA\\d+$", - "prefix": "bactibase", - "uri_format": "http://bactibase.pfba-lab-tun.org/$1" - }, - "uri_format": "http://bactibase.hammamilab.org/$1" - }, - "bams": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "deprecated": true, - "description": "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.", - "homepage": "https://bams1.org", - "name": "Brain Architecture Knowledge Management System Neuroanatomical Ontology", - "references": [ - "https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full" - ] - }, - "bao": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "BAO", - "uri_format": "http://identifiers.org/bao/$1" - }, - "bioportal": { - "name": "BioAssay Ontology", - "prefix": "BAO" - }, - "fairsharing": { - "abbreviation": "BAO", - "description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.", - "id": "874", - "name": "BioAssay Ontology", - "prefix": "FAIRsharing.mye76w", - "subjects": [ - "Biochemistry", - "Life Science", - "Biomedical Science" - ] - }, - "mappings": { - "biocontext": "BAO", - "bioportal": "BAO", - "fairsharing": "FAIRsharing.mye76w", - "miriam": "bao", - "n2t": "bao", - "ols": "bao", - "ontobee": "BAO" - }, - "miriam": { - "deprecated": false, - "description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.", - "homepage": "http://bioportal.bioontology.org/ontologies/BAO/", - "id": "00000597", - "name": "BioAssay Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{7}$", - "prefix": "bao", - "sampleId": "0002989", - "uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1" - }, - "n2t": { - "description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.", - "example": "0002989", - "homepage": "http://bioportal.bioontology.org/ontologies/BAO/", - "name": "BioAssay Ontology through BioPortal", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{7}$", - "prefix": "bao", - "uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1" - }, - "ols": { - "description": "The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. 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Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.", - "download": "http://www.bioassayontology.org/bao/", - "homepage": "http://bioassayontology.org", - "name": "BioAssay Ontology", - "prefix": "bao", - "version": "2.7.2", - "version.iri": "http://www.bioassayontology.org/bao/bao_complete.owl" - }, - "ontobee": { - "library": "Not Specified/No", - "name": "BioAssay Ontology", - "prefix": "BAO" - }, - "synonyms": [ - "BAO" - ] - }, - "bbkg": { - "mappings": { - "miriam": "bbkg" - }, - "miriam": { - "deprecated": false, - "description": "Blue Brain Project's published data as knowledge graphs and Web Studios.", - "homepage": "https://portal.bluebrain.epfl.ch", - "id": "00000903", - "name": "Blue Brain Project Knowledge Graph", - "namespaceEmbeddedInLui": false, - "pattern": "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$", - "prefix": "bbkg", - "sampleId": "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", - "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/$1" - } - }, - "bbtp": { - "mappings": { - "miriam": "bbtp" - }, - "miriam": { - "deprecated": false, - "description": "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).", - "homepage": "https://portal.bluebrain.epfl.ch", - "id": "00000889", - "name": "Blue Brain Project Topological sampling Knowledge Graph", - "namespaceEmbeddedInLui": false, - "pattern": "\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b", - "prefix": "bbtp", - "sampleId": "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", - "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1" - } - }, - "bcgo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "BCGO", - "uri_format": "http://purl.obolibrary.org/obo/BCGO_$1" - }, - "bioportal": { - "name": "Breast Cancer Grading Ontology", - "prefix": "BCGO" - }, - "cellosaurus": { - "category": "Anatomy/cell type resources", - "homepage": "https://github.com/obi-bcgo/bcgo", - "name": "Beta Cell Genomics Ontology", - "prefix": "BCGO", - "uri_format": "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1" - }, - "download_owl": "https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl", - "mappings": { - "biocontext": "BCGO", - "bioportal": "BCGO", - "cellosaurus": "BCGO", - "obofoundry": "bcgo", - "ontobee": "BCGO" - }, - "obofoundry": { - "contact": "jiezheng@pennmedicine.upenn.edu", - "contact.github": "zhengj2007", - "contact.label": "Jie Zheng", - "contact.orcid": "0000-0002-2999-0103", - "deprecated": true, - "description": "An application ontology built for beta cell genomics studies.", - "download.owl": "http://purl.obolibrary.org/obo/bcgo.owl", - "homepage": "https://github.com/obi-bcgo/bcgo", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Beta Cell Genomics Ontology", - "prefix": "bcgo", - "repository": "https://github.com/obi-bcgo/bcgo" - }, - "ontobee": { - "library": "Library", - "name": "Beta Cell Genomics Ontology", - "prefix": "BCGO" - } - }, - "bcio": { - "bioportal": { - "name": "Brain-Computer Interaction (BCI) Ontology", - "prefix": "BCI-O" - }, - "download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl", - "example": "040000", - "mappings": { - "bioportal": "BCI-O", - "ols": "bcio" - }, - "ols": { - "description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.", - "download": "http://humanbehaviourchange.org/ontology/bcio.owl", - "homepage": "https://www.humanbehaviourchange.org/", - "name": "The Behaviour Change Intervention Ontology", - "prefix": "bcio", - "version.iri": "http://humanbehaviourchange.org/ontology/bcio.owl/2022-04-30" - }, - "pattern": "^\\d{6}$" - }, - "bco": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "BCO", - "uri_format": "http://purl.obolibrary.org/obo/BCO_$1" - }, - "bioportal": { - "name": "Biological Collections Ontology", - "prefix": "BCO" - }, - "example": "0000081", - "fairsharing": { - "abbreviation": "BCO", - "description": "The Biological Collections Ontology (BCO) supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of \"samples\". Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.", - "id": "1080", - "name": "Biological Collections Ontology", - "prefix": "FAIRsharing.8ktkqy", - "subjects": [ - "Metagenomics", - "Taxonomy", - "Ecology", - "Biodiversity" - ] - }, - "mappings": { - "biocontext": "BCO", - "bioportal": "BCO", - "fairsharing": "FAIRsharing.8ktkqy", - "obofoundry": "bco", - "ols": "bco", - "ontobee": "BCO" - }, - "obofoundry": { - "appears_in": [ - "fovt" - ], - "contact": "rlwalls2008@gmail.com", - "contact.github": "ramonawalls", - "contact.label": "Ramona Walls", - "contact.orcid": "0000-0001-8815-0078", - "deprecated": false, - "description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.", - "download.owl": "http://purl.obolibrary.org/obo/bco.owl", - "homepage": "https://github.com/BiodiversityOntologies/bco", - "license": "CC0 1.0", - "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", - "name": "Biological Collections Ontology", - "preferredPrefix": "BCO", - "prefix": "bco", - "repository": "https://github.com/BiodiversityOntologies/bco" - }, - "ols": { - "description": "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.", - "download": "http://purl.obolibrary.org/obo/bco.owl", - "homepage": "https://github.com/BiodiversityOntologies/bco", - "name": "Biological Collections Ontology", - "prefix": "bco", - "version": "2021-11-14", - "version.iri": "http://purl.obolibrary.org/obo/bco/releases/2021-11-14/bco.owl" - }, - "ontobee": { - "library": "Library", - "name": "Biological Collections Ontology", - "prefix": "BCO" - }, - "pattern": "^\\d{7}$" - }, - "bcrc": { - "cellosaurus": { - "category": "Cell line collections", - "homepage": "https://catalog.bcrc.firdi.org.tw/", - "name": "Taiwan Bioresource Collection and Research Center", - "prefix": "BCRC", - "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "example": "60316", - "homepage": "https://catalog.bcrc.firdi.org.tw", - "mappings": { - "cellosaurus": "BCRC" - }, - "name": "BCRC Strain Collection Catalog", - "pattern": "^\\d+$", - "uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1" - }, - "bcrj": { - "cellosaurus": { - "category": "Cell line collections", - "homepage": "http://bcrj.org.br/celula/bcrj", - "name": "Banco de Celulas do Rio de Janeiro", - "prefix": "BCRJ", - "uri_format": "http://bcrj.org.br/celula/$1" - }, - "example": "0278", - "mappings": { - "cellosaurus": "BCRJ" - }, - "pattern": "^\\d{4}$" - }, - "bdgp.est": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "BDGP.EST", - "uri_format": "http://identifiers.org/bdgp.est/$1" - }, - "has_canonical": "dbest", - "mappings": { - "biocontext": "BDGP.EST", - "miriam": "bdgp.est", - "n2t": "bdgp.est", - "ncbi": "BDGP_EST" - }, - "miriam": { - "deprecated": false, - "description": "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. 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Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", - "example": "CVCL_0030", - "homepage": "https://web.expasy.org/cellosaurus/", - "name": "Cellosaurus through SIB", - "namespaceEmbeddedInLui": false, - "pattern": "CVCL_[A-Z0-9]{4}", - "prefix": "cellosaurus", - "uri_format": "https://web.expasy.org/cellosaurus/$1" - }, - "name": "Cellosaurus", - "pattern": "^CVCL_[A-Z0-9]{4}$", - "synonyms": [ - "CVCL" - ], - "wikidata": { - "database": "Q24691710", - "database.homepage": "https://web.expasy.org/cellosaurus/", - "database.label": "Cellosaurus", - "name": "Cellosaurus ID", - "pattern": "CVCL_[A-Z\\d][A-Z\\d][A-Z\\d][A-Z\\d]", - "prefix": "P3289", - "uri_format": "https://web.expasy.org/cellosaurus/$1" - } - }, - "cellosaurus.resource": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "The set of prefixes used in the Cellosaurus resource", - "example": "4DN", - "homepage": "https://web.expasy.org/cellosaurus/", - "name": "Cellosaurus Registry", - "uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1" - }, - "cellrepo": { - "mappings": { - "miriam": "cellrepo" - }, - "miriam": { - "deprecated": false, - "description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines", - "homepage": "https://cellrepo.ico2s.org/", - "id": "00000829", - "name": "Cell Version Control Repository", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "cellrepo", - "sampleId": "82", - "uri_format": "https://cellrepo.ico2s.org/repositories/$1" - } - }, - "ceph": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "CEPH", - "uri_format": "http://purl.obolibrary.org/obo/CEPH_$1" - }, - "bioportal": { - "name": "Cephalopod Ontology", - "prefix": "CEPH" - }, - "download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo", - "example": "0000109", - "fairsharing": { - "abbreviation": "CEPH", - "description": "An anatomical and developmental ontology for cephalopods", - "id": "668", - "name": "Cephalopod Ontology", - "prefix": "FAIRsharing.p58bm4", - "subjects": [] - }, - "mappings": { - "biocontext": "CEPH", - "bioportal": "CEPH", - "fairsharing": "FAIRsharing.p58bm4", - "obofoundry": "ceph", - "ols": "ceph", - "ontobee": "CEPH" - }, - "obofoundry": { - "contact": "cjmungall@lbl.gov", - "contact.github": "cmungall", - "contact.label": "Chris Mungall", - "contact.orcid": "0000-0002-6601-2165", - "deprecated": true, - "description": "An anatomical and developmental ontology for cephalopods", - "download.obo": "http://purl.obolibrary.org/obo/ceph.obo", - "download.owl": "http://purl.obolibrary.org/obo/ceph.owl", - "homepage": "https://github.com/obophenotype/cephalopod-ontology", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Cephalopod Ontology", - "prefix": "ceph", - "repository": "https://github.com/obophenotype/cephalopod-ontology" - }, - "ols": { - "description": "An anatomical and developmental ontology for cephalopods", - "download": "http://purl.obolibrary.org/obo/ceph.owl", - "homepage": "https://github.com/obophenotype/cephalopod-ontology", - "name": "Cephalopod Ontology", - "prefix": "ceph", - "version": "2016-01-12", - "version.iri": "http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl" - }, - "ontobee": { - "library": "Library", - "name": "Cephalopod Ontology", - "prefix": "CEPH" - }, - "pattern": "^\\d{7}$" - }, - "cgd": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "CGD", - "uri_format": "http://identifiers.org/cgd/$1" - }, - "fairsharing": { - "abbreviation": "CGD", - "description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. 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Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", - "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "id": "00000596", - "name": "ClinVar Variant", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "clinvar", - "sampleId": "12345", - "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1" - }, - "n2t": { - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", - "example": "12345", - "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "name": "ClinVar Variant at NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "clinvar", - "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1" - }, - "name": "ClinVar Variation", - "wikidata": { - "database": "Q20023123", - "database.homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "database.label": "ClinVar", - "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "name": "ClinVar Variation ID", - "prefix": "P1929", - "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/variation/$1/" - } - }, - "clinvar.record": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "CLINVAR.RECORD", - "uri_format": "http://identifiers.org/clinvar.record/$1" - }, - "mappings": { - "biocontext": "CLINVAR.RECORD", - "miriam": "clinvar.record", - "n2t": "clinvar.record" - }, - "miriam": { - "deprecated": false, - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", - "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "id": "00000534", - "name": "ClinVar Record", - "namespaceEmbeddedInLui": false, - "pattern": "^RCV\\d+(\\.\\d+)?$", - "prefix": "clinvar.record", - "sampleId": "RCV000033555.3", - "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1/" - }, - "n2t": { - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", - "example": "RCV000033555.3", - "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "name": "ClinVar Record at NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^RCV\\d+(\\.\\d+)?$", - "prefix": "clinvar.record", - "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1/" - }, - "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1" - }, - "clinvar.submission": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "CLINVAR.SUBMISSION", - "uri_format": "http://identifiers.org/clinvar.submission/$1" - }, - "mappings": { - "biocontext": "CLINVAR.SUBMISSION", - "miriam": "clinvar.submission", - "n2t": "clinvar.submission" - }, - "miriam": { - "deprecated": false, - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.", - "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "id": "00000595", - "name": "ClinVar Submission", - "namespaceEmbeddedInLui": false, - "pattern": "^SCV\\d+(\\.\\d+)?$", - "prefix": "clinvar.submission", - "sampleId": "SCV000151292", - "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1" - }, - "n2t": { - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.", - "example": "SCV000151292", - "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", - "name": "ClinVar Submission at NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^SCV\\d+(\\.\\d+)?$", - "prefix": "clinvar.submission", - "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1" - } - }, - "clinvar.submitter": { - "mappings": { - "miriam": "clinvar.submitter" - }, - "miriam": { - "deprecated": false, - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).", - "homepage": "https://www.ncbi.nlm.nih.gov/clinvar/", - "id": "00000769", - "name": "ClinVar Submitter", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "clinvar.submitter", - "sampleId": "26957", - "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1" - } - }, - "clo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "CLO", - "uri_format": "http://purl.obolibrary.org/obo/CLO_$1" - }, - "bioportal": { - "name": "Cell Line Ontology", - "prefix": "CLO" - }, - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "http://www.clo-ontology.org", - "name": "Cell Line Ontology", - "prefix": "CLO", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1" - }, - "example": "0000091", - "fairsharing": { - "abbreviation": "CLO", - "description": "The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Thousands of cell lines have been artificially developed and used for different applications. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. CLO is a community-based effort to represent all cell lines in a standard ontology approach.", - "id": "1012", - "name": "Cell Line Ontology", - "prefix": "FAIRsharing.4dvtcz", - "subjects": [ - "Life Science", - "Cell Biology" - ] - }, - "mappings": { - "biocontext": "CLO", - "bioportal": "CLO", - "cellosaurus": "CLO", - "fairsharing": "FAIRsharing.4dvtcz", - "obofoundry": "clo", - "ols": "clo", - "ontobee": "CLO", - "prefixcommons": "clo" - }, - "obofoundry": { - "appears_in": [ - "mco" - ], - "contact": "siiraa@umich.edu", - "contact.github": "siiraa", - "contact.label": "Sirarat Sarntivijai", - "contact.orcid": "0000-0002-2548-641X", - "depends_on": [ - "cl", - "doid", - "ncbitaxon", - "uberon" - ], - "deprecated": false, - "description": "An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.", - "download.owl": "http://purl.obolibrary.org/obo/clo.owl", - "homepage": "http://www.clo-ontology.org", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Cell Line Ontology", - "preferredPrefix": "CLO", - "prefix": "clo", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/25852852", - "title": "CLO: The Cell Line Ontology" - } - ], - "repository": "https://github.com/CLO-Ontology/CLO" - }, - "ols": { - "description": "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.", - "download": "http://purl.obolibrary.org/obo/clo.owl", - "homepage": "http://www.clo-ontology.org", - "name": "CLO: Cell Line Ontology", - "prefix": "clo", - "version": "2.1.178" - }, - "ontobee": { - "library": "Library", - "name": "Cell Line Ontology", - "prefix": "CLO" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1314", - "description": "The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.", - "example": "CL:0000232", - "homepage": "http://sourceforge.net/projects/clo-ontology/", - "keywords": [ - "ontology" - ], - "name": "Cell Line Ontology", - "pattern": "^CL:\\d{7}$", - "prefix": "clo", - "pubmed_ids": [ - "15693950" - ] - }, - "synonyms": [ - "CLO" - ], - "wikidata": { - "prefix": "P2158" - } - }, - "cls": { - "cellosaurus": { - "category": "Cell line collections", - "homepage": "https://cls.shop/", - "name": "Cell Lines Service", - "prefix": "CLS", - "uri_format": "https://www.clsgmbh.de/$1.html" - }, - "example": "300108/p3934_A-172", - "mappings": { - "cellosaurus": "CLS" - } - }, - "clyh": { - "bioportal": { - "name": "Clytia hemisphaerica Development and Anatomy Ontology", - "prefix": "CLYH" - }, - "example": "1000100", - "mappings": { - "bioportal": "CLYH", - "obofoundry": "clyh", - "ols": "clyh", - "ontobee": "CLYH" - }, - "obofoundry": { - "contact": "lucas.leclere@obs-vlfr.fr", - "contact.github": "L-Leclere", - "contact.label": "Lucas Leclere", - "contact.orcid": "0000-0002-7440-0467", - "depends_on": [ - "iao", - "ro", - "uberon" - ], - "deprecated": false, - "description": "The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.", - "download.obo": "http://purl.obolibrary.org/obo/clyh.obo", - "download.owl": "http://purl.obolibrary.org/obo/clyh.owl", - "homepage": "https://github.com/EBISPOT/clyh_ontology", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Clytia hemisphaerica Development and Anatomy Ontology", - "preferredPrefix": "CLYH", - "prefix": "clyh", - "repository": "https://github.com/EBISPOT/clyh_ontology" - }, - "ols": { - "description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.", - "download": "https://raw.githubusercontent.com/EBISPOT/clyh_ontology/master/clyh.owl", - "name": "Clytia hemisphaerica Development and Anatomy Ontology (CLYH)", - "prefix": "clyh", - "version": "2020-05-29", - "version.iri": "http://purl.obolibrary.org/obo/clyh/releases/2020-05-29/clyh.owl" - }, - "ontobee": { - "library": "Library", - "name": "Clytia hemisphaerica Development and Anatomy Ontology", - "prefix": "CLYH" - }, - "pattern": "^\\d+$" - }, - "cmecs": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", - "example": "595", - "homepage": "https://cmecscatalog.org/cmecs", - "name": "Costal and Marine Ecological Classification Standard", - "pattern": "^\\d+$", - "references": [ - "http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf" - ], - "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" - }, - "cmf": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "CMF", - "uri_format": "http://purl.obolibrary.org/obo/CMF_$1" - }, - "deprecated": true, - "description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain", - "mappings": { - "biocontext": "CMF", - "obofoundry": "cmf", - "ontobee": "CMF" - }, - "obofoundry": { - "contact": "engelsta@ohsu.edu", - "contact.label": "Mark Engelstad", - "contact.orcid": "0000-0001-5889-4463", - "deprecated": true, - "homepage": "https://code.google.com/p/craniomaxillofacial-ontology/", - "name": "CranioMaxilloFacial ontology", - "prefix": "cmf" - }, - "ontobee": { - "library": "Library", - "name": "CranioMaxilloFacial ontology", - "prefix": "CMF" - } - }, - "cmo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "CMO", - "uri_format": "http://purl.obolibrary.org/obo/CMO_$1" - }, - "bioportal": { - "name": "Clinical Measurement Ontology", - "prefix": "CMO" - }, - "example": "0001350", - "fairsharing": { - "abbreviation": "CMO", - "description": "The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.", - "id": "885", - "name": "Clinical Measurement Ontology", - "prefix": "FAIRsharing.dq78pn", - "subjects": [ - "Life Science", - "Biomedical Science", - "Preclinical Studies" - ] - }, - "mappings": { - "biocontext": "CMO", - "bioportal": "CMO", - "fairsharing": "FAIRsharing.dq78pn", - "obofoundry": "cmo", - "ols": "cmo", - "ontobee": "CMO" - }, - "obofoundry": { - "appears_in": [ - "scdo" - ], - "contact": "jrsmith@mcw.edu", - "contact.github": "jrsjrs", - "contact.label": "Jennifer Smith", - "contact.orcid": "0000-0002-6443-9376", - "deprecated": false, - "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", - "download.obo": "http://purl.obolibrary.org/obo/cmo.obo", - "download.owl": "http://purl.obolibrary.org/obo/cmo.owl", - "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", - "license": "CC0 1.0", - "license.url": "http://creativecommons.org/publicdomain/zero/1.0/", - "name": "Clinical measurement ontology", - "preferredPrefix": "CMO", - "prefix": "cmo", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/22654893", - "title": "Three ontologies to define phenotype measurement data." - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/24103152", - "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications." - } - ], - "repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology" - }, - "ols": { - "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", - "download": "http://purl.obolibrary.org/obo/cmo.owl", - "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", - "name": "Clinical measurement ontology", - "prefix": "cmo", - "version": "2019-02-19", - "version.iri": "http://purl.obolibrary.org/obo/cmo/releases/2019-02-19/cmo.owl" - }, - "ontobee": { - "library": "Library", - "name": "Clinical measurement ontology", - "prefix": "CMO" - }, - "pattern": "^\\d{7}$" - }, - "cmpo": { - "bioportal": { - "name": "Cellular microscopy phenotype ontology", - "prefix": "CMPO" - }, - "example": "0000435", - "fairsharing": { - "abbreviation": "CMPO", - "description": "Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations", - "id": "157", - "name": "Cellular Microscopy Phenotype Ontology", - "prefix": "FAIRsharing.knp11s", - "subjects": [ - "Cell Biology" - ] - }, - "mappings": { - "bioportal": "CMPO", - "fairsharing": "FAIRsharing.knp11s", - "ols": "cmpo" - }, - "ols": { - "contact": "jupp@ebi.ac.uk", - "description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.", - "download": "http://www.ebi.ac.uk/cmpo/cmpo.owl", - "homepage": "http://www.ebi.ac.uk/cmpo", - "name": "Cellular Microscopy Phenotype Ontology", - "prefix": "cmpo", - "version": "2017-12-19", - "version.iri": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl" - }, - "pattern": "^\\d{7}$" - }, - "co_320": { - "example": "0000618", - "fairsharing": { - "abbreviation": "CO_320", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The IBP Rice Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor and IRIS DB.", - "id": "832", - "name": "Rice Ontology", - "prefix": "FAIRsharing.2jkxp5", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.2jkxp5", - "ols": "co_320" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables", - "download": "https://cropontology.org/ontology/CO_320/Rice/owl", - "homepage": "https://cropontology.org/ontology/CO_320/Rice", - "name": "Rice ontology", - "prefix": "co_320", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_320:$1" - }, - "co_321": { - "example": "0000449", - "fairsharing": { - "abbreviation": "CO_321", - "description": "This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "728", - "name": "Wheat Ontology", - "prefix": "FAIRsharing.czzmpg", - "subjects": [ - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.czzmpg", - "ols": "co_321" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "July 2018", - "download": "https://cropontology.org/ontology/CO_321/Wheat/owl", - "homepage": "https://cropontology.org/ontology/CO_321/Wheat", - "name": "Wheat ontology", - "prefix": "co_321", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_321:$1" - }, - "co_322": { - "example": "0000773", - "fairsharing": { - "abbreviation": "CO_322", - "description": "The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "925", - "name": "Maize Ontology", - "prefix": "FAIRsharing.eeyne8", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.eeyne8", - "ols": "co_322" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016", - "download": "https://cropontology.org/ontology/CO_322/Maize/owl", - "homepage": "https://cropontology.org/ontology/CO_322/Maize", - "name": "Maize ontology", - "prefix": "co_322", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_322:$1" - }, - "co_323": { - "example": "0000252", - "fairsharing": { - "abbreviation": "CO_323", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding.", - "id": "872", - "name": "Barley Ontology", - "prefix": "FAIRsharing.f69084", - "subjects": [ - "Botany", - "Agriculture" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.f69084", - "ols": "co_323" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "ICARDA - TDv5 - Sept 2018", - "download": "https://cropontology.org/ontology/CO_323/Barley/owl", - "homepage": "https://cropontology.org/ontology/CO_323/Barley", - "name": "Barley ontology", - "prefix": "co_323", - "version": "2019-11-20" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_323:$1" - }, - "co_324": { - "example": "0000111", - "fairsharing": { - "abbreviation": "CO_324", - "description": "The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "1077", - "name": "Sorghum Ontology", - "prefix": "FAIRsharing.dxx0c", - "subjects": [ - "Botany", - "Agriculture" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.dxx0c", - "ols": "co_324" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Sorghum TDv5 - Oct 2019", - "download": "https://cropontology.org/ontology/CO_324/Sorghum/owl", - "homepage": "https://cropontology.org/ontology/CO_324/Sorghum", - "name": "Sorghum ontology", - "prefix": "co_324", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_324:$1" - }, - "co_325": { - "example": "0000519", - "fairsharing": { - "abbreviation": "CO_325", - "description": "The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "642", - "name": "Banana Ontology", - "prefix": "FAIRsharing.gdszhh", - "subjects": [ - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.gdszhh", - "ols": "co_325" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019", - "download": "https://cropontology.org/ontology/CO_325/Banana/owl", - "homepage": "https://cropontology.org/ontology/CO_325/Banana", - "name": "Banana ontology", - "prefix": "co_325", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_325:$1" - }, - "co_326": { - "example": "0000254", - "mappings": { - "ols": "co_326" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Draft version", - "download": "https://cropontology.org/ontology/CO_326/Coconut/owl", - "homepage": "https://cropontology.org/ontology/CO_326/Coconut", - "name": "Coconut ontology", - "prefix": "co_326" - }, - "pattern": "^\\d{7}$" - }, - "co_327": { - "example": "0000095", - "fairsharing": { - "abbreviation": "CO_327", - "description": "The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies.", - "id": "495", - "name": "Pearl Millet Ontology", - "prefix": "FAIRsharing.4e3qh9", - "subjects": [ - "Botany", - "Agriculture" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.4e3qh9", - "ols": "co_327" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016", - "download": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl", - "homepage": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet", - "name": "Pearl millet ontology", - "prefix": "co_327" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_327:$1" - }, - "co_330": { - "example": "0000106", - "fairsharing": { - "abbreviation": "CO_330", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1307", - "name": "Potato Ontology", - "prefix": "FAIRsharing.4fa657", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.4fa657", - "ols": "co_330" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "CIP - potato ontology - december 2018", - "download": "https://cropontology.org/ontology/CO_330/Potato/owl", - "homepage": "https://cropontology.org/ontology/CO_330/Potato", - "name": "Potato ontology", - "prefix": "co_330", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_330:$1" - }, - "co_331": { - "example": "0000088", - "fairsharing": { - "abbreviation": "CO_331", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "496", - "name": "Sweet Potato Ontology", - "prefix": "FAIRsharing.4g5qcw", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.4g5qcw", - "ols": "co_331" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019", - "download": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl", - "homepage": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato", - "name": "Sweet Potato ontology", - "prefix": "co_331" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_331:$1" - }, - "co_333": { - "example": "3000045", - "fairsharing": { - "abbreviation": "CO_333", - "description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Beet Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1079", - "name": "Beet Ontology", - "prefix": "FAIRsharing.af5655", - "subjects": [ - "Botany", - "Plant Breeding", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.af5655", - "ols": "co_333" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.", - "download": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl", - "homepage": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology", - "name": "Beet Ontology ontology", - "prefix": "co_333" - }, - "pattern": "^\\d+$", - "uri_format": "https://www.cropontology.org/rdf/CO_333:$1" - }, - "co_334": { - "example": "0000070", - "fairsharing": { - "abbreviation": "CO_334", - "description": "Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive.", - "id": "1099", - "name": "IBP Cassava Trait Ontology", - "prefix": "FAIRsharing.v06c4q", - "subjects": [ - "Botany", - "Agriculture", - "Nutritional Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.v06c4q", - "ols": "co_334" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016", - "download": "https://cropontology.org/ontology/CO_334/Cassava/owl", - "homepage": "https://cropontology.org/ontology/CO_334/Cassava", - "name": "Cassava ontology", - "prefix": "co_334", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_334:$1" - }, - "co_335": { - "example": "0000189", - "fairsharing": { - "abbreviation": "CO_335", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1096", - "name": "Common Bean Ontology", - "prefix": "FAIRsharing.a14123", - "subjects": [ - "Botany", - "Agriculture" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.a14123", - "ols": "co_335" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "CIAT Common bean trait dictionary - version August 2014", - "download": "http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl", - "homepage": "http://www.cropontology.org/ontology/CO_335/Common%20Bean", - "name": "Common Bean ontology", - "prefix": "co_335" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_335:$1" - }, - "co_336": { - "example": "0000339", - "fairsharing": { - "abbreviation": "CO_336", - "description": "The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "669", - "name": "Soybean Ontology", - "prefix": "FAIRsharing.j75srj", - "subjects": [ - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.j75srj", - "ols": "co_336" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Soybean Trait Dictionary in template v5 - IITA - July 2015", - "download": "https://cropontology.org/ontology/CO_336/Soybean/owl", - "homepage": "https://cropontology.org/ontology/CO_336/Soybean", - "name": "Soybean ontology", - "prefix": "co_336" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_336:$1" - }, - "co_337": { - "example": "0000054", - "fairsharing": { - "abbreviation": "CO_337", - "description": "The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "40", - "name": "Groundnut Ontology", - "prefix": "FAIRsharing.ge8y23", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.ge8y23", - "ols": "co_337" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015", - "download": "https://cropontology.org/ontology/CO_337/Groundnut/owl", - "homepage": "https://cropontology.org/ontology/CO_337/Groundnut", - "name": "Groundnut ontology", - "prefix": "co_337", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_337:$1" - }, - "co_338": { - "example": "0000138", - "fairsharing": { - "abbreviation": "CO_338", - "description": "Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "1321", - "name": "Chickpea Ontology", - "prefix": "FAIRsharing.js20q3", - "subjects": [ - "Botany", - "Agriculture" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.js20q3", - "ols": "co_338" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015", - "download": "https://cropontology.org/ontology/CO_338/Chickpea/owl", - "homepage": "https://cropontology.org/ontology/CO_338/Chickpea", - "name": "Chickpea ontology", - "prefix": "co_338", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_338:$1" - }, - "co_339": { - "example": "0000032", - "fairsharing": { - "abbreviation": "CO_339", - "description": "The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "1352", - "name": "Lentil Ontology", - "prefix": "FAIRsharing.ry1ezg", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.ry1ezg", - "ols": "co_339" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Lentil Trait Dictionary in template v5 - ICARDA - July 2015", - "download": "https://cropontology.org/ontology/CO_339/Lentil/owl", - "homepage": "https://cropontology.org/ontology/CO_339/Lentil", - "name": "Lentil ontology", - "prefix": "co_339", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_339:$1" - }, - "co_340": { - "example": "0000639", - "fairsharing": { - "abbreviation": "CO_340", - "description": "The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information.", - "id": "1302", - "name": "IBP Cowpea Trait Ontology", - "prefix": "FAIRsharing.31apg2", - "subjects": [ - "Botany", - "Agriculture" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.31apg2", - "ols": "co_340" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Cowpea Trait Dictionary in template v5 - IITA - August 2015", - "download": "https://cropontology.org/ontology/CO_340/Cowpea/owl", - "homepage": "https://cropontology.org/ontology/CO_340/Cowpea", - "name": "Cowpea ontology", - "prefix": "co_340", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_340:$1" - }, - "co_341": { - "example": "0000140", - "fairsharing": { - "abbreviation": "CO_341", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Pigeon Pea Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1078", - "name": "Pigeon Pea Ontology", - "prefix": "FAIRsharing.ehe3yp", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.ehe3yp", - "ols": "co_341" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015", - "download": "https://cropontology.org/ontology/CO_341/Pigeonpea/owl", - "homepage": "https://cropontology.org/ontology/CO_341/Pigeonpea", - "name": "Pigeonpea ontology", - "prefix": "co_341", - "version": "2019-11-18" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_341:$1" - }, - "co_343": { - "example": "0100010", - "fairsharing": { - "abbreviation": "CO_343", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Yam Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "838", - "name": "Yam Ontology", - "prefix": "FAIRsharing.7e9cff", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.7e9cff", - "ols": "co_343" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "version 2019 - pvs", - "download": "https://cropontology.org/ontology/CO_343/Yam/owl", - "homepage": "https://cropontology.org/ontology/CO_343/Yam", - "name": "Yam ontology", - "prefix": "co_343", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_343:$1" - }, - "co_345": { - "example": "0000127", - "fairsharing": { - "abbreviation": "CO_345", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Brachiaria Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "494", - "name": "Brachiaria Ontology", - "prefix": "FAIRsharing.9e9683", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.9e9683", - "ols": "co_345" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Brachiaria (forages) ontology TD v5 - Version Oct 2016", - "download": "https://cropontology.org/ontology/CO_345/Brachiaria/owl", - "homepage": "https://cropontology.org/ontology/CO_345/Brachiaria", - "name": "Brachiaria ontology", - "prefix": "co_345", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_345:$1" - }, - "co_346": { - "example": "0000199", - "fairsharing": { - "abbreviation": "CO_346", - "description": "The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.", - "id": "1100", - "name": "Mungbean Ontology", - "prefix": "FAIRsharing.fgd5gq", - "subjects": [ - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.fgd5gq", - "ols": "co_346" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "oct 2016", - "download": "https://cropontology.org/ontology/CO_346/Mungbean/owl", - "homepage": "https://cropontology.org/ontology/CO_346/Mungbean", - "name": "Mungbean ontology", - "prefix": "co_346", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_346:$1" - }, - "co_347": { - "example": "0000108", - "fairsharing": { - "abbreviation": "CO_347", - "description": "The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data.", - "id": "1070", - "name": "Castor Bean Ontology", - "prefix": "FAIRsharing.qrrvyk", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.qrrvyk", - "ols": "co_347" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "March 2017 version ", - "download": "http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl", - "homepage": "http://www.cropontology.org/ontology/CO_347/Castor%20bean", - "name": "Castor bean ontology", - "prefix": "co_347" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_347:$1" - }, - "co_348": { - "example": "1100107", - "fairsharing": { - "abbreviation": "CO_348", - "description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1019", - "name": "Brassica Ontology", - "prefix": "FAIRsharing.af7a2d", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.af7a2d", - "ols": "co_348" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).", - "download": "https://cropontology.org/ontology/CO_348/Brassica/owl", - "homepage": "https://cropontology.org/ontology/CO_348/Brassica", - "name": "Brassica ontology", - "prefix": "co_348", - "version": "2019-11-29" - }, - "pattern": "^\\d+$", - "uri_format": "https://www.cropontology.org/rdf/CO_348:$1" - }, - "co_350": { - "example": "0000215", - "fairsharing": { - "abbreviation": "CO_350", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Oat Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. The Oat Trait Dictionary was commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/).", - "id": "652", - "name": "Oat Trait Ontology", - "prefix": "FAIRsharing.35e1c3", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.35e1c3", - "ols": "co_350" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo", - "download": "https://cropontology.org/ontology/CO_350/Oat/owl", - "homepage": "https://cropontology.org/ontology/CO_350/Oat", - "name": "Oat ontology", - "prefix": "co_350", - "version": "2019-10-09" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_350:$1" - }, - "co_356": { - "example": "4000027", - "fairsharing": { - "abbreviation": "CO_356", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1092", - "name": "Vitis Ontology", - "prefix": "FAIRsharing.c7f4d7", - "subjects": [ - "Botany", - "Agriculture", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.c7f4d7", - "ols": "co_356" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017", - "download": "https://cropontology.org/ontology/CO_356/Vitis/owl", - "homepage": "https://cropontology.org/ontology/CO_356/Vitis", - "name": "Vitis ontology", - "prefix": "co_356", - "version": "2019-11-29" - }, - "pattern": "^\\d+$", - "uri_format": "https://www.cropontology.org/rdf/CO_356:$1" - }, - "co_357": { - "example": "1000290", - "fairsharing": { - "abbreviation": "CO_357", - "description": "The Woody Plant Ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Woody Plant Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1103", - "name": "Woody Plant Ontology", - "prefix": "FAIRsharing.2b04ae", - "subjects": [ - "Botany", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.2b04ae", - "ols": "co_357" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.", - "download": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl", - "homepage": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology", - "name": "Woody Plant Ontology ontology", - "prefix": "co_357" - }, - "pattern": "^\\d+$", - "uri_format": "https://www.cropontology.org/rdf/CO_357:$1" - }, - "co_358": { - "example": "0000139", - "mappings": { - "ols": "co_358" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Cotton ontology from CottonGen database - June 2019", - "download": "https://cropontology.org/ontology/CO_358/Cotton/owl", - "homepage": "https://cropontology.org/ontology/CO_358/Cotton", - "name": "Cotton ontology", - "prefix": "co_358", - "version": "2020-01-03" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_358:$1" - }, - "co_359": { - "example": "0000947", - "mappings": { - "ols": "co_359" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "December 2019", - "download": "https://cropontology.org/ontology/CO_359/Sunflower/owl", - "homepage": "https://cropontology.org/ontology/CO_359/Sunflower", - "name": "Sunflower ontology", - "prefix": "co_359" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_359:$1" - }, - "co_360": { - "example": "0000071", - "fairsharing": { - "abbreviation": "CO_360", - "description": "Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders\u2019 trait names, measurement methods, scales and standard variables for many crops. The Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology.", - "id": "1093", - "name": "Sugar Kelp Trait Ontology", - "prefix": "FAIRsharing.1c1738", - "subjects": [ - "Botany", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.1c1738", - "ols": "co_360" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "Sugar Kelp trait ontology", - "download": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl", - "homepage": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait", - "name": "Sugar Kelp trait ontology", - "prefix": "co_360" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_360:$1" - }, - "co_365": { - "example": "0000205", - "mappings": { - "ols": "co_365" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "developed by ICARDA - Dec 2018", - "download": "https://cropontology.org/ontology/CO_365/Fababean/owl", - "homepage": "https://cropontology.org/ontology/CO_365/Fababean", - "name": "Fababean ontology", - "prefix": "co_365", - "version": "2019-10-15" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_365:$1" - }, - "co_366": { - "example": "0000072", - "mappings": { - "ols": "co_366" - }, - "ols": { - "contact": "helpdesk@cropontology-curationtool.org", - "description": "version Dec 2019", - "download": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl", - "homepage": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut", - "name": "Bambara groundnut ontology", - "prefix": "co_366" - }, - "pattern": "^\\d{7}$", - "uri_format": "https://www.cropontology.org/rdf/CO_366:$1" - }, - "cob": { - "bioportal": { - "name": "Core Ontology for Biology and Biomedicine", - "prefix": "COB" - }, - "example": "0000080", - "mappings": { - "bioportal": "COB", - "obofoundry": "cob", - "ols": "cob", - "ontobee": "COB" - }, - "obofoundry": { - "contact": "bpeters@lji.org", - "contact.github": "bpeters42", - "contact.label": "Bjoern Peters", - "contact.orcid": "0000-0002-8457-6693", - "deprecated": false, - "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", - "download.owl": "http://purl.obolibrary.org/obo/cob.owl", - "homepage": "https://github.com/OBOFoundry/COB", - "license": "CC0 1.0", - "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", - "name": "Core Ontology for Biology and Biomedicine", - "preferredPrefix": "COB", - "prefix": "cob", - "repository": "https://github.com/OBOFoundry/COB" - }, - "ols": { - "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", - "download": "http://purl.obolibrary.org/obo/cob.owl", - "homepage": "https://github.com/OBOFoundry/COB", - "name": "Core Ontology for Biology and Biomedicine", - "prefix": "cob", - "version": "2022-05-02", - "version.iri": "http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob.owl" - }, - "ontobee": { - "library": "Library", - "name": "Core Ontology for Biology and Biomedicine", - "prefix": "COB" - }, - "pattern": "^\\d{7}$" - }, - "coconut": { - "comment": "@mSorok is the dev of the resource, hope I got it right!", - "contributor": { - "github": "adafede", - "name": "Adriano Rutz", - "orcid": "0000-0003-0443-9902" - }, - "description": "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.", - "example": "CNP0171505", - "homepage": "https://coconut.naturalproducts.net", - "name": "COlleCtion of Open Natural ProdUcTs", - "pattern": "^CNP\\d{7}$", - "reviewer": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "uri_format": "https://coconut.naturalproducts.net/compound/coconut_id/$1" - }, - "codelink": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).", - "example": "GE86325", - "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt", - "name": "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray", - "pattern": "^GE\\d+$", - "references": [ - "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt", - "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt" - ] - }, - "cog": { - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "COG", - "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog-project/$1" - }, - "contact": { - "email": "cogs@ncbi.nlm.nih.gov", - "name": "Michael Y Galperin", - "orcid": "0000-0002-2265-5572" - }, - "description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.", - "example": "COG0001", - "fairsharing": { - "abbreviation": "COG", - "description": "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.", - "id": "1968", - "name": "Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes", - "prefix": "FAIRsharing.djsbw2", - "subjects": [ - "Life Science" - ] - }, - "go": { - "homepage": "http://www.ncbi.nlm.nih.gov/COG/", - "name": "NCBI COG cluster", - "prefix": "COG_Cluster", - "uri_format": "http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=$1" - }, - "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", - "mappings": { - "biolink": "COG", - "fairsharing": "FAIRsharing.djsbw2", - "go": "COG_Cluster", - "prefixcommons": "cog" - }, - "name": "Cluster of orthologous genes", - "pattern": "^COG\\d+$", - "prefixcommons": { - "description": "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.", - "example": "145262", - "homepage": "http://www.ncbi.nlm.nih.gov/COG", - "keywords": [ - "protein", - "genome" - ], - "name": "Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes", - "pattern": "^\\d+$", - "prefix": "cog", - "uri_format": "http://www.ncbi.nlm.nih.gov/COG/grace/cogenome.cgi?g=$1" - }, - "synonyms": [ - "COG_Cluster" - ], - "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1" - }, - "cog.category": { - "contact": { - "email": "cogs@ncbi.nlm.nih.gov", - "name": "Michael Y Galperin", - "orcid": "0000-0002-2265-5572" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Higher-level classifications of COG Pathways", - "example": "K", - "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", - "name": "COG Categories", - "part_of": "cog", - "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1" - }, - "cog.pathway": { - "contact": { - "email": "cogs@ncbi.nlm.nih.gov", - "name": "Michael Y Galperin", - "orcid": "0000-0002-2265-5572" - }, - "description": "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.", - "example": "NAD%20biosynthesis", - "go": { - "homepage": "http://www.ncbi.nlm.nih.gov/COG/", - "name": "NCBI COG pathway", - "prefix": "COG_Pathway", - "uri_format": "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=$1" - }, - "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways", - "mappings": { - "go": "COG_Pathway" - }, - "name": "COG Pathways", - "part_of": "cog", - "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1" - }, - "cohd": { - "comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012", - "homepage": "https://github.com/MIT-LCP/mimic-omop", - "name": "MIMIC III Database", - "no_own_terms": true, - "repository": "https://github.com/MIT-LCP/mimic-omop" - }, - "colao": { - "bioportal": { - "name": "Coleoptera Anatomy Ontology", - "prefix": "COLAO" - }, - "example": "0000000", - "mappings": { - "bioportal": "COLAO", - "obofoundry": "colao", - "ols": "colao", - "ontobee": "COLAO" - }, - "name": "Coleoptera Anatomy Ontology", - "obofoundry": { - "contact": "entiminae@gmail.com", - "contact.github": "JCGiron", - "contact.label": "Jennifer C. Giron", - "contact.orcid": "0000-0002-0851-6883", - "depends_on": [ - "aism", - "bfo", - "bspo", - "caro", - "pato", - "ro", - "uberon" - ], - "deprecated": false, - "description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone.", - "download.obo": "http://purl.obolibrary.org/obo/colao.obo", - "download.owl": "http://purl.obolibrary.org/obo/colao.owl", - "homepage": "https://github.com/insect-morphology/colao", - "license": "CC BY 4.0", - "license.url": "https://creativecommons.org/licenses/by/4.0/", - "name": "Coleoptera Anatomy Ontology (COLAO)", - "preferredPrefix": "COLAO", - "prefix": "colao", - "repository": "https://github.com/insect-morphology/colao" - }, - "ols": { - "description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.", - "download": "http://purl.obolibrary.org/obo/colao.owl", - "homepage": "https://github.com/insect-morphology/colao", - "name": "Coleoptera Anatomy Ontology", - "prefix": "colao", - "version": "2021-12-14", - "version.iri": "http://purl.obolibrary.org/obo/colao/releases/2021-12-14/colao.owl" - }, - "ontobee": { - "library": "Library", - "name": "Coleoptera Anatomy Ontology", - "prefix": "COLAO" - }, - "pattern": "^\\d{7}$" - }, - "colonatlas": { - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "http://www.coloncanceratlas.org", - "name": "Colorectal Cancer Atlas", - "prefix": "ColonAtlas", - "uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1" - }, - "example": "ALA", - "mappings": { - "cellosaurus": "ColonAtlas" - } - }, - "combine.specifications": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "COMBINE.SPECIFICATIONS", - "uri_format": "http://identifiers.org/combine.specifications/$1" - }, - "mappings": { - "biocontext": "COMBINE.SPECIFICATIONS", - "miriam": "combine.specifications", - "n2t": "combine.specifications" - }, - "miriam": { - "deprecated": false, - "description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.", - "homepage": "https://co.mbine.org/standards/", - "id": "00000258", - "name": "COMBINE specifications", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+(\\-|\\.|\\w)*$", - "prefix": "combine.specifications", - "sampleId": "sbgn.er.level-1.version-1.2", - "uri_format": "https://co.mbine.org/specifications/$1" - }, - "n2t": { - "description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.", - "example": "sbgn.er.level-1.version-1.2", - "homepage": "https://co.mbine.org/standards/", - "name": "COMBINE at EBI", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+(\\-|\\.|\\w)*$", - "prefix": "combine.specifications", - "uri_format": "https://co.mbine.org/specifications/$1" - } - }, - "come": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.", - "example": "MOL000160", - "homepage": "https://www.flymine.org/come", - "mappings": { - "prefixcommons": "come" - }, - "name": "The Bioinorganic Motif Database", - "prefixcommons": { - "description": "COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif.", - "example": "BIM000347", - "homepage": "http://www.flymine.org/come/", - "keywords": [ - "protein" - ], - "name": "COMe", - "pattern": "^BIM\\d+$", - "prefix": "come", - "uri_format": "http://www.flymine.org/come/entry?gn=$1" - }, - "uri_format": "https://www.flymine.org/come/entry?gn=$1" - }, - "complexportal": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "COMPLEXPORTAL", - "uri_format": "http://identifiers.org/complexportal/$1" - }, - "example": "CPX-263", - "go": { - "homepage": "https://www.ebi.ac.uk/complexportal", - "name": "Complex Portal database of macromolecular complexes", - "prefix": "ComplexPortal", - "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" - }, - "mappings": { - "biocontext": "COMPLEXPORTAL", - "go": "ComplexPortal", - "miriam": "complexportal", - "n2t": "complexportal", - "uniprot": "ComplexPortal", - "wikidata": "P7718" - }, - "miriam": { - "deprecated": false, - "description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.", - "homepage": "https://www.ebi.ac.uk/complexportal", - "id": "00000657", - "name": "Complex Portal", - "namespaceEmbeddedInLui": false, - "pattern": "^CPX-[0-9]+$", - "prefix": "complexportal", - "sampleId": "CPX-2158", - "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" - }, - "n2t": { - "description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.", - "example": "CPX-2158", - "homepage": "https://www.ebi.ac.uk/complexportal", - "name": "Complex Portal", - "namespaceEmbeddedInLui": false, - "pattern": "^CPX-[0-9]+$", - "prefix": "complexportal", - "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" - }, - "name": "Complex Portal", - "synonyms": [ - "ComplexPortal" - ], - "uniprot": { - "category": "Protein-protein interaction databases", - "identifier": "228", - "link_is_explicit": "true", - "name": "ComplexPortal: manually curated resource of macromolecular complexes", - "prefix": "ComplexPortal", - "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" - }, - "wikidata": { - "database": "Q47196990", - "database.homepage": "https://www.ebi.ac.uk/complexportal/home", - "database.label": "Complex Portal", - "homepage": "https://www.ebi.ac.uk/complexportal/home", - "name": "Complex Portal accession ID", - "pattern": "^CPX-[0-9]+$", - "prefix": "P7718", - "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" - } - }, - "comptox": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "COMPTOX", - "uri_format": "http://identifiers.org/comptox/$1" - }, - "mappings": { - "biocontext": "COMPTOX", - "miriam": "comptox", - "n2t": "comptox" - }, - "miriam": { - "deprecated": false, - "description": "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. 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Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.", - "example": "ECMDB00005", - "homepage": "https://ecmdb.ca", - "name": "E. coli Metabolite Database", - "pattern": "^ECMDB\\d+$", - "synonyms": [ - "ECMDB" - ], - "uri_format": "http://ecmdb.ca/compounds/$1", - "wikidata": { - "database": "Q17052437" - } - }, - "eco": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "ECO", - "uri_format": "http://purl.obolibrary.org/obo/ECO_$1" - }, - "bioportal": { - "name": "Evidence and Conclusion Ontology", - "prefix": "ECO" - }, - "example": "0007807", - "fairsharing": { - "abbreviation": "ECO", - "description": "The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). 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This allows inference of a 'level of support' between an entity and an annotation made to an entity.", - "example": "ECO:0000006", - "keywords": [ - "obo", - "ontology" - ], - "name": "Evidence Code Ontology", - "pattern": "^ECO:\\d{7}$", - "prefix": "eco", - "uri_format": "http://www.ebi.ac.uk/ontology-lookup/?termId=$1" - } - }, - "ecocore": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "ECOCORE", - "uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1" - }, - "bioportal": { - "name": "An ontology of core ecological entities", - "prefix": "ECOCORE" - }, - "example": "00000001", - "mappings": { - "biocontext": "ECOCORE", - "bioportal": "ECOCORE", - "obofoundry": "ecocore", - "ols": "ecocore", - "ontobee": "ECOCORE" - }, - "obofoundry": { - "contact": "p.buttigieg@gmail.com", - "contact.github": "pbuttigieg", - "contact.label": "Pier Luigi Buttigieg", - "contact.orcid": "0000-0002-4366-3088", - "depends_on": [ - "bfo", - "chebi", - "envo", - "go", - "iao", - "pato", - "pco", - "po", - "ro", - "uberon" - ], - "deprecated": false, - "description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.", - "download.obo": "http://purl.obolibrary.org/obo/ecocore.obo", - "download.owl": "http://purl.obolibrary.org/obo/ecocore.owl", - "homepage": "https://github.com/EcologicalSemantics/ecocore", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "An ontology of core ecological entities", - "preferredPrefix": "ECOCORE", - "prefix": "ecocore", - "repository": "https://github.com/EcologicalSemantics/ecocore" - }, - "ols": { - "description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.", - "download": "http://purl.obolibrary.org/obo/ecocore.owl", - "homepage": "https://github.com/EcologicalSemantics/ecocore", - "name": "An ontology of core ecological entities", - "prefix": "ecocore", - "version": "2022-03-09", - "version.iri": "http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl" - }, - "ontobee": { - "library": "Library", - "name": "An ontology of core ecological entities", - "prefix": "ECOCORE" - }, - "pattern": "^\\d+$" - }, - "ecocyc": { - "description": "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. 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The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc.", - "id": "2054", - "name": "EcoCyc E. coli Database", - "prefix": "FAIRsharing.65dmtr", - "subjects": [ - "Biology" - ] - }, - "go": { - "homepage": "http://ecocyc.org/", - "name": "Encyclopedia of E. coli metabolism", - "prefix": "EcoCyc", - "uri_format": "http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=$1" - }, - "mappings": { - "fairsharing": "FAIRsharing.65dmtr", - "go": "EcoCyc", - "ncbi": "ECOCYC" - }, - "name": "EcoCyc", - "ncbi": { - "example": "sroC", - "homepage": "https://ecocyc.org/", - "name": "E. coli database", - "prefix": "ECOCYC" - }, - "uri_format": "https://biocyc.org/gene?id=$1" - }, - "ecogene": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "EcoGene", - "uri_format": "http://ecogene.org/gene/$1" - }, - "fairsharing": { - "abbreviation": "EcoGene", - "description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. 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The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).", - "download.json": "http://purl.obolibrary.org/obo/ecto.json", - "download.obo": "http://purl.obolibrary.org/obo/ecto.obo", - "download.owl": "http://purl.obolibrary.org/obo/ecto.owl", - "homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", - "license": "CC0 1.0", - "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", - "name": "Environmental conditions, treatments and exposures ontology", - "preferredPrefix": "ECTO", - "prefix": "ecto", - "repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology" - }, - "ols": { - "description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. 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It allows models to be represented at different levels of abstraction \u2014 as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.", - "homepage": "http://www.e-cyanobacterium.org/bcs/entity/", - "id": "00000585", - "name": "E-cyanobacterium entity", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "ecyano.entity", - "sampleId": "23", - "uri_format": "http://e-cyanobacterium.org/bcs/entity/$1/" - }, - "n2t": { - "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. 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This collection references models.", - "example": "26", - "homepage": "http://e-cyanobacterium.org/models/", - "name": "e-cyanobacterium entity at Masaryk University Brno", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "ecyano.model", - "uri_format": "http://e-cyanobacterium.org/models/model/$1/" - }, - "uri_format": "https://e-cyanobacterium.org/models/model/$1" - }, - "ecyano.rule": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "ECYANO.RULE", - "uri_format": "http://identifiers.org/ecyano.rule/$1" - }, - "mappings": { - "biocontext": "ECYANO.RULE", - "miriam": "ecyano.rule", - "n2t": "ecyano.rule" - }, - "miriam": { - "deprecated": false, - "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. 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EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", - "homepage": "http://bioportal.bioontology.org/ontologies/EDAM", - "id": "00000189", - "name": "EDAM Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^(data|topic|operation|format)\\_\\d{4}$", - "prefix": "edam", - "sampleId": "data_1664", - "uri_format": "http://purl.bioontology.org/ontology/EDAM/$1" - }, - "n2t": { - "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", - "example": "data_1664", - "homepage": "http://bioportal.bioontology.org/ontologies/EDAM", - "name": "EDAM through BioPortal", - "namespaceEmbeddedInLui": false, - "pattern": "^(data|topic|operation|format)\\_\\d{4}$", - "prefix": "edam", - "uri_format": "http://purl.bioontology.org/ontology/EDAM/$1" - }, - "ols": { - "contact": "edam@elixir-dk.org", - "description": "EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use.", - "download": "https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl", - "homepage": "http://edamontology.org", - "name": "Bioinformatics operations, data types, formats, identifiers and topics", - "prefix": "edam", - "version": "2019-07-17" - }, - "ontobee": { - "library": "Not Specified/No", - "name": "EMBRACE Data and Methods", - "prefix": "EDAM" - }, - "prefixcommons": { - "bioportal": "1498", - "description": "EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.", - "example": "EDAM_data:1664", - "homepage": "https://sourceforge.net/projects/edamontology/", - "keywords": [ - "obo", - "ontology" - ], - "name": "Bioinformatics operations, types of data, data formats and topics", - "pattern": "^EDAM_(data|topic)\\:\\d{4}$", - "prefix": "edam", - "uri_format": "http://www.ebi.ac.uk/ontology-lookup/?termId=$1" - }, - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1" - }, - "edda": { - "bioportal": { - "name": "EDDA Study Designs Taxonomy", - "prefix": "EDDA" - }, - "description": "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.", - "example": "health_care_quality_assessment", - "fairsharing": { - "abbreviation": "EDDA", - "description": "Terminology of study designs and publication types (beta version). Developed by the Evidence in Documents, Discovery, and Analysis (EDDA) Group. Tanja Bekhuis (PI); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist). Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pennsylvania, US. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Based on research described in Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. The terminology appearing in JMLA has been enriched with terms from MeSH, NCI Thesaurus (NCIT), and Emtree, the controlled vocabularies for MEDLINE, the National Cancer Institute, and Embase, respectively, as well as from published research literature. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and medical dictionaries. A class for Publication Type is included because investigators consider type and design when screening reports for inclusion in comparative effectiveness research. EDDA Study Designs and Publications by Tanja Bekhuis is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.", - "id": "1289", - "name": "EDDA Study Designs Taxonomy", - "prefix": "FAIRsharing.2ffmsb", - "subjects": [] - }, - "homepage": "https://bioportal.bioontology.org/ontologies/EDDA", - "mappings": { - "bioportal": "EDDA", - "fairsharing": "FAIRsharing.2ffmsb" - } - }, - "efo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "EFO", - "uri_format": "http://purl.obolibrary.org/obo/EFO_$1" - }, - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "EFO", - "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1" - }, - "bioportal": { - "name": "Experimental Factor Ontology", - "prefix": "EFO" - }, - "cellosaurus": { - "category": "Experimental variables resources", - "homepage": "https://www.ebi.ac.uk/efo/", - "name": "Experimental Factor Ontology", - "prefix": "EFO", - "uri_format": "https://www.ebi.ac.uk/efo/$1" - }, - "contact": { - "email": "plwhetzel@gmail.com", - "github": "twhetzel", - "name": "Trish Whetzel", - "orcid": "0000-0002-3458-4839" - }, - "download_obo": "http://www.ebi.ac.uk/efo/efo.obo", - "example": "0005147", - "fairsharing": { - "abbreviation": "EFO", - "description": "The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and the Centre for Therapeutic Target Validation. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype.", - "id": "1498", - "name": "Experimental Factor Ontology", - "prefix": "FAIRsharing.1gr4tz", - "subjects": [ - "Functional Genomics" - ] - }, - "mappings": { - "biocontext": "EFO", - "biolink": "EFO", - "bioportal": "EFO", - "cellosaurus": "EFO", - "fairsharing": "FAIRsharing.1gr4tz", - "miriam": "efo", - "n2t": "efo", - "ols": "efo", - "ontobee": "EFO" - }, - "miriam": { - "deprecated": false, - "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/efo", - "id": "00000391", - "name": "Experimental Factor Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{7}$", - "prefix": "efo", - "providers": [ - { - "code": "ebi", - "description": "EFO through Functional Genomics Group (EBI)", - "homepage": "https://www.ebi.ac.uk/efo/", - "name": "EFO through Functional Genomics Group (EBI)", - "uri_format": "https://www.ebi.ac.uk/efo/EFO_$1" - } - ], - "sampleId": "0004859", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=EFO:$1" - }, - "n2t": { - "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", - "example": "0004859", - "homepage": "http://bioportal.bioontology.org/ontologies/EFO", - "name": "EFO through BioPortal", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{7}$", - "prefix": "efo", - "uri_format": "http://purl.bioontology.org/ontology/EFO/efo:EFO_$1" - }, - "ols": { - "contact": "efo-users@lists.sourceforge.net", - "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org", - "download": "http://www.ebi.ac.uk/efo/efo.owl", - "homepage": "http://www.ebi.ac.uk/efo", - "name": "Experimental Factor Ontology", - "prefix": "efo", - "version": "3.42.0", - "version.iri": "http://www.ebi.ac.uk/efo/releases/v3.42.0/efo.owl" - }, - "ontobee": { - "library": "Not Specified/No", - "name": "Experimental Factor Ontology", - "prefix": "EFO" - }, - "preferred_prefix": "EFO", - "repository": "https://github.com/EBISPOT/efo/", - "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1" - }, - "ega.dataset": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "EGA.DATASET", - "uri_format": "http://identifiers.org/ega.dataset/$1" - }, - "fairsharing": { - "abbreviation": "EGA", - "description": "The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. Access to data must be approved by the specified Data Access Committee (DAC).", - "id": "1865", - "name": "The European Genome-phenome Archive", - "prefix": "FAIRsharing.mya1ff", - "subjects": [ - "Genomics", - "Phenomics", - "Biomedical Science", - "Biology" - ] - }, - "homepage": "https://ega-archive.org/", - "mappings": { - "biocontext": "EGA.DATASET", - "fairsharing": "FAIRsharing.mya1ff", - "miriam": "ega.dataset", - "n2t": "ega.dataset" - }, - "miriam": { - "deprecated": false, - "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", - "homepage": "https://www.ebi.ac.uk/ega/dataset", - "id": "00000512", - "name": "European Genome-phenome Archive Dataset", - "namespaceEmbeddedInLui": false, - "pattern": "^EGAD\\d{11}$", - "prefix": "ega.dataset", - "providers": [ - { - "code": "omicsdi", - "description": "EGA Dataset through OmicsDI", - "homepage": "https://www.omicsdi.org/", - "name": "EGA Dataset through OmicsDI", - "uri_format": "https://www.omicsdi.org/dataset/ega/$1" - } - ], - "sampleId": "EGAD00000000001", - "uri_format": "https://www.ebi.ac.uk/ega/datasets/$1" - }, - "n2t": { - "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", - "example": "EGAD00000000001", - "homepage": "https://www.ebi.ac.uk/ega/dataset", - "name": "EGA Dataset at European Bioinformatics Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^EGAD\\d{11}$", - "prefix": "ega.dataset", - "uri_format": "https://www.ebi.ac.uk/ega/datasets/$1" - } - }, - "ega.study": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "EGA.STUDY", - "uri_format": "http://identifiers.org/ega.study/$1" - }, - "mappings": { - "biocontext": "EGA.STUDY", - "miriam": "ega.study", - "n2t": "ega.study" - }, - "miriam": { - "deprecated": false, - "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", - "homepage": "https://www.ebi.ac.uk/ega/studies", - "id": "00000511", - "name": "European Genome-phenome Archive Study", - "namespaceEmbeddedInLui": false, - "pattern": "^EGAS\\d{11}$", - "prefix": "ega.study", - "providers": [ - { - "code": "omicsdi", - "description": "EGA Study through OmicsDI", - "homepage": "https://www.omicsdi.org/", - "name": "EGA Study through OmicsDI", - "uri_format": "https://www.omicsdi.org/dataset/ega/$1" - } - ], - "sampleId": "EGAS00000000001", - "uri_format": "https://www.ebi.ac.uk/ega/studies/$1" - }, - "n2t": { - "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", - "example": "EGAS00000000001", - "homepage": "https://www.ebi.ac.uk/ega/studies", - "name": "EGA Study at European Bioinformatics Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^EGAS\\d{11}$", - "prefix": "ega.study", - "uri_format": "https://www.ebi.ac.uk/ega/studies/$1" - } - }, - "eggnog": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "EGGNOG", - "uri_format": "http://identifiers.org/eggnog/$1" - }, - "fairsharing": { - "abbreviation": "eggNOG", - "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", - "id": "1577", - "name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups", - "prefix": "FAIRsharing.j1wj7d", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "EGGNOG", - "fairsharing": "FAIRsharing.j1wj7d", - "miriam": "eggnog", - "n2t": "eggnog", - "prefixcommons": "eggnog", - "uniprot": "eggNOG" - }, - "miriam": { - "deprecated": false, - "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", - "homepage": "http://eggnog.embl.de/version_3.0/", - "id": "00000201", - "name": "eggNOG", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "eggnog", - "sampleId": "veNOG12876", - "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1" - }, - "n2t": { - "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", - "example": "veNOG12876", - "homepage": "http://eggnog.embl.de/version_3.0/", - "name": "eggNOG Version 3 at European Molecular Biology Laboratory", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "eggnog", - "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1" - }, - "prefixcommons": { - "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", - "example": "NOG80852", - "homepage": "http://eggnog.embl.de", - "keywords": [ - "gene" - ], - "name": "Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups", - "pattern": "^\\w+$", - "prefix": "eggnog", - "pubmed_ids": [ - "19900971" - ], - "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1" - }, - "uniprot": { - "category": "Phylogenomic databases", - "identifier": "152", - "link_is_explicit": "true", - "name": "evolutionary genealogy of genes: Non-supervised Orthologous Groups", - "prefix": "eggNOG", - "uri_format": "http://eggnogdb.embl.de/#/app/results?seqid=%u&target_nogs=%s" - } - }, - "ehda": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "EHDA", - "uri_format": "http://purl.obolibrary.org/obo/EHDA_$1" - }, - "bioportal": { - "name": "Human Developmental Anatomy Ontology, timed version", - "prefix": "EHDA" - }, - "example": "1", - "mappings": { - "biocontext": "EHDA", - "bioportal": "EHDA", - "obofoundry": "ehda", - "prefixcommons": "ehda" - }, - "obofoundry": { - "contact": "J.Bard@ed.ac.uk", - "contact.label": "Jonathan Bard", - "deprecated": true, - "homepage": "http://genex.hgu.mrc.ac.uk/", - "name": "Human developmental anatomy, timed version", - "prefix": "ehda" - }, - "pattern": "^\\d+$", - "prefixcommons": { - "bioportal": "1022", - "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20).", - "example": "EHDAA_1", - "homepage": "http://genex.hgu.mrc.ac.uk/", - "keywords": [ - "obo", - "anatomy", - "development", - "human" - ], - "name": "Human developmental anatomy, timed version", - "pattern": "^EHDA_\\d+$", - "prefix": "ehda" - } - }, - "ehdaa": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "EHDAA", - "uri_format": "http://purl.obolibrary.org/obo/EHDAA_$1" - }, - "bioportal": { - "name": "Human Developmental Anatomy Ontology, abstract version 1", - "prefix": "EHDAA" - }, - "example": "1", - "mappings": { - "biocontext": "EHDAA", - "bioportal": "EHDAA", - "obofoundry": "ehdaa", - "prefixcommons": "ehdaa" - }, - "obofoundry": { - "contact": "J.Bard@ed.ac.uk", - "contact.label": "Jonathan Bard", - "deprecated": true, - "name": "Human developmental anatomy, abstract version", - "prefix": "ehdaa" - }, - "pattern": "^\\d+$", - "prefixcommons": { - "bioportal": "1021", - "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20).", - "example": "EHDAA_573", - "homepage": "http://genex.hgu.mrc.ac.uk/", - "keywords": [ - "obo", - "anatomy", - "development", - "human" - ], - "name": "Human developmental anatomy, abstract version", - "pattern": "^EHDAA_\\d+$", - "prefix": "ehdaa" - } - }, - "ehdaa2": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "EHDAA2", - "uri_format": "http://purl.obolibrary.org/obo/EHDAA2_$1" - }, - "bioportal": { - "name": "Human Developmental Anatomy Ontology, abstract version 2", - "prefix": "EHDAA2" - }, - "example": "0000000", - "fairsharing": { - "abbreviation": "EHDAA2", - "description": "The EHDAA2 ontology is a human developmental anatomy covering the first 49 days [Carnegie stages (CS)1\u201320], primarily structured around the parts of organ systems and their development. The ontology includes more than 2000 anatomical entities (AEs) that range from the whole embryo, through organ systems and organ parts down to simple or leaf tissues (groups of cells with the same morphological phenotype), as well as features such as cavities. It represents a complete rebuilding of the EHDA intended to meet current standards. The intention has been to include as much information about human developmental anatomy as is practical and as is available in the literature.", - "id": "199", - "name": "Edinburgh human developmental anatomy abstract version 2", - "prefix": "FAIRsharing.7zxrs6", - "subjects": [ - "Anatomy", - "Life Science", - "Biomedical Science" - ] - }, - "mappings": { - "biocontext": "EHDAA2", - "bioportal": "EHDAA2", - "fairsharing": "FAIRsharing.7zxrs6", - "obofoundry": "ehdaa2", - "ols": "ehdaa2", - "ontobee": "EHDAA2" - }, - "obofoundry": { - "contact": "J.Bard@ed.ac.uk", - "contact.label": "Jonathan Bard", - "depends_on": [ - "aeo", - "caro", - "cl" - ], - "deprecated": true, - "description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.", - "download.obo": "http://purl.obolibrary.org/obo/ehdaa2.obo", - "download.owl": "http://purl.obolibrary.org/obo/ehdaa2.owl", - "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology", - "license": "CC BY 4.0", - "license.url": "https://creativecommons.org/licenses/by/4.0/", - "name": "Human developmental anatomy, abstract", - "prefix": "ehdaa2", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/22973865", - "title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)." - } - ], - "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology" - }, - "ols": { - "description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.", - "download": "http://purl.obolibrary.org/obo/ehdaa2.owl", - "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology", - "name": "Human developmental anatomy, abstract", - "prefix": "ehdaa2", - "version": "2013-07-04", - "version.iri": "http://purl.obolibrary.org/obo/ehdaa2/releases/2013-07-04/ehdaa2.owl" - }, - "ontobee": { - "library": "Library", - "name": "Human developmental anatomy, abstract", - "prefix": "EHDAA2" - }, - "pattern": "^\\d{7}$", - "synonyms": [ - "EHDAA2_RETIRED", - "HDAA2", - "RETIRED_EHDAA2" - ] - }, - "elm": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "ELM", - "uri_format": "http://identifiers.org/elm/$1" - }, - "fairsharing": { - "abbreviation": "ELM", - "description": "This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. 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It provides access to individual reconstructed HERV elements, their sequence, structure and features.", - "example": "THE1B", - "homepage": "https://herv.img.cas.cz/", - "name": "Human Endogenous Retrovirus Database", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9\\-\\_]+$", - "prefix": "erv", - "uri_format": "https://herv.img.cas.cz/s/$1" - } - }, - "estdab": { - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "https://www.ebi.ac.uk/ipd/estdab/", - "name": "European Searchable Tumour Line Database", - "prefix": "ESTDAB", - "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1" - }, - "comment": "Website is dead", - "deprecated": true, - "example": "046", - "mappings": { - "cellosaurus": "ESTDAB" - }, - "pattern": "^\\d{3}$", - "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1" - }, - "eu89h": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "EU89H", - "uri_format": "http://identifiers.org/eu89h/$1" - }, - "mappings": { - "biocontext": "EU89H", - "miriam": "eu89h", - "n2t": "eu89h" - }, - "miriam": { - "deprecated": false, - "description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.", - "homepage": "http://data.jrc.ec.europa.eu/", - "id": "00000644", - "name": "JRC Data Catalogue", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9\\-_]+$", - "prefix": "eu89h", - "sampleId": "jrc-eurl-ecvam-chemagora", - "uri_format": "http://data.europa.eu/89h/$1" - }, - "n2t": { - "description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.", - "example": "jrc-eurl-ecvam-chemagora", - "homepage": "http://data.jrc.ec.europa.eu/", - "name": "JRC Data Catalogue", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9\\-_]+$", - "prefix": "eu89h", - "uri_format": "http://data.europa.eu/89h/$1" - } - }, - "euclinicaltrials": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "EUCLINICALTRIALS", - "uri_format": "http://identifiers.org/euclinicaltrials/$1" - }, - "mappings": { - "biocontext": "EUCLINICALTRIALS", - "miriam": "euclinicaltrials", - "n2t": "euclinicaltrials" - }, - "miriam": { - "deprecated": false, - "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", - "homepage": "https://www.clinicaltrialsregister.eu/", - "id": "00000536", - "name": "EU Clinical Trials", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", - "prefix": "euclinicaltrials", - "sampleId": "2008-005144-16", - "uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1" - }, - "n2t": { - "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. 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One of the missions of this consortium is to facilitate cooperation and collaboration between projects.", - "example": "FB00000917", - "homepage": "https://www.facebase.org", - "name": "FaceBase Data Repository", - "namespaceEmbeddedInLui": false, - "pattern": "^FB\\d{8}$", - "prefix": "facebase", - "uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1" - } - }, - "fairsharing": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "FAIRSHARING", - "uri_format": "http://identifiers.org/fairsharing/$1" - }, - "fairsharing": { - "abbreviation": "FAIRsharing", - "description": "FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in FAIRsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the FAIRsharing registry is accurate and timely. Every record is manually reviewed at least once a year. 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FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned \u201comics\u201d areas. 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}, - "ols": { - "description": "A structured controlled vocabulary for the anatomy of fungi.", - "download": "http://purl.obolibrary.org/obo/fao.owl", - "homepage": "https://github.com/obophenotype/fungal-anatomy-ontology/", - "name": "Fungal gross anatomy", - "prefix": "fao", - "version": "2020-05-07", - "version.iri": "http://purl.obolibrary.org/obo/fao/releases/2020-05-07/fao.owl" - }, - "ontobee": { - "library": "Library", - "name": "Fungal gross anatomy", - "prefix": "FAO" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1019", - "description": "The project aims to develop a controlled vocabulary to describe the 'anatomy' of fungi and other microbes, called the fungal anatomy ontology (FAO).", - "example": "FAO_0000001", - "homepage": "http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/", - "keywords": [ - "obo", - "anatomy", - "fungi" - ], - "name": "Fungal Anatomy Ontology", - "pattern": "^FAO_\\d+$", - "prefix": "fao" - } - }, - "fbbi": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "FBbi", - "uri_format": "http://purl.obolibrary.org/obo/FBbi_$1" - }, - "bioportal": { - "name": "Biological Imaging Methods Ontology", - "prefix": "FBbi" - }, - "example": "00000268", - "fairsharing": { - "abbreviation": "FBbi", - "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", - "id": "33", - "name": "Biological Imaging methods Ontology", - "prefix": "FAIRsharing.ny3z9j", - "subjects": [ - "Life Science", - "Biomedical Science" - ] - }, - "mappings": { - "biocontext": "FBbi", - "bioportal": "FBbi", - "fairsharing": "FAIRsharing.ny3z9j", - "obofoundry": "fbbi", - "ols": "fbbi", - "ontobee": "FBBI", - "prefixcommons": "fbbi" - }, - "obofoundry": { - "contact": "wawong@gmail.com", - "contact.github": "wawong", - "contact.label": "Willy Wong", - "contact.orcid": "0000-0002-8841-5870", - "deprecated": false, - "description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.", - 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This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs.", - "id": "1582", - "name": "FlyBase", - "prefix": "FAIRsharing.wrvze3", - "subjects": [ - "Functional Genomics", - "Anatomy", - "Molecular biology", - "Genomics", - "Bioinformatics", - "Genetics", - "Life Science", - "Molecular Genetics", - "Comparative Genomics" - ] - }, - "go": { - "homepage": "http://flybase.org/", - "name": "FlyBase", - "prefix": "FB", - "synonyms": [ - "FlyBase", - "FLYBASE" - ], - "uri_format": "http://flybase.org/reports/$1.html" - }, - "mappings": { - "biocontext": "FlyBase", - "cellosaurus": "FlyBase", - "fairsharing": "FAIRsharing.wrvze3", - "go": "FB", - "miriam": "fb", - "n2t": "fb", - "ncbi": "FLYBASE", - "prefixcommons": "flybase", - "uniprot": "FlyBase", - "wikidata": "P3852" - }, - "miriam": { - "deprecated": false, - "description": "FlyBase is the database of the Drosophila Genome Projects and of associated literature.", - "homepage": "http://flybase.org/", - "id": "00000030", - "name": "FlyBase", - "namespaceEmbeddedInLui": false, - "pattern": "^FB\\w{2}\\d{7}$", - "prefix": "fb", - "providers": [ - { - "code": "bioentitylink", - "description": "FlyBase through BioEntity Link", - "homepage": "https://bioentity.link/", - "name": "FlyBase through BioEntity Link", - "uri_format": "https://bioentity.link/#/lexicon/public/$1" - }, - { - "code": "agr", - "description": "FlyBase through the Alliance of Genome Resources", - "homepage": "https://www.alliancegenome.org", - "name": "FlyBase through the Alliance of Genome Resources", - "uri_format": "https://www.alliancegenome.org/gene/FB:$1" - } - ], - "sampleId": "FBgn0011293", - "uri_format": "http://flybase.org/reports/$1.html" - }, - "n2t": { - "description": "FlyBase is the database of the Drosophila Genome Projects and of associated literature.", - "example": "FBgn0011293", - "homepage": "https://www.alliancegenome.org", - "name": "FlyBase through the Alliance of Genome Resources", - "namespaceEmbeddedInLui": false, - "pattern": "^FB\\w{2}\\d{7}$", - "prefix": "fb", - "uri_format": "https://www.alliancegenome.org/gene/FB:$1" - }, - "name": "FlyBase Gene", - "ncbi": { - "example": "FBgn0000024", - "homepage": "http://www.flybase.org/", - "name": "Database of Genetic and molecular data of Drosophila.", - "prefix": "FLYBASE" - }, - "preferred_prefix": "FlyBase", - "prefixcommons": { - "description": "FlyBase is an integrated resource for genetic, molecular, and descriptive data concerning the Drosophilidae, including interactive genomic maps, gene product descriptions, mutant allele phenotypes, genetic interactions, expression patterns, transgenic constructs and their insertions, anatomy and images, and genetic stock collections.", - "example": "FBgn0011293", - "homepage": "http://flybase.org/", - "keywords": [ - "genome", - "interaction", - "anatomy", - "DNA" - ], - "name": "Drosophila genome database", - "pattern": "^FB\\w{2}\\d{7}$", - "prefix": "flybase", - "uri_format": "http://flybase.org/reports/$1.html" - }, - "synonyms": [ - "FB", - "FlyBase" - ], - "uniprot": { - "category": "Organism-specific databases", - "comment": "Replacement for DMAP", - "identifier": "26", - "link_is_explicit": "true", - "name": "Drosophila genome database", - "prefix": "FlyBase", - "uri_format": "http://flybase.org/reports/$1.html" - }, - "uri_format": "https://flybase.org/reports/$1", - "wikidata": { - "database": "Q3074571", - "database.homepage": "https://flybase.org/", - "database.label": "FlyBase", - "homepage": "http://flybase.org/", - "name": "FlyBase Gene ID", - "pattern": "FBgn\\d{7}", - "prefix": "P3852", - "uri_format": "http://flybase.org/reports/$1" - } - }, - "flybrain.ndb": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "A database of fly neurons and pathways with an associated 3D viewer.", - "example": "10531", - "homepage": "https://flybrain-ndb.virtualflybrain.org", - "name": "FlyBrain Neuron Database", - "pattern": "^\\d+$", - "uri_format": "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html" - }, - "fma": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "FMA", - "uri_format": "http://purl.obolibrary.org/obo/FMA_$1" - }, - "bioportal": { - "name": "Foundational Model of Anatomy", - "prefix": "FMA" - }, - "example": "63189", - "fairsharing": { - "abbreviation": "FMA", - "description": "The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species", - "id": "683", - "name": "Foundational Model of Anatomy", - "prefix": "FAIRsharing.x56jsy", - "subjects": [ - "Anatomy", - "Radiology", - "Biomedical Science" - ] - }, - "go": { - "homepage": "http://sig.biostr.washington.edu/projects/fm/index.html", - "name": "Foundational Model of Anatomy", - "prefix": "FMA" - }, - "mappings": { - "biocontext": "FMA", - "bioportal": "FMA", - "fairsharing": "FAIRsharing.x56jsy", - "go": "FMA", - "miriam": "fma", - "n2t": "fma", - "obofoundry": "fma", - "ols": "fma", - "ontobee": "FMA", - "prefixcommons": "fma" - }, - "miriam": { - "deprecated": false, - "description": "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/fma/", - "id": "00000067", - "name": "FMA", - "namespaceEmbeddedInLui": true, - "pattern": "^FMA:\\d+$", - "prefix": "fma", - "sampleId": "67112", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1" - }, - "n2t": { - "description": "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.", - "example": "67112", - "homepage": "http://bioportal.bioontology.org/ontologies/FMA", - "name": "Foundational Model of Anatomy through BioPortal", - "namespaceEmbeddedInLui": true, - "pattern": "^FMA:\\d+$", - "prefix": "fma", - "uri_format": "http://purl.bioontology.org/ontology/FMA_subset/FMA:$1" - }, - "name": "Foundational Model of Anatomy", - "obofoundry": { - "contact": "mejino@u.washington.edu", - "contact.label": "Onard Mejino", - "deprecated": true, - "description": "This is currently a slimmed down version of FMA", - "download.owl": "http://purl.obolibrary.org/obo/fma.owl", - "homepage": "http://si.washington.edu/projects/fma", - "license": "CC BY 3.0", - "license.url": "https://creativecommons.org/licenses/by/3.0/", - "name": "Foundational Model of Anatomy Ontology (subset)", - "preferredPrefix": "FMA", - "prefix": "fma", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/18688289", - "title": "Translating the Foundational Model of Anatomy into OWL" - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/18360535", - "title": "The foundational model of anatomy in OWL: Experience and perspectives" - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/16779026", - "title": "Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study" - } - ], - "repository": "https://bitbucket.org/uwsig/fma" - }, - "ols": { - "description": "This is currently a slimmed down version of FMA", - "download": "http://purl.obolibrary.org/obo/fma.owl", - "homepage": "http://si.washington.edu/projects/fma", - "name": "Foundational Model of Anatomy Ontology (subset)", - "prefix": "fma", - "version": "2020-04-13", - "version.iri": "http://purl.obolibrary.org/obo/fma/releases/2020-04-13/fma.owl" - }, - "ontobee": { - "library": "Library", - "name": "Foundational Model of Anatomy Ontology (subset)", - "prefix": "FMA" - }, - "pattern": "^\\d+$", - "prefixcommons": { - "bioportal": "1053", - "description": "FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy.", - "example": "FMA:67112", - "homepage": "http://sig.biostr.washington.edu/projects/fm/", - "keywords": [ - "owl", - "anatomy", - "human" - ], - "name": "The Foundational Model of Anatomy Ontology", - "pattern": "^FMA:\\d+$", - "prefix": "fma", - "pubmed_ids": [ - "17271570" - ] - }, - "synonyms": [ - "FMAID", - "FMA_RETIRED" - ] - }, - "foaf": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "foaf", - "uri_format": "http://xmlns.com/foaf/0.1/$1" - }, - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "foaf", - "uri_format": "http://xmlns.com/foaf/0.1/$1" - }, - "bioportal": { - "name": "Friend of a Friend Vocabulary", - "prefix": "FOAF" - }, - "description": "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world.", - "example": "familyName", - "homepage": "http://xmlns.com/foaf/spec/", - "mappings": { - "biocontext": "foaf", - "biolink": "foaf", - "bioportal": "FOAF" - }, - "name": "Friend of a Friend", - "uri_format": "http://xmlns.com/foaf/0.1/$1" - }, - "fobi": { - "bioportal": { - "name": "FOBI (Food-Biomarker Ontology)", - "prefix": "FOBI" - }, - "example": "030719", - "homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology", - "mappings": { - "bioportal": "FOBI", - "obofoundry": "fobi", - "ols": "fobi", - "ontobee": "FOBI" - }, - "name": "Food-Biomarker Ontology", - "obofoundry": { - "contact": "polcaes@gmail.com", - "contact.github": "pcastellanoescuder", - "contact.label": "Pol Castellano Escuder", - "contact.orcid": "0000-0001-6466-877X", - "depends_on": [ - "chebi", - "foodon" - ], - "deprecated": false, - "description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data", - "download.owl": "http://purl.obolibrary.org/obo/fobi.owl", - "homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Food-Biomarker Ontology", - "preferredPrefix": "FOBI", - "prefix": "fobi", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/32556148", - "title": "FOBI: an ontology to represent food intake data and associate it with metabolomic data" - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/34601570", - "title": "The fobitools framework: the first steps towards food enrichment analysis" - } - ], - "repository": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology" - }, - "ols": { - "description": "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data", - "download": "http://purl.obolibrary.org/obo/fobi.owl", - "homepage": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology", - "name": "Food-Biomarker Ontology", - "prefix": "fobi", - "version.iri": "http://purl.obolibrary.org/obo/fobi/fobi.owl" - }, - "ontobee": { - "library": "Library", - "name": "FOBI", - "prefix": "FOBI" - }, - "pattern": "^\\d{6}$" - }, - "foodb.compound": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "FOODB.COMPOUND", - "uri_format": "http://identifiers.org/foodb.compound/$1" - }, - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "foodb.compound", - "uri_format": "http://foodb.ca/foods/$1" - }, - "homepage": "https://foodb.ca/", - "mappings": { - "biocontext": "FOODB.COMPOUND", - "biolink": "foodb.compound", - "miriam": "foodb.compound", - "n2t": "foodb.compound" - }, - "miriam": { - "deprecated": false, - "description": "FooDB is resource on food and its constituent compounds. It includes data on the compound\u2019s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.", - "homepage": "http://foodb.ca/foods", - "id": "00000530", - "name": "FooDB Compound", - "namespaceEmbeddedInLui": false, - "pattern": "^FDB\\d+$", - "prefix": "foodb.compound", - "sampleId": "FDB002100", - "uri_format": "http://foodb.ca/compounds/$1" - }, - "n2t": { - "description": "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.", - "example": "FDB002100", - "homepage": "http://foodb.ca/foods", - "name": "FooDB database of food additives at University of Alberta", - "namespaceEmbeddedInLui": false, - "pattern": "^FDB\\d+$", - "prefix": "foodb.compound", - "uri_format": "http://foodb.ca/compounds/$1" - }, - "synonyms": [ - "foodb" - ] - }, - "foodon": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "FOODON", - "uri_format": "http://purl.obolibrary.org/obo/FOODON_$1" - }, - "bioportal": { - "name": "The FoodOn Food Ontology", - "prefix": "FOODON" - }, - "fairsharing": { - "abbreviation": "FOODON", - "description": "The need to represent knowledge about food is central to many human activities including agriculture, medicine, food safety inspection, shopping patterns, and sustainable development. FoodOn is built to interoperate with the OBO Library and to represent entities which bear a food role. Initially the ontology will focus on the human-centric categorization and handling of food, but in the future it will also encompass materials in natural ecosystems and food webs. We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes.", - "id": "638", - "name": "FoodOn", - "prefix": "FAIRsharing.dzxae", - "subjects": [ - "Botany", - "Environmental Science", - "Medicine", - "Agriculture" - ] - }, - "mappings": { - "biocontext": "FOODON", - "bioportal": "FOODON", - "fairsharing": "FAIRsharing.dzxae", - "miriam": "foodon", - "n2t": "foodon", - "obofoundry": "foodon", - "ols": "foodon", - "ontobee": "FOODON" - }, - "miriam": { - "deprecated": false, - "description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.", - "homepage": "https://foodon.org", - "id": "00000661", - "name": "FoodOn Food Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^FOODON:[0-9]{8}$", - "prefix": "foodon", - "sampleId": "03307879", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1" - }, - "n2t": { - "description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.", - "example": "03307879", - "homepage": "https://foodon.org", - "name": "FoodOn Food Ontology through OLS", - "namespaceEmbeddedInLui": true, - "pattern": "^FOODON:[0-9]{8}$", - "prefix": "foodon", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1" - }, - "name": "The Food Ontology", - "obofoundry": { - "appears_in": [ - "agro", - "envo", - "fobi", - "maxo", - "one", - "ons" - ], - "contact": "damion_dooley@sfu.ca", - "contact.github": "ddooley", - "contact.label": "Damion Dooley", - "contact.orcid": "0000-0002-8844-9165", - "depends_on": [ - "bfo", - "chebi", - "envo", - "eo", - "ncbitaxon", - "obi", - "ro", - "uberon" - ], - "deprecated": false, - "description": "A broadly scoped ontology representing entities which bear a \u201cfood role\u201d. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research", - "download.owl": "http://purl.obolibrary.org/obo/foodon.owl", - "homepage": "https://foodon.org/", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Food Ontology", - "preferredPrefix": "FOODON", - "prefix": "foodon", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/31304272", - "title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration" - } - ], - "repository": "https://github.com/FoodOntology/foodon" - }, - "ols": { - "description": "FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world.", - "download": "http://purl.obolibrary.org/obo/foodon.owl", - "homepage": "https://foodon.org/", - "name": "Food Ontology", - "prefix": "foodon", - "version": "2022-02-01", - "version.iri": "http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl" - }, - "ontobee": { - "library": "Library", - "name": "FOODON", - "prefix": "FOODON" - }, - "pattern": "^[0-9]{8}$" - }, - "fovt": { - "bioportal": { - "name": "FuTRES Ontology of Vertebrate Traits", - "prefix": "FOVT" - }, - "example": "0000009", - "mappings": { - "bioportal": "FOVT", - "obofoundry": "fovt", - "ols": "fovt", - "ontobee": "FOVT" - }, - "obofoundry": { - "contact": "meghan.balk@gmail.com", - "contact.github": "megbalk", - "contact.label": "Meghan Balk", - "contact.orcid": "0000-0003-2699-3066", - "depends_on": [ - "bco", - "bfo", - "bspo", - "iao", - "oba", - "pato", - "ro", - "uberon" - ], - "deprecated": false, - "description": "FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. 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The FYECO namespace shows up in data ingests from PomBase.", - "example": "0000003", - "homepage": "https://github.com/pombase/fypo", - "mappings": { - "biolink": "FYECO" - }, - "name": "Fission Yeast Experimental Conditions Ontology", - "pattern": "^\\d{7}$", - "preferred_prefix": "FYECO", - "repository": "https://github.com/pombase/fypo", - "reviewer": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - } - }, - "fyler": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "A hierarchical classification of congenital heart disease ", - "example": "4447", - "homepage": "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906", - "name": "Fyler", - "pattern": "^\\d+$", - "references": [ - "https://github.com/obophenotype/human-phenotype-ontology/issues/2568", - "https://github.com/obophenotype/human-phenotype-ontology/issues/2511" - ] - }, - "fypo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "FYPO", - "uri_format": "http://purl.obolibrary.org/obo/FYPO_$1" - }, - "biolink": { - "is_identifiers": false, - "is_obo": true, - "prefix": "FYPO", - "uri_format": "http://purl.obolibrary.org/obo/FYPO_$1" - }, - "bioportal": { - "name": "Fission Yeast Phenotype Ontology", - "prefix": "FYPO" - }, - "download_obo": "http://purl.obolibrary.org/obo/fypo.obo", - "example": "0001707", - "fairsharing": { - "abbreviation": "FYPO", - "description": "FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource (www.pombase.org). 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These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.", - "homepage": "http://www.gabipd.org/", - "id": "00000164", - "name": "GABI", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "gabi", - "sampleId": "2679240", - "uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" - }, - "n2t": { - "description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.", - "example": "2679240", - "homepage": "http://www.gabipd.org/", - "name": "GABI at Max Planck", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "gabi", - "uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" - }, - "ncbi": { - "example": "HA05J18", - "homepage": "http://www.gabipd.org/information/about.shtml", - "name": "Network of Different Plant Genomic Research Projects", - "prefix": "GABI" - }, - "prefixcommons": { - "description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.", - "example": "2679240", - "homepage": "http://www.gabi.de/", - "keywords": [ - "gene", - "genome", - "plant" - ], - "name": "Network of Different Plant Genomic Research Projects", - "pattern": "^\\w+$", - "prefix": "gabi", - "pubmed_ids": [ - "18812395" - ], - "uri_format": "http://gabi.rzpd.de/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" - } - }, - "galen": { - "bioportal": { - "name": "Galen Ontology", - "prefix": "GALEN" - }, - "comment": "I really tried, but could not figure out what GALEN stands for", - "deprecated": true, - "example": "MagnitudeValueType", - "homepage": "https://www.opengalen.org", - "mappings": { - "bioportal": "GALEN" - }, - "name": "GALEN" - }, - "gard": { - "description": "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.", - "example": "6038", - "homepage": "https://rarediseases.info.nih.gov/diseases", - "name": "Genetic and Rare Diseases Information Center", - "pattern": "^\\d+$", - "synonyms": [ - "GARD", - "Genetic and Rare Diseases Information Center" - ], - "wikidata": { - "prefix": "P4317" - } - }, - "gateway": { - "mappings": { - "miriam": "gateway" - }, - "miriam": { - "deprecated": false, - "description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.", - "homepage": "https://www.hdruk.ac.uk", - "id": "00000796", - "name": "gateway", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", - "prefix": "gateway", - "sampleId": "fd8d0743-344a-4758-bb97-f8ad84a37357", - "uri_format": "https://web.www.healthdatagateway.org/dataset/$1" - }, - "name": "Health Data Research Innovation Gateway" - }, - "gaz": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "GAZ", - "uri_format": "http://purl.obolibrary.org/obo/GAZ_$1" - }, - "bioportal": { - "name": "Gazetteer", - "prefix": "GAZ" - }, - "download_obo": "http://purl.obolibrary.org/obo/gaz.obo", - "example": "00620027", - "fairsharing": { - "abbreviation": "GAZ", - "description": "A controlled vocabulary following ontological rules that describes named geographical locations. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles, that describes places and place names and the relations between them.", - "id": "384", - "name": "Gazetteer", - "prefix": "FAIRsharing.wkdjpb", - "subjects": [ - "Environmental Science" - ] - }, - "mappings": { - "biocontext": "GAZ", - "bioportal": "GAZ", - "fairsharing": "FAIRsharing.wkdjpb", - "obofoundry": "gaz", - "ols": "gaz", - "ontobee": "GAZ" - }, - "obofoundry": { - "appears_in": [ - "scdo" - ], - "contact": "lschriml@som.umaryland.edu", - "contact.github": "lschriml", - "contact.label": "Lynn Schriml", - "contact.orcid": "0000-0001-8910-9851", - "deprecated": true, - "description": "A gazetteer constructed on ontological principles", - "download.obo": "http://purl.obolibrary.org/obo/gaz.obo", - "download.owl": "http://purl.obolibrary.org/obo/gaz.owl", - "homepage": "http://environmentontology.github.io/gaz/", - "license": "CC0 1.0", - "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", - "name": "Gazetteer", - "prefix": "gaz", - "repository": "https://github.com/EnvironmentOntology/gaz" - }, - "ols": { - "download": "http://purl.obolibrary.org/obo/gaz.obo", - "name": "gaz", - "prefix": "gaz" - }, - "ontobee": { - "library": "Library", - "name": "Gazetteer", - "prefix": "GAZ" - }, - "pattern": "^\\d{8}$", - "wikidata": { - "prefix": "P6778" - } - }, - "gbif": { - "description": "Database of living organisms, taxonomic. \n The GBIF\u2014the Global Biodiversity Information Facility\u2014is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.", - "example": "4238", - "fairsharing": { - "abbreviation": "GBIF.org", - "description": "GBIF\u2014the Global Biodiversity Information Facility\u2014is an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.\n\nStrictly speaking, GBIF is not a data repository. Rather, GBIF indexes thousands of datasets through a distributed infrastructure involving more than 100 formal participants that supports hundreds of data-publishing institutions worldwide. GBIF.org makes the FAIR and open data discoverable and citable, assigning each download a DOI and storing it for an extended period of time. More than three peer-reviewed research articles make use of data from the GBIF network every day, in studies spanning the impacts of climate change, the spread of pests and diseases, priority areas for conservation and food security. \n\nTo share data with GBIF, follow this quick guide: http://www.gbif.org/publishing-data/quick-guide. To deposit or host data, we suggest using one of the trusted data hosting centres (DHC) listed in FAIRsharing.org that uses GBIF's IPT (Integrated Publishing Toolkit) software. The DHC provides data publishers with a hosted IPT account enabling them to manage and publish datasets through GBIF.org.", - "id": "2163", - "name": "GBIF.org", - "prefix": "FAIRsharing.zv11j3", - "subjects": [ - "Metagenomics", - "Bioinformatics", - "Taxonomy", - "Marine Biology", - "Biodiversity", - "Natural Science", - "Natural History" - ] - }, - "homepage": "https://www.gbif.org/species", - "mappings": { - "fairsharing": "FAIRsharing.zv11j3" - }, - "name": "Global Biodiversity Information Facility", - "pattern": "^\\d+$", - "uri_format": "https://www.gbif.org/species/$1", - "wikidata": { - "prefix": "P846" - } - }, - "gc": { - "comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.", - "example": "11", - "homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html", - "name": "Genetic Code", - "pattern": "^\\d+$", - "references": [ - "https://github.com/obophenotype/ncbitaxon/issues/47" - ], - "synonyms": [ - "gc_id" - ], - "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1" - }, - "gcst": { - "mappings": { - "miriam": "gcst", - "n2t": "gcst" - }, - "miriam": { - "deprecated": false, - "description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.", - "homepage": "https://www.ebi.ac.uk", - "id": "00000715", - "name": "GWAS Catalog", - "namespaceEmbeddedInLui": false, - "pattern": "^GCST\\d{6}\\d*$", - "prefix": "gcst", - "sampleId": "GCST000035", - "uri_format": "https://www.ebi.ac.uk/gwas/studies/$1" - }, - "n2t": { - "description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.", - "example": "GCST000035", - "homepage": "https://www.ebi.ac.uk/gwas/studies", - "name": "GWAS Catalog", - "namespaceEmbeddedInLui": false, - "pattern": "^GCST\\d{6}$", - "prefix": "gcst", - "uri_format": "https://www.ebi.ac.uk/gwas/studies/$1" - } - }, - "gdc": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GDC", - "uri_format": "http://identifiers.org/gdc/$1" - }, - "mappings": { - "biocontext": "GDC", - "miriam": "gdc", - "n2t": "gdc" - }, - "miriam": { - "deprecated": false, - "description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.", - "homepage": "https://gdc.cancer.gov", - "id": "00000604", - "name": "Genomic Data Commons Data Portal", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$", - "prefix": "gdc", - "sampleId": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef", - "uri_format": "https://portal.gdc.cancer.gov/cases/$1" - }, - "n2t": { - "description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.", - "example": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef", - "homepage": "https://gdc.cancer.gov", - "name": "Genomic Data Commons", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$", - "prefix": "gdc", - "uri_format": "https://portal.gdc.cancer.gov/cases/$1" - } - }, - "gdsc": { - "cellosaurus": { - "category": "Chemistry resources", - "homepage": "https://www.cancerrxgene.org", - "name": "Genomics of Drug Sensitivity in Cancer Project", - "prefix": "GDSC", - "uri_format": "https://www.cancerrxgene.org/translation/CellLine/$1" - }, - "mappings": { - "cellosaurus": "GDSC", - "miriam": "gdsc", - "n2t": "gdsc" - }, - "miriam": { - "deprecated": false, - "description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.", - "homepage": "https://www.cancerrxgene.org", - "id": "00000678", - "name": "Genomics of Drug Sensitivity in Cancer", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "gdsc", - "sampleId": "1242", - "uri_format": "https://www.cancerrxgene.org/translation/Drug/$1" - }, - "n2t": { - "description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.", - "example": "1242", - "homepage": "https://www.cancerrxgene.org", - "name": "Genomics of Drug Sensitivity in Cancer", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "gdsc", - "uri_format": "https://www.cancerrxgene.org/translation/Drug/$1" - } - }, - "gecko": { - "bioportal": { - "name": "Genomics Cohorts Knowledge Ontology", - "prefix": "GECKO" - }, - "example": "0000044", - "fairsharing": { - "abbreviation": "GECKO", - "description": "GECKO is an ontology to represent genomics cohort attributes. The GECKO is maintained by the CINECA project, and standardises attributes commonly used for genomics cohort description as well as individual-level data items.", - "id": "3626", - "name": "Genomics Cohorts Knowledge Ontology", - "prefix": "FAIRsharing.3da56b", - "subjects": [ - "Genomics", - "Statistics", - "Life Science" - ] - }, - "mappings": { - "bioportal": "GECKO", - "fairsharing": "FAIRsharing.3da56b", - "obofoundry": "gecko", - "ols": "gecko", - "ontobee": "GECKO" - }, - "obofoundry": { - "contact": "rbca.jackson@gmail.com", - "contact.github": "beckyjackson", - "contact.label": "Rebecca Jackson", - "contact.orcid": "0000-0003-4871-5569", - "deprecated": false, - "description": "An ontology to represent genomics cohort attributes", - "download.owl": "http://purl.obolibrary.org/obo/gecko.owl", - "homepage": "https://github.com/IHCC-cohorts/GECKO", - "license": "CC BY 4.0", - "license.url": "https://creativecommons.org/licenses/by/4.0/", - "name": "Genomics Cohorts Knowledge Ontology", - "preferredPrefix": "GECKO", - "prefix": "gecko", - "repository": "https://github.com/IHCC-cohorts/GECKO" - }, - "ols": { - "description": "An ontology to represent genomics cohort attributes.", - "download": "http://purl.obolibrary.org/obo/gecko.owl", - "homepage": "https://github.com/IHCC-cohorts/GECKO", - "name": "Genomics Cohorts Knowledge Ontology", - "prefix": "gecko", - "version": "2021-01-18", - "version.iri": "http://purl.obolibrary.org/obo/gecko/releases/2021-01-18/gecko.owl" - }, - "ontobee": { - "library": "Library", - "name": "Genomics Cohorts Knowledge Ontology", - "prefix": "GECKO" - }, - "pattern": "^\\d{7}$" - }, - "gemet": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. 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}, - "mappings": { - "biocontext": "GENPROP", - "miriam": "genprop", - "n2t": "genprop" - }, - "miriam": { - "deprecated": false, - "description": "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.", - "homepage": "https://www.ebi.ac.uk/interpro/genomeproperties/", - "id": "00000443", - "name": "Genome Properties", - "namespaceEmbeddedInLui": false, - "pattern": "^GenProp\\d+$", - "prefix": "genprop", - "sampleId": "GenProp0699", - "uri_format": "https://www.ebi.ac.uk/interpro/genomeproperties/#$1" - }, - "n2t": { - "description": "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome.", - "example": "GenProp0699", - "homepage": "https://www.ebi.ac.uk/interpro/genomeproperties/", - "name": "Genome Properties", - "namespaceEmbeddedInLui": false, - 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It provides a number of different access levels, from free through to a number of paid services.", - "id": "3277", - "name": "GitLab", - "prefix": "FAIRsharing.530e61", - "subjects": [ - "Knowledge and Information Systems", - "Subject Agnostic", - "Software Engineering" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.530e61", - "miriam": "gitlab" - }, - "miriam": { - "deprecated": false, - "description": "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. 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It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.", - "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", - "id": "00000494", - "name": "GLIDA Ligand", - "namespaceEmbeddedInLui": false, - "pattern": "^L\\d+$", - "prefix": "glida.ligand", - "sampleId": "L000001", - "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1" - }, - "n2t": { - "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. 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This collection references Glycoepitopes.", - "homepage": "https://www.glycoepitope.jp/epitopes/", - "id": "00000478", - "name": "GlycoEpitope", - "namespaceEmbeddedInLui": false, - "pattern": "^EP\\d{4}$", - "prefix": "glycoepitope", - "sampleId": "EP0311", - "uri_format": "https://www.glycoepitope.jp/epitopes/$1" - }, - "n2t": { - "description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.", - "example": "EP0311", - "homepage": "https://www.glycoepitope.jp/epitopes/", - "name": "GlycoEpitope at Ritsumeikan University", - "namespaceEmbeddedInLui": false, - "pattern": "^EP\\d{4}$", - "prefix": "glycoepitope", - "uri_format": "https://www.glycoepitope.jp/epitopes/$1" - } - }, - "glycomedb": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GLYCOMEDB", - "uri_format": "http://identifiers.org/glycomedb/$1" - }, - "comment": "this is exactly the same as glytoucan. Idk why there are two different ones", - "fairsharing": { - "abbreviation": "GlycomeDB", - "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", - "id": "1888", - "name": "GlycomeDB", - "prefix": "FAIRsharing.k5k0yh", - "subjects": [ - "Life Science" - ] - }, - "has_canonical": "glytoucan", - "mappings": { - "biocontext": "GLYCOMEDB", - "fairsharing": "FAIRsharing.k5k0yh", - "miriam": "glycomedb", - "n2t": "glycomedb", - "prefixcommons": "glycomedb" - }, - "miriam": { - "deprecated": false, - "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", - "homepage": "https://glytoucan.org/", - "id": "00000114", - "name": "GlycomeDB", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "glycomedb", - "sampleId": "G77500AY", - "uri_format": "https://glytoucan.org/Structures/Glycans/$1" - }, - "n2t": { - "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", - "example": "G77500AY", - "homepage": "https://glytoucan.org/", - "name": "GlycomeDB carbohydrate structure database", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "glycomedb", - "uri_format": "https://glytoucan.org/Structures/Glycans/$1" - }, - "prefixcommons": { - "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", - "example": "1", - "homepage": "http://www.glycome-db.org/showMenu.action?major=database", - "keywords": [ - "molecules", - "small molecules", - "structure" - ], - "name": "GlycomeDB Carbohydrate Structure Database", - "pattern": "^\\d+$", - "prefix": "glycomedb", - "pubmed_ids": [ - "19759275" - ], - "uri_format": "http://www.glycome-db.org/database/showStructure.action?glycomeId=$1" - } - }, - "glyconavi": { - "example_extras": [ - "GN_GlyTouCan_G03681DA" - ], - "fairsharing": { - "abbreviation": "GlycoNAVI", - "description": "GlycoNAVI is a repository of data relevant to carbohydrate research. It contains a free suite of carbohydrate research tools organized by domain, including glycans, proteins, lipids, genes, diseases and samples.", - "id": "1548", - "name": "GlycoNAVI", - "prefix": "FAIRsharing.wvp1t7", - "subjects": [ - "Organic Chemistry", - "Chemistry", - "Life Science", - "Glycomics" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.wvp1t7", - "miriam": "glyconavi" - }, - "miriam": { - "deprecated": false, - "description": "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.", - "homepage": "https://www.noguchi.or.jp/", - "id": "00000830", - "name": "GlycoNAVI", - "namespaceEmbeddedInLui": false, - "pattern": "^GN_[A-Za-z0-9]+$", - "prefix": "glyconavi", - "sampleId": "GN_G03681DA", - "uri_format": "https://glyconavi.org/hub/?id=$1" - }, - "pattern": "^GN_[A-Za-z0-9_:]+$" - }, - "glycopost": { - "fairsharing": { - "abbreviation": "GlycoPOST", - "description": "GlycoPOST is a mass spectrometry data repository for glycomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.", - "id": "3185", - "name": "GlycoPOST", - "prefix": "FAIRsharing.2y1KMt", - "subjects": [ - "Life Science", - "Glycomics" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.2y1KMt", - "miriam": "glycopost" - }, - "miriam": { - "deprecated": false, - "description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.", - "homepage": "https://glycopost.glycosmos.org", - "id": "00000721", - "name": "GlycoPOST", - "namespaceEmbeddedInLui": false, - "pattern": "^GPST[0-9]{6}$", - "prefix": "glycopost", - "sampleId": "GPST000024", - "uri_format": "https://glycopost.glycosmos.org/entry/$1" - } - }, - "glygen": { - "description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data.", - "example": "G24361QY", - "fairsharing": { - "abbreviation": "GlyGen", - "description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone.", - "id": "2874", - "name": "GlyGen: Computational and Informatics Resources for Glycoscience", - "prefix": "FAIRsharing.aI1J5W", - "subjects": [ - "Life Science", - "Glycomics" - ] - }, - "homepage": "https://glygen.org/glycan/", - "mappings": { - "fairsharing": "FAIRsharing.aI1J5W", - "uniprot": "GlyGen" - }, - "name": "Computational and Informatics Resources for Glycoscience", - "uniprot": { - "category": "PTM databases", - "identifier": "254", - "link_is_explicit": "true", - "name": "GlyGen: Computational and Informatics Resources for Glycoscience", - "prefix": "GlyGen", - "uri_format": "https://glygen.org/protein/$1#glycosylation" - }, - "uri_format": "https://glygen.org/glycan/$1" - }, - "glytoucan": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GLYTOUCAN", - "uri_format": "http://identifiers.org/glytoucan/$1" - }, - "mappings": { - "biocontext": "GLYTOUCAN", - "miriam": "glytoucan", - "n2t": "glytoucan" - }, - "miriam": { - "deprecated": false, - "description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.", - "homepage": "https://glytoucan.org", - "id": "00000608", - "name": "GlyTouCan", - "namespaceEmbeddedInLui": false, - "pattern": "^G[0-9]{5}[A-Z]{2}$", - "prefix": "glytoucan", - "sampleId": "G00054MO", - "uri_format": "https://glytoucan.org/Structures/Glycans/$1" - }, - "n2t": { - "description": "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data.", - "example": "G00054MO", - "homepage": "https://glytoucan.org", - "name": "The Glycan Repository", - "namespaceEmbeddedInLui": false, - "pattern": "^G[0-9]{5}[A-Z]{2}$", - "prefix": "glytoucan", - "uri_format": "https://glytoucan.org/Structures/Glycans/$1" - } - }, - "gmd": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GMD", - "uri_format": "http://identifiers.org/gmd/$1" - }, - "fairsharing": { - "abbreviation": "GMD", - "description": "The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.", - "id": "1729", - "name": "Golm Metabolome Database", - "prefix": "FAIRsharing.jykmkw", - "subjects": [ - "Life Science", - "Metabolomics" - ] - }, - "mappings": { - "biocontext": "GMD", - "fairsharing": "FAIRsharing.jykmkw", - "miriam": "gmd", - "n2t": "gmd" - }, - "miriam": { - "deprecated": false, - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.", - "homepage": "http://gmd.mpimp-golm.mpg.de/", - "id": "00000274", - "name": "Golm Metabolome Database", - "namespaceEmbeddedInLui": false, - "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", - "prefix": "gmd", - "sampleId": "68513255-fc44-4041-bc4b-4fd2fae7541d", - "uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx" - }, - "n2t": { - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.", - "example": "68513255-fc44-4041-bc4b-4fd2fae7541d", - "homepage": "http://gmd.mpimp-golm.mpg.de/", - "name": "Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology", - "namespaceEmbeddedInLui": false, - "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", - "prefix": "gmd", - "uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx" - } - }, - "gmd.analyte": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GMD.ANALYTE", - "uri_format": "http://identifiers.org/gmd.analyte/$1" - }, - "mappings": { - "biocontext": "GMD.ANALYTE", - "miriam": "gmd.analyte", - "n2t": "gmd.analyte" - }, - "miriam": { - "deprecated": false, - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.", - "homepage": "http://gmd.mpimp-golm.mpg.de/", - "id": "00000426", - "name": "Golm Metabolome Database Analyte", - "namespaceEmbeddedInLui": false, - "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", - "prefix": "gmd.analyte", - "sampleId": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", - "uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1" - }, - "n2t": { - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. 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It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.", - "example": "1466", - "homepage": "https://link.springer.com/bookseries/562", - "name": "Gmelins Handbuch der anorganischen Chemie", - "pattern": "^[1-9][0-9]{3,6}$", - "references": [ - "https://en.wikipedia.org/wiki/Gmelin_database" - ], - "wikidata": { - "prefix": "P1578" - } - }, - "gno": { - "bioportal": { - "name": "Glycan Naming Ontology", - "prefix": "GNO" - }, - "example": "10004892", - "mappings": { - "bioportal": "GNO", - "obofoundry": "gno", - "ols": "gno", - "ontobee": "GNO" - }, - "name": "Glycan Naming and Subsumption Ontology", - "obofoundry": { - "contact": "nje5@georgetown.edu", - "contact.github": "edwardsnj", - "contact.label": "Nathan Edwards", - "contact.orcid": "0000-0001-5168-3196", - "deprecated": false, - "description": "GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). 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You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.", - "example": "PjrpzUIAAAAJ", - "homepage": "https://scholar.google.com/", - "mappings": { - "biolink": "GSID" - }, - "name": "Google Scholar Researcher" - }, - "gorel": { - "biolink": { - "is_identifiers": false, - "is_obo": true, - "prefix": "GOREL", - "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" - }, - "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", - "download_owl": "ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl", - "example": "0002005", - "go": { - "description": "Additional relations pending addition into RO", - "name": "GO Extensions to OBO Relation Ontology Ontology", - "prefix": "GOREL" - }, - "homepage": "http://geneontology.org/docs/ontology-relations/", - "mappings": { - "biolink": "GOREL", - "go": "GOREL" - }, - "name": "GO Relations", - "pattern": "^\\d{7}$" - }, - "gpcrdb": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GPCRDB", - "uri_format": "http://identifiers.org/gpcrdb/$1" - }, - "fairsharing": { - "abbreviation": "GPCRdb", - "description": "The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.", - "id": "1832", - "name": "Information system for G protein-coupled receptors", - "prefix": "FAIRsharing.e4n3an", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "GPCRDB", - "fairsharing": "FAIRsharing.e4n3an", - "miriam": "gpcrdb", - "n2t": "gpcrdb", - "prefixcommons": "gpcrdb", - "uniprot": "GPCRDB" - }, - "miriam": { - "deprecated": false, - "description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.", - "homepage": "http://www.gpcrdb.org/", - "id": "00000212", - "name": "GPCRDB", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "gpcrdb", - "sampleId": "RL3R1_HUMAN", - "uri_format": "http://www.gpcrdb.org/protein/$1/" - }, - "n2t": { - "description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.", - "example": "RL3R1_HUMAN", - "homepage": "http://www.gpcrdb.org/", - "name": "GPCRDB at Radboud University", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "gpcrdb", - "uri_format": "http://www.gpcrdb.org/protein/$1/" - }, - "name": "G protein-coupled receptor database", - "prefixcommons": { - "description": "The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models.", - "example": "RL3R1_HUMAN", - "homepage": "http://www.gpcr.org/7tm/", - "keywords": [ - "small molecule", - "protein" - ], - "name": "Information system for G protein-coupled receptors (GPCRs)", - "pattern": "^\\w+$", - "prefix": "gpcrdb", - "pubmed_ids": [ - "21045054" - ], - "uri_format": "http://www.gpcr.org/7tm/proteins/$1" - }, - "uniprot": { - "category": "Protein family/group databases", - "identifier": "38", - "name": "Information system for G protein-coupled receptors (GPCRs)", - "prefix": "GPCRDB", - "uri_format": "https://gpcrdb.org/protein/$1/" - }, - "uri_format": "https://gpcrdb.org/protein/$1" - }, - "gpmdb": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GPMDB", - "uri_format": "http://identifiers.org/gpmdb/$1" - }, - "fairsharing": { - "abbreviation": "gpmDB", - "description": "The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.", - "id": "1949", - "name": "The Global Proteome Machine Database", - "prefix": "FAIRsharing.fhcmwq", - "subjects": [ - "Bioinformatics", - "Proteomics" - ] - }, - "mappings": { - "biocontext": "GPMDB", - "fairsharing": "FAIRsharing.fhcmwq", - "miriam": "gpmdb", - "n2t": "gpmdb" - }, - "miriam": { - "deprecated": false, - "description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.", - "homepage": "http://gpmdb.thegpm.org/", - "id": "00000649", - "name": "GPMDB", - "namespaceEmbeddedInLui": false, - "pattern": "^GPM\\d+$", - "prefix": "gpmdb", - "providers": [ - { - "code": "omicsdi", - "description": "GPMDB through OmicsDI", - "homepage": "https://www.omicsdi.org/", - "name": "GPMDB through OmicsDI", - "uri_format": "https://www.omicsdi.org/dataset/gpmdb/$1" - } - ], - "sampleId": "GPM32310002988", - "uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1" - }, - "n2t": { - "description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.", - "example": "GPM32310002988", - "homepage": "http://gpmdb.thegpm.org/", - "name": "GPMDB", - "namespaceEmbeddedInLui": false, - "pattern": "^GPM\\d+$", - "prefix": "gpmdb", - "uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1" - }, - "name": "Global Proteome Machine Database" - }, - "graingenes.reference": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "A database for Triticeae and Avena references.", - "example": "WGS-95-1333", - "homepage": "http://wheat.pw.usda.gov", - "name": "GrainGenes", - "uri_format": "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1" - }, - "graingenes.symbol": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "A database for Triticeae and Avena gene symbols.", - "example": "1-FEH+w3", - "homepage": "http://wheat.pw.usda.gov", - "name": "GrainGenes", - "uri_format": "http://wheat.pw.usda.gov/report?class=gene;name=$1" - }, - "gramene.gene": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRAMENE.GENE", - "uri_format": "http://identifiers.org/gramene.gene/$1" - }, - "go": { - "homepage": "http://www.gramene.org/", - "name": "Gramene", - "prefix": "GR_GENE", - "synonyms": [ - "GR_gene" - ], - "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" - }, - "mappings": { - "biocontext": "GRAMENE.GENE", - "go": "GR_GENE", - "miriam": "gramene.gene", - "n2t": "gramene.gene" - }, - "miriam": { - "deprecated": false, - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.", - "homepage": "http://www.gramene.org/", - "id": "00000182", - "name": "Gramene genes", - "namespaceEmbeddedInLui": false, - "pattern": "^GR\\:\\d+$", - "prefix": "gramene.gene", - "sampleId": "GR:0080039", - "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" - }, - "n2t": { - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.", - "example": "GR:0080039", - "homepage": "http://www.gramene.org/", - "name": "Gramene Genes at Cold Spring Harbor", - "namespaceEmbeddedInLui": false, - "pattern": "^GR\\:\\d+$", - "prefix": "gramene.gene", - "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" - }, - "name": "Gramene Gene", - "synonyms": [ - "GR_GENE" - ] - }, - "gramene.growthstage": { - "banana": "gramene.growthstage:GRO\\", - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRAMENE.GROWTHSTAGE", - "uri_format": "http://identifiers.org/gramene.growthstage/$1" - }, - "mappings": { - "biocontext": "GRAMENE.GROWTHSTAGE", - "miriam": "gramene.growthstage", - "n2t": "gramene.growthstage" - }, - "miriam": { - "deprecated": false, - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", - "homepage": "http://www.gramene.org/", - "id": "00000508", - "name": "Gramene Growth Stage Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^GRO\\:\\d+$", - "prefix": "gramene.growthstage", - "sampleId": "0007133", - "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" - }, - "n2t": { - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene.", - "example": "0007133", - "homepage": "http://www.gramene.org/", - "name": "Gramene Growth Stage Ontology at Cold Spring Harbor", - "namespaceEmbeddedInLui": true, - "pattern": "^GRO\\:\\d+$", - "prefix": "gramene.growthstage", - "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" - }, - "name": "Gramene Growth Stage Ontology", - "namespace_in_lui": false, - "pattern": "^\\d{7}$", - "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" - }, - "gramene.protein": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRAMENE.PROTEIN", - "uri_format": "http://identifiers.org/gramene.protein/$1" - }, - "go": { - "homepage": "http://www.gramene.org/", - "name": "Gramene", - "prefix": "GR_PROTEIN", - "synonyms": [ - "GR_protein" - ], - "uri_format": "http://www.gramene.org/db/protein/protein_search?acc=$1" - }, - "mappings": { - "biocontext": "GRAMENE.PROTEIN", - "go": "GR_PROTEIN", - "miriam": "gramene.protein", - "n2t": "gramene.protein" - }, - "miriam": { - "deprecated": false, - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.", - "homepage": "http://www.gramene.org/", - "id": "00000181", - "name": "Gramene protein", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "gramene.protein", - "sampleId": "78073", - "uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1" - }, - "n2t": { - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.", - "example": "78073", - "homepage": "http://www.gramene.org/", - "name": "Gramene Protein at Cold Spring Harbor", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "gramene.protein", - "uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1" - }, - "name": "Gramene protein", - "synonyms": [ - "GR_PROTEIN" - ] - }, - "gramene.qtl": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRAMENE.QTL", - "uri_format": "http://identifiers.org/gramene.qtl/$1" - }, - "go": { - "homepage": "http://www.gramene.org/", - "name": "Gramene", - "prefix": "GR_QTL", - "uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1" - }, - "mappings": { - "biocontext": "GRAMENE.QTL", - "go": "GR_QTL", - "miriam": "gramene.qtl", - "n2t": "gramene.qtl" - }, - "miriam": { - "deprecated": false, - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.", - "homepage": "http://www.gramene.org/", - "id": "00000184", - "name": "Gramene QTL", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "gramene.qtl", - "sampleId": "CQG5", - "uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1" - }, - "n2t": { - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.", - "example": "CQG5", - "homepage": "http://www.gramene.org/", - "name": "Gramene Quantitative Trait Loci at Cold Spring Harbor", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "gramene.qtl", - "uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1" - }, - "name": "Gramene QTL", - "synonyms": [ - "GR_QTL" - ] - }, - "gramene.reference": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Literature references in Gramene", - "example": "6200", - "homepage": "http://www.gramene.org", - "name": "Gramene Reference", - "pattern": "^\\d+$", - "synonyms": [ - "gramene.ref" - ], - "uri_format": "http://www.gramene.org/db/literature/pub_search?ref_id=$1" - }, - "gramene.taxonomy": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRAMENE.TAXONOMY", - "uri_format": "http://identifiers.org/gramene.taxonomy/$1" - }, - "mappings": { - "biocontext": "GRAMENE.TAXONOMY", - "miriam": "gramene.taxonomy", - "n2t": "gramene.taxonomy" - }, - "miriam": { - "deprecated": false, - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.", - "homepage": "http://www.gramene.org/", - "id": "00000183", - "name": "Gramene Taxonomy", - "namespaceEmbeddedInLui": false, - "pattern": "^GR\\_tax\\:\\d+$", - "prefix": "gramene.taxonomy", - "sampleId": "GR_tax:013681", - "uri_format": "http://www.gramene.org/db/ontology/search?id=$1" - }, - "n2t": { - "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.", - "example": "GR_tax:013681", - "homepage": "http://www.gramene.org/", - "name": "Gramene Taxonomy at Cold Spring Harbor", - "namespaceEmbeddedInLui": false, - "pattern": "^GR\\_tax\\:\\d+$", - "prefix": "gramene.taxonomy", - "uri_format": "http://www.gramene.org/db/ontology/search?id=$1" - } - }, - "grassbase": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.", - "example": "imp10873", - "homepage": "https://www.kew.org/data/grasses-syn/index.htm", - "name": "GrassBase", - "pattern": "^(imp|gen)\\d{5}$", - "uri_format": "https://www.kew.org/data/grasses-db/www/$1" - }, - "greengenes": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GREENGENES", - "uri_format": "http://identifiers.org/greengenes/$1" - }, - "fairsharing": { - "abbreviation": "Greengenes", - "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", - "id": "1947", - "name": "Greengenes", - "prefix": "FAIRsharing.bpxgb6", - "subjects": [ - "Genetics", - "Life Science" - ] - }, - "mappings": { - "biocontext": "GREENGENES", - "fairsharing": "FAIRsharing.bpxgb6", - "miriam": "greengenes", - "n2t": "greengenes", - "ncbi": "Greengenes", - "prefixcommons": "greengenes" - }, - "miriam": { - "deprecated": false, - "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", - "homepage": "http://greengenes.lbl.gov/", - "id": "00000165", - "name": "GreenGenes", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "greengenes", - "sampleId": "100000", - "uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1" - }, - "n2t": { - "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", - "example": "100000", - "homepage": "http://greengenes.lbl.gov/", - "name": "GreenGenes at Lawrence Berkeley", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "greengenes", - "uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1" - }, - "ncbi": { - "example": "269185", - "homepage": "http://greengenes.lbl.gov/", - "name": "16S rRNA gene database", - "prefix": "Greengenes" - }, - "prefixcommons": { - "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", - "example": "100000", - "homepage": "http://greengenes.lbl.gov", - "keywords": [ - "RNA" - ], - "name": "Greengenes:16S rRNA gene database", - "pattern": "^\\d+$", - "prefix": "greengenes", - "pubmed_ids": [ - "16820507" - ], - "uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1" - } - }, - "grid": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRID", - "uri_format": "http://identifiers.org/grid/$1" - }, - "fairsharing": { - "abbreviation": "GRID", - "description": "Global Research Identifier Database (GRID) stores information on research-related organisations worldwide. GRID record contains a unique GRID ID, relevant metadata, and relationships between associated institutions.", - "id": "3040", - "name": "Global Research Identifier Database", - "prefix": "FAIRsharing.0pUMYW", - "subjects": [ - "Data Management" - ] - }, - "mappings": { - "biocontext": "GRID", - "fairsharing": "FAIRsharing.0pUMYW", - "miriam": "grid", - "n2t": "grid" - }, - "miriam": { - "deprecated": false, - "description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.", - "homepage": "https://www.grid.ac/", - "id": "00000593", - "name": "GRID", - "namespaceEmbeddedInLui": false, - "pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$", - "prefix": "grid", - "sampleId": "grid.225360.0", - "uri_format": "https://www.grid.ac/institutes/$1" - }, - "n2t": { - "description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.", - "example": "grid.225360.0", - "homepage": "https://www.grid.ac/", - "name": "GRID at Digital Science & Research Ltd.", - "namespaceEmbeddedInLui": false, - "pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$", - "prefix": "grid", - "uri_format": "https://www.grid.ac/institutes/$1" - }, - "name": "Global Research Identifier Database" - }, - "grin.taxonomy": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRIN.TAXONOMY", - "uri_format": "http://identifiers.org/grin.taxonomy/$1" - }, - "go": { - "homepage": "https://www.ars-grin.gov/", - "name": "Germplasm Resources Information Network", - "prefix": "GRIN", - "synonyms": [ - "grin" - ], - "uri_format": "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=$1" - }, - "mappings": { - "biocontext": "GRIN.TAXONOMY", - "go": "GRIN", - "miriam": "grin.taxonomy", - "n2t": "grin.taxonomy", - "ncbi": "GRIN" - }, - "miriam": { - "deprecated": false, - "description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.", - "homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en", - "id": "00000166", - "name": "GRIN Plant Taxonomy", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "grin.taxonomy", - "sampleId": "19333", - "uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1" - }, - "n2t": { - "description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.", - "example": "19333", - "homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en", - "name": "GRIN at Maryland", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "grin.taxonomy", - "uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1" - }, - "ncbi": { - "example": "1005973", - "homepage": "http://www.ars-grin.gov/", - "name": "Germplasm Resources Information Network", - "prefix": "GRIN" - } - }, - "gro": { - "bioportal": { - "name": "Gene Regulation Ontology", - "prefix": "GRO" - }, - "deprecated": true, - "mappings": { - "bioportal": "GRO" - } - }, - "grsdb": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "GRSDB", - "uri_format": "http://identifiers.org/grsdb/$1" - }, - "mappings": { - "biocontext": "GRSDB", - "miriam": "grsdb", - "n2t": "grsdb", - "prefixcommons": "grsdb" - }, - "miriam": { - "deprecated": false, - "description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). 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HGNC identifiers refer to records in the HGNC symbol database.", - "example": "2674", - "homepage": "https://www.genenames.org", - "name": "HUGO Genome Nomenclature Committee", - "namespaceEmbeddedInLui": false, - "pattern": "^((HGNC|hgnc):)?\\d{1,5}$", - "prefix": "hgnc", - "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1" - }, - "name": "HUGO Gene Nomenclature Committee", - "ncbi": { - "example": "HGNC:2041", - "homepage": "http://www.genenames.org/cgi-bin/search", - "name": "Human Gene Nomenclature Database", - "prefix": "HGNC" - }, - "prefixcommons": { - "bioportal": "1528", - "description": "The HGNC gives unique and meaningful names to every human gene. For each known human gene we approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database.", - "example": "7", - "homepage": "http://www.genenames.org/", - "keywords": [ - "classification", - "gene" - ], - "name": "HUGO Gene Nomenclature Committee", - "pattern": "^\\d+$", - "prefix": "hgnc", - "uri_format": "http://www.genenames.org/data/hgnc_data.php?hgnc_id=$1" - }, - "providers": [ - { - "code": "indra", - "description": "A large scale database of biomedical statements.", - "homepage": "https://db.indra.bio", - "name": "INDRA Database", - "uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC" - }, - { - "code": "gencc", - "description": "The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI\u2019s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women\u2019s Health, Mass General Brigham Laboratory for Molecular Medicine).", - "homepage": "https://thegencc.org", - "name": "The Gene Curation Coalition", - "uri_format": "https://search.thegencc.org/genes/HGNC:$1" - } - ], - "uniprot": { - "category": "Organism-specific databases", - "comment": "Replacement for Genew", - "identifier": "42", - "link_is_explicit": "true", - "name": "Human Gene Nomenclature Database", - "prefix": "HGNC", - "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1" - }, - "wikidata": { - "prefix": "P354" - } - }, - "hgnc.genefamily": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HGNC.GENEFAMILY", - "uri_format": "http://identifiers.org/hgnc.genefamily/$1" - }, - "example": "2029", - "has_canonical": "hgnc.genegroup", - "homepage": "http://www.genenames.org", - "mappings": { - "biocontext": "HGNC.GENEFAMILY", - "miriam": "hgnc.family", - "n2t": "hgnc.genefamily" - }, - "miriam": { - "deprecated": true, - "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol.", - "id": "00000520", - "name": "HGNC Family", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z0-9-]+(#[A-Z0-9-]+)?$", - "prefix": "hgnc.family", - "sampleId": "PADI" - }, - "n2t": { - "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", - "example": "141", - "homepage": "https://www.genenames.org/", - "name": "HGNC gene family at HUGO Genome Nomenclature Committee", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "hgnc.genefamily", - "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" - }, - "synonyms": [ - "GFAM", - "HGNC_GROUP", - "hgnc.family" - ] - }, - "hgnc.genegroup": { - "mappings": { - "miriam": "hgnc.genegroup" - }, - "miriam": { - "deprecated": false, - "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", - "homepage": "https://www.genenames.org", - "id": "00000709", - "name": "HGNC Gene Group", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "hgnc.genegroup", - "sampleId": "141", - "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" - } - }, - "hgnc.symbol": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HGNC.SYMBOL", - "uri_format": "http://identifiers.org/hgnc.symbol/$1" - }, - "mappings": { - "biocontext": "HGNC.SYMBOL", - "miriam": "hgnc.symbol", - "n2t": "hgnc.symbol" - }, - "miriam": { - "deprecated": false, - "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.", - "homepage": "https://www.genenames.org/", - "id": "00000362", - "name": "HGNC Symbol", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z-0-9_]+(\\@)?$", - "prefix": "hgnc.symbol", - "sampleId": "DAPK1", - "uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1" - }, - "n2t": { - "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.", - "example": "DAPK1", - "homepage": "https://www.genenames.org/", - "name": "HGNC Symbol at HUGO Genome Nomenclature Committee", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z-0-9_]+(\\@)?$", - "prefix": "hgnc.symbol", - "uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1" - }, - "providers": [ - { - "code": "depmap", - "description": "DepMap summary of the given gene", - "homepage": "https://depmap.org", - "name": "DepMap Gene Summary", - "uri_format": "https://depmap.org/portal/gene/$1" - }, - { - "code": "pathwaycommons", - "description": "Interactions between a given gene and other molecular entities", - "homepage": "https://www.pathwaycommons.org/", - "name": "Pathway Commons Gene Interations", - "uri_format": "https://apps.pathwaycommons.org/interactions?source=$1" - }, - { - "code": "oncomx", - "description": "Mutation profiles for a gene", - "homepage": "https://oncomx.org", - "name": "OncoMX", - "uri_format": "https://oncomx.org/searchview/?gene=$1" - } - ] - }, - "hinv.locus": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HINV.LOCUS", - "uri_format": "http://identifiers.org/hinv.locus/$1" - }, - "mappings": { - "biocontext": "HINV.LOCUS", - "miriam": "hinv.locus", - "n2t": "hinv.locus" - }, - "miriam": { - "deprecated": false, - "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.", - "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", - "id": "00000167", - "name": "H-InvDb Locus", - "namespaceEmbeddedInLui": false, - "pattern": "^HIX\\d{7}(\\.\\d+)?$", - "prefix": "hinv.locus", - "sampleId": "HIX0004394", - "uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1" - }, - "n2t": { - "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.", - "example": "HIX0004394", - "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", - "name": "H-Invitational Locus View at BIRC", - "namespaceEmbeddedInLui": false, - "pattern": "^HIX\\d{7}(\\.\\d+)?$", - "prefix": "hinv.locus", - "uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1" - } - }, - "hinv.protein": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HINV.PROTEIN", - "uri_format": "http://identifiers.org/hinv.protein/$1" - }, - "mappings": { - "biocontext": "HINV.PROTEIN", - "miriam": "hinv.protein", - "n2t": "hinv.protein" - }, - "miriam": { - "deprecated": false, - "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.", - "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", - "id": "00000169", - "name": "H-InvDb Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^HIP\\d{9}(\\.\\d+)?$", - "prefix": "hinv.protein", - "sampleId": "HIP000030660", - "uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1" - }, - "n2t": { - "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.", - "example": "HIP000030660", - "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", - "name": "H-Invitational Protein View at BIRC", - "namespaceEmbeddedInLui": false, - "pattern": "^HIP\\d{9}(\\.\\d+)?$", - "prefix": "hinv.protein", - "uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1" - } - }, - "hinv.transcript": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HINV.TRANSCRIPT", - "uri_format": "http://identifiers.org/hinv.transcript/$1" - }, - "mappings": { - "biocontext": "HINV.TRANSCRIPT", - "miriam": "hinv.transcript", - "n2t": "hinv.transcript" - }, - "miriam": { - "deprecated": false, - "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.", - "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", - "id": "00000168", - "name": "H-InvDb Transcript", - "namespaceEmbeddedInLui": false, - "pattern": "^HIT\\d{9}(\\.\\d+)?$", - "prefix": "hinv.transcript", - "sampleId": "HIT000195363", - "uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1" - }, - "n2t": { - "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.", - "example": "HIT000195363", - "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", - "name": "H-Invitational Transcript View at BIRC", - "namespaceEmbeddedInLui": false, - "pattern": "^HIT\\d{9}(\\.\\d+)?$", - "prefix": "hinv.transcript", - "uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1" - } - }, - "hipsci": { - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "http://www.hipsci.org", - "name": "Human Induced Pluripotent Stem Cells Initiative", - "prefix": "HipSci", - "uri_format": "http://www.hipsci.org/lines/#/lines/$1" - }, - "example": "HPSI0114i-bezi_1", - "mappings": { - "cellosaurus": "HipSci" - } - }, - "hivreagentprogram": { - "cellosaurus": { - "category": "Cell line collections", - "homepage": "https://www.hivreagentprogram.org/Home.aspx", - "name": "NIH HIV Reagent Program", - "prefix": "HIVReagentProgram", - "uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx" - }, - "example": "ARP-1513", - "mappings": { - "cellosaurus": "HIVReagentProgram" - } - }, - "hmdb": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "HMDB", - "uri_format": "http://www.hmdb.ca/metabolites/$1" - }, - "cheminf": { - "description": "Database identifier used by Human Metabolome Database.", - "name": "HMDB", - "obsolete": false, - "prefix": "000408" - }, - "fairsharing": { - "abbreviation": "HMDB", - "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", - "id": "2084", - "name": "The Human Metabolome Database", - "prefix": "FAIRsharing.sye5js", - "subjects": [ - "Molecular biology", - "Biochemistry", - "Life Science", - "Metabolomics" - ] - }, - "mappings": { - "biocontext": "HMDB", - "cheminf": "000408", - "fairsharing": "FAIRsharing.sye5js", - "miriam": "hmdb", - "n2t": "hmdb", - "prefixcommons": "hmdb", - "wikidata": "P2057" - }, - "miriam": { - "deprecated": false, - "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", - "homepage": "http://www.hmdb.ca/", - "id": "00000051", - "name": "HMDB", - "namespaceEmbeddedInLui": false, - "pattern": "^HMDB\\d+$", - "prefix": "hmdb", - "sampleId": "HMDB00001", - "uri_format": "http://www.hmdb.ca/metabolites/$1" - }, - "n2t": { - "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", - "example": "HMDB00001", - "homepage": "http://www.hmdb.ca/", - "name": "The Human Metabolome Database", - "namespaceEmbeddedInLui": false, - "pattern": "^HMDB\\d+$", - "prefix": "hmdb", - "uri_format": "http://www.hmdb.ca/metabolites/$1" - }, - "name": "Human Metabolome Database", - "prefixcommons": { - "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", - "example": "HMDB00001", - "homepage": "http://www.hmdb.ca", - "keywords": [ - "chemical", - "human", - "metabolite" - ], - "name": "The Human Metabolome Database", - "pattern": "^HMDB\\d{5}$", - "prefix": "hmdb", - "pubmed_ids": [ - "17202168" - ], - "uri_format": "http://www.hmdb.ca/metabolites/$1" - }, - "synonyms": [ - "HMDB" - ], - "wikidata": { - "database": "Q5937262", - "database.homepage": "https://hmdb.ca", - "database.label": "Human Metabolome Database", - "name": "Human Metabolome Database ID", - "pattern": "HMDB\\d+", - "prefix": "P2057", - "uri_format": "https://www.hmdb.ca/metabolites/$1" - } - }, - "hms.lincs.compound": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", - "example": "10001-101", - "homepage": "https://lincs.hms.harvard.edu/db/sm/", - "name": "HMS LINCS Compound", - "synonyms": [ - "HMS-LINCS", - "hmsl_id" - ], - "uri_format": "https://lincs.hms.harvard.edu/db/sm/$1" - }, - "hog": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.", - "download_obo": "ftp://ftp.bgee.org/general/ontologies/HOG.obo", - "example": "0000255", - "homepage": "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships", - "name": "Homologous Organ Groups", - "pattern": "^\\d{7}$" - }, - "hogenom": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HOGENOM", - "uri_format": "http://identifiers.org/hogenom/$1" - }, - "fairsharing": { - "abbreviation": "HOGENOM", - "description": "HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.", - "id": "2033", - "name": "HOGENOM", - "prefix": "FAIRsharing.qe8tz8", - "subjects": [ - "Phylogeny", - "Phylogenetics", - "Life Science" - ] - }, - "mappings": { - "biocontext": "HOGENOM", - "fairsharing": "FAIRsharing.qe8tz8", - "miriam": "hogenom", - "n2t": "hogenom", - "prefixcommons": "hogenom", - "uniprot": "HOGENOM" - }, - "miriam": { - "deprecated": false, - "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", - "homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/", - "id": "00000213", - "name": "HOGENOM", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "hogenom", - "sampleId": "HBG284870", - "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1" - }, - "n2t": { - "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", - "example": "HBG284870", - "homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/", - "name": "HOGENOM at CNRS", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "hogenom", - "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1" - }, - "name": "Database of Complete Genome Homologous Genes Families", - "prefixcommons": { - "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", - "example": "HBG284870", - "homepage": "http://pbil.univ-lyon1.fr/databases/hogenom.php", - "keywords": [ - "classification", - "sequence" - ], - "name": "The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms", - "pattern": "^\\w+$", - "prefix": "hogenom", - "pubmed_ids": [ - "19534752" - ], - "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1" - }, - "uniprot": { - "category": "Phylogenomic databases", - "identifier": "44", - "link_is_explicit": "true", - "name": "The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms", - "prefix": "HOGENOM", - "uri_format": "http://hogenom.univ-lyon1.fr/query_sequence?seq=$1" - } - }, - "hom": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "HOM", - "uri_format": "http://purl.obolibrary.org/obo/HOM_$1" - }, - "bioportal": { - "name": "Ontology of Homology and Related Concepts in Biology", - "prefix": "HOM" - }, - "example": "0000049", - "fairsharing": { - "abbreviation": "HOM", - "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", - "id": "48", - "name": "HOMology", - "prefix": "FAIRsharing.efv7gw", - "subjects": [ - "Anatomy", - "Life Science" - ] - }, - "mappings": { - "biocontext": "HOM", - "bioportal": "HOM", - "fairsharing": "FAIRsharing.efv7gw", - "obofoundry": "hom", - "ols": "hom", - "ontobee": "HOM" - }, - "obofoundry": { - "contact": "bgee@sib.swiss", - "contact.github": "fbastian", - "contact.label": "Frederic Bastian", - "contact.orcid": "0000-0002-9415-5104", - "deprecated": false, - "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", - "download.owl": "http://purl.obolibrary.org/obo/hom.owl", - "homepage": "https://github.com/BgeeDB/homology-ontology", - "license": "CC0 1.0", - "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", - "name": "Homology Ontology", - "preferredPrefix": "HOM", - "prefix": "hom", - "repository": "https://github.com/BgeeDB/homology-ontology" - }, - "ols": { - "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", - "download": "http://purl.obolibrary.org/obo/hom.owl", - "homepage": "https://github.com/BgeeDB/homology-ontology", - "name": "Homology Ontology", - "prefix": "hom", - "version": "2015-01-07", - "version.iri": "http://purl.obolibrary.org/obo/hom/releases/2015-01-07/hom.owl" - }, - "ontobee": { - "library": "Library", - "name": "Homology Ontology", - "prefix": "HOM" - }, - "pattern": "^\\d{7}$" - }, - "homd.seq": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HOMD.SEQ", - "uri_format": "http://identifiers.org/homd.seq/$1" - }, - "mappings": { - "biocontext": "HOMD.SEQ", - "miriam": "homd.seq", - "n2t": "homd.seq", - "prefixcommons": "homd.seq" - }, - "miriam": { - "deprecated": false, - "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", - "homepage": "http://www.homd.org/index.php", - "id": "00000170", - "name": "HOMD Sequence Metainformation", - "namespaceEmbeddedInLui": false, - "pattern": "^SEQF\\d+$", - "prefix": "homd.seq", - "sampleId": "SEQF1003", - "uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1" - }, - "n2t": { - "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", - "example": "SEQF1003", - "homepage": "http://www.homd.org/index.php", - "name": "HOMD sequence metainformation at The Forsyth Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^SEQF\\d+$", - "prefix": "homd.seq", - "uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1" - }, - "prefixcommons": { - "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", - "example": "SEQF1003", - "keywords": [ - "genome", - "microbial" - ], - "name": "HOMD Sequence Metainformation", - "pattern": "^SEQF\\d+$", - "prefix": "homd.seq", - "pubmed_ids": [ - "20624719" - ], - "uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1" - } - }, - "homd.taxon": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HOMD.TAXON", - "uri_format": "http://identifiers.org/homd.taxon/$1" - }, - "mappings": { - "biocontext": "HOMD.TAXON", - "miriam": "homd.taxon", - "n2t": "homd.taxon", - "prefixcommons": "homd.taxon" - }, - "miriam": { - "deprecated": false, - "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", - "homepage": "http://www.homd.org/index.php", - "id": "00000171", - "name": "HOMD Taxonomy", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "homd.taxon", - "sampleId": "811", - "uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic" - }, - "n2t": { - "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", - "example": "811", - "homepage": "http://www.homd.org/index.php", - "name": "HOMD taxon information at The Forsyth Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "homd.taxon", - "uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic" - }, - "prefixcommons": { - "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", - "example": "811", - "keywords": [ - "microbial", - "taxonomy" - ], - "name": "HOMD Taxonomy", - "pattern": "^\\d+$", - "prefix": "homd.taxon", - "pubmed_ids": [ - "20624719" - ], - "uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic" - }, - "uri_format": "www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1" - }, - "homologene": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "HOMOLOGENE", - "uri_format": "http://www.ncbi.nlm.nih.gov/homologene/$1" - }, - "fairsharing": { - "abbreviation": "HomoloGene", - "description": "HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) and matches are placed into groups, using a tree built from sequence similarity to guide the process, where closer related organisms are matched up first, and then further organisms are added as the tree is traversed toward the root. The protein alignments are mapped back to their corresponding DNA sequences, where distance metrics can be calculated (e.g. molecular distance, Ka/Ks ratio). Sequences are matched using synteny when applicable. Remaining sequences are matched up by using an algorithm for maximizing the score globally, rather than locally, in a bipartite matching. Cutoffs on bits per position and Ks values are set to prevent unlikely \"orthologs\" from being grouped together. These cutoffs are calculated based on the respective score distribution for the given groups of organisms. Paralogs are identified by finding sequences that are closer within species than other species.", - "id": "1977", - "name": "NCBI HomoloGene Database", - "prefix": "FAIRsharing.mzc066", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "HOMOLOGENE", - "fairsharing": "FAIRsharing.mzc066", - "miriam": "homologene", - "n2t": "homologene", - "prefixcommons": "homologene", - "wikidata": "P593" - }, - "miriam": { - "deprecated": false, - "description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.", - "homepage": "https://www.ncbi.nlm.nih.gov/homologene/", - "id": "00000275", - "name": "HomoloGene", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "homologene", - "providers": [ - { - "code": "CURATOR_REVIEW", - "description": "Bio2RDF", - "homepage": "http://homologene.bio2rdf.org/fct", - "name": "Bio2RDF", - "uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1" - } - ], - "sampleId": "1000", - "uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1" - }, - "n2t": { - "description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.", - "example": "1000", - "homepage": "https://www.ncbi.nlm.nih.gov/homologene/", - "name": "Homologene at NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "homologene", - "uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1" - }, - "name": "HomoloGene", - "prefixcommons": { - "description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.", - "example": "1000", - "homepage": "http://wwww.ncbi.nlm.nih.gov/homologene", - "keywords": [ - "gene", - "genome" - ], - "name": "NCBI Homologene", - "pattern": "^\\d+$", - "prefix": "homologene", - "pubmed_ids": [ - "21097890" - ], - "uri_format": "http://www.ncbi.nlm.nih.gov/homologene/[?id]" - }, - "wikidata": { - "database": "Q468215", - "database.homepage": "http://www.ncbi.nlm.nih.gov/homologene", - "database.label": "HomoloGene", - "homepage": "http://www.ncbi.nlm.nih.gov/homologene", - "name": "HomoloGene ID", - "pattern": "[1-9]\\d{0,5}", - "prefix": "P593", - "uri_format": "https://www.ncbi.nlm.nih.gov/homologene?term=$1" - } - }, - "horizon_discovery": { - "cellosaurus": { - "category": "Cell line collections", - "homepage": "https://horizondiscovery.com/", - "name": "Horizon Discovery cell line collection", - "prefix": "Horizon_Discovery", - "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" - }, - "example": "HD+118-001", - "mappings": { - "cellosaurus": "Horizon_Discovery" - } - }, - "hovergen": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HOVERGEN", - "uri_format": "http://identifiers.org/hovergen/$1" - }, - "fairsharing": { - "abbreviation": "HOVERGEN", - "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", - "id": "2034", - "name": "Homologous Vertebrate Genes Database", - "prefix": "FAIRsharing.dg1f0e", - "subjects": [ - "Life Science" - ] - }, - "homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php", - "mappings": { - "biocontext": "HOVERGEN", - "fairsharing": "FAIRsharing.dg1f0e", - "miriam": "hovergen", - "n2t": "hovergen", - "prefixcommons": "hovergen" - }, - "miriam": { - "deprecated": false, - "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", - "homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php", - "id": "00000074", - "name": "HOVERGEN", - "namespaceEmbeddedInLui": false, - "pattern": "^HBG\\d+$", - "prefix": "hovergen", - "sampleId": "HBG004341", - "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN" - }, - "n2t": { - "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", - "example": "HBG004341", - "homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.php", - "name": "Hovergen", - "namespaceEmbeddedInLui": false, - "pattern": "^HBG\\d+$", - "prefix": "hovergen", - "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN" - }, - "name": "Homologous Vertebrate Genes Database", - "prefixcommons": { - "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", - "example": "HBG004341", - "homepage": "http://pbil.univ-lyon1.fr/databases/hovergen.html", - "keywords": [ - "gene", - "DNA", - "protein" - ], - "name": "HOVERGEN: Homologous Vertebrate Genes Database", - "pattern": "^HBG\\d+$", - "prefix": "hovergen", - "pubmed_ids": [ - "15713731" - ], - "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN" - } - }, - "hp": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "HPO", - "uri_format": "http://human-phenotype-ontology.org/$1" - }, - "bioportal": { - "name": "Human Phenotype Ontology", - "prefix": "HP" - }, - "download_obo": "http://purl.obolibrary.org/obo/hp.obo", - "example": "0011140", - "fairsharing": { - "abbreviation": "HP", - "description": "The Human Phenotype Ontology has been developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. The goal is to provide resource for the computational analysis of the human phenome, with a focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) and Orphanet databases, for which annotations are also provided.", - "id": "757", - "name": "Human Phenotype Ontology", - "prefix": "FAIRsharing.kbtt7f", - "subjects": [ - "Genetics", - "Phenomics", - "Biomedical Science", - "Preclinical Studies" - ] - }, - "mappings": { - "biocontext": "HPO", - "bioportal": "HP", - "fairsharing": "FAIRsharing.kbtt7f", - "miriam": "hp", - "n2t": "hp", - "obofoundry": "hp", - "ols": "hp", - "ontobee": "HP", - "wikidata": "P3841" - }, - "miriam": { - "deprecated": false, - "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", - "homepage": "http://human-phenotype-ontology.github.io/", - "id": "00000571", - "name": "Human Phenotype Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^HP:\\d{7}$", - "prefix": "hp", - "sampleId": "0000118", - "uri_format": "https://hpo.jax.org/app/browse/term/HP:$1" - }, - "n2t": { - "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", - "example": "0000118", - "homepage": "http://human-phenotype-ontology.github.io/", - "name": "Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics", - "namespaceEmbeddedInLui": true, - "pattern": "^HP:\\d{7}$", - "prefix": "hp", - "uri_format": "http://compbio.charite.de/hpoweb/showterm?id=HP:$1" - }, - "obofoundry": { - "appears_in": [ - "chiro", - "scdo" - ], - "contact": "dr.sebastian.koehler@gmail.com", - "contact.github": "drseb", - "contact.label": "Sebastian Koehler", - "contact.orcid": "0000-0002-5316-1399", - "deprecated": false, - "description": "A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.", - "download.obo": "http://purl.obolibrary.org/obo/hp.obo", - "download.owl": "http://purl.obolibrary.org/obo/hp.owl", - "homepage": "http://www.human-phenotype-ontology.org/", - "license": "hpo", - "license.url": "https://hpo.jax.org/app/license", - "name": "Human Phenotype Ontology", - "preferredPrefix": "HP", - "prefix": "hp", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/18950739", - "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease." - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/26119816", - "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease." - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/24217912", - "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data." - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/30476213", - "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources." - } - ], - "repository": "https://github.com/obophenotype/human-phenotype-ontology", - "twitter": "hp_ontology" - }, - "ols": { - "description": "The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease.", - "download": "http://purl.obolibrary.org/obo/hp.owl", - "homepage": "http://www.human-phenotype-ontology.org/", - "name": "Human Phenotype Ontology", - "prefix": "hp", - "version": "2022-04-14", - "version.iri": "http://purl.obolibrary.org/obo/hp/releases/2022-04-14/hp.owl" - }, - "ontobee": { - "library": "Library", - "name": "Human Phenotype Ontology", - "prefix": "HP" - }, - "pattern": "^\\d{7}$", - "synonyms": [ - "hpo" - ], - "wikidata": { - "database": "Q17027854", - "database.homepage": "http://www.human-phenotype-ontology.org/", - "database.label": "Human Phenotype Ontology", - "homepage": "http://human-phenotype-ontology.github.io/about.html", - "name": "Human Phenotype Ontology ID", - "pattern": "HP:[0-9]{7}", - "prefix": "P3841", - "uri_format": "https://hpo.jax.org/app/browse/term/$1" - } - }, - "hpa": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HPA", - "uri_format": "http://identifiers.org/hpa/$1" - }, - "fairsharing": { - "abbreviation": "HPA", - "description": "The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in a number of different wild-type tissues, cancer types and human cell lines. The goal of the HPA is to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas, the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.", - "id": "1945", - "name": "Human Protein Atlas", - "prefix": "FAIRsharing.j0t0pe", - "subjects": [ - "Proteomics", - "Transcriptomics", - "Biomedical Science", - "Systems Biology" - ] - }, - "go": { - "homepage": "http://www.proteinatlas.org/", - "name": "Human Protein Atlas tissue profile information", - "prefix": "HPA", - "uri_format": "http://www.proteinatlas.org/tissue_profile.php?antibody_id=$1" - }, - "mappings": { - "biocontext": "HPA", - "fairsharing": "FAIRsharing.j0t0pe", - "go": "HPA", - "miriam": "hpa", - "n2t": "hpa", - "prefixcommons": "hpa", - "uniprot": "HPA" - }, - "miriam": { - "deprecated": false, - "description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers.", - "homepage": "http://www.proteinatlas.org/", - "id": "00000336", - "name": "HPA", - "namespaceEmbeddedInLui": false, - "pattern": "^ENSG\\d{11}$", - "prefix": "hpa", - "sampleId": "ENSG00000026508", - "uri_format": "http://www.proteinatlas.org/$1" - }, - "n2t": { - "description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. 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The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.", - "download": "https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo", - "homepage": "https://github.com/Novartis/hpath", - "name": "Histopathology Ontology", - "prefix": "hpath", - "version": "2019-07-05" - }, - "pattern": "^\\d+$", - "repository": "https://github.com/Novartis/hpath", - "synonyms": [ - "MC" - ] - }, - "hpm.peptide": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "HPM.PEPTIDE", - "uri_format": "http://identifiers.org/hpm.peptide/$1" - }, - "mappings": { - "biocontext": "HPM.PEPTIDE", - "miriam": "hpm.peptide", - "n2t": "hpm.peptide" - }, - "miriam": { - "deprecated": false, - "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. 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Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases.", - "id": "1275", - "name": "Infectious Disease Ontology Core", - "prefix": "FAIRsharing.aae3v6", - "subjects": [ - "Molecular Infection Biology", - "Biomedical Science", - "Preclinical Studies" - ] - }, - "mappings": { - "biocontext": "IDO", - "bioportal": "IDO", - "fairsharing": "FAIRsharing.aae3v6", - "miriam": "ido", - "n2t": "ido", - "obofoundry": "ido", - "ols": "ido", - "ontobee": "IDO" - }, - "miriam": { - "deprecated": false, - "description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/ido", - "id": "00000677", - "name": "Infectious Disease Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "ido", - "sampleId": "0000504", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1" - }, - "n2t": { - "description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.", - "example": "0000504", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/ido", - "name": "IDO through OLS", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "ido", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1" - }, - "obofoundry": { - "appears_in": [ - "scdo" - ], - "contact": "Lindsay.Cowell@utsouthwestern.edu", - "contact.github": "lgcowell", - "contact.label": "Lindsay Cowell", - "contact.orcid": "0000-0003-1617-8244", - "deprecated": false, - "description": "A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain.", - "download.owl": "http://purl.obolibrary.org/obo/ido.owl", - "homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology", - "license": "CC BY 3.0", - "license.url": "https://creativecommons.org/licenses/by/3.0/", - "name": "Infectious Disease Ontology", - "preferredPrefix": "IDO", - "prefix": "ido", - "repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology" - }, - "ols": { - "description": "A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain.", - "download": "http://purl.obolibrary.org/obo/ido.owl", - "homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology", - "name": "Infectious Disease Ontology", - "prefix": "ido", - "version": "2017-11-03", - "version.iri": "http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl" - }, - "ontobee": { - "library": "Library", - "name": "Infectious Disease Ontology", - "prefix": "IDO" - } - }, - "idocovid19": { - "bioportal": { - "name": "The COVID-19 Infectious Disease Ontology", - "prefix": "IDO-COVID-19" - }, - "contact": { - "email": "johnbeverley2021@u.northwestern.edu", - "github": "johnbeve", - "name": "John Beverly", - "orcid": "0000-0002-1118-1738" - }, - "example": "0001191", - "mappings": { - "bioportal": "IDO-COVID-19", - "ols": "idocovid19" - }, - "ols": { - "contact": "johnbeverley2021@u.northwestern.edu", - "description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.", - "download": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19", - "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", - "name": "The COVID-19 Infectious Disease Ontology", - "prefix": "idocovid19", - "version": "2020-07-21", - "version.iri": "http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl" - }, - "pattern": "^\\d{7}$", - "repository": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19" - }, - "idoden": { - "bioportal": { - "name": "Dengue Fever Ontology", - "prefix": "IDODEN" - }, - "description": "An ontology for dengue fever.", - "example": "0003463", - "fairsharing": { - "abbreviation": "IDODEN", - "description": "An ontology for dengue fever.", - "id": "756", - "name": "Dengue Fever Ontology", - "prefix": "FAIRsharing.askzq4", - "subjects": [] - }, - "homepage": "https://bioportal.bioontology.org/ontologies/IDODEN", - "mappings": { - "bioportal": "IDODEN", - "fairsharing": "FAIRsharing.askzq4" - }, - "name": "Dengue Fever Ontology", - "pattern": "^\\d{7}$", - "references": [ - "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479" - ] - }, - "idomal": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "IDOMAL", - "uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1" - }, - "bioportal": { - "name": "Malaria Ontology", - "prefix": "IDOMAL" - }, - "download_obo": "http://purl.obolibrary.org/obo/idomal.obo", - "example": "0002350", - "fairsharing": { - "abbreviation": "IDOMAL", - "description": "An application ontology for malaria extending the infectious disease ontology (IDO). With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated.", - "id": "549", - "name": "Infection Disease Ontology Malaria", - "prefix": "FAIRsharing.2q8c28", - "subjects": [ - "Molecular Infection Biology", - "Life Science", - "Biomedical Science" - ] - }, - "mappings": { - "biocontext": "IDOMAL", - "bioportal": "IDOMAL", - "fairsharing": "FAIRsharing.2q8c28", - "obofoundry": "idomal", - "ols": "idomal", - "ontobee": "IDOMAL" - }, - "obofoundry": { - "appears_in": [ - "scdo" - ], - "contact": "topalis@imbb.forth.gr", - "contact.label": "Pantelis Topalis", - "deprecated": true, - "description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.", - "download.obo": "http://purl.obolibrary.org/obo/idomal.obo", - "download.owl": "http://purl.obolibrary.org/obo/idomal.owl", - "homepage": "https://www.vectorbase.org/ontology-browser", - "license": "CC0 1.0", - "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", - "name": "Malaria Ontology", - "prefix": "idomal", - "repository": "https://github.com/VEuPathDB-ontology/IDOMAL" - }, - "ols": { - "description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.", - "download": "http://purl.obolibrary.org/obo/idomal.owl", - "homepage": "https://www.vectorbase.org/ontology-browser", - "name": "Malaria Ontology", - "prefix": "idomal", - "version": "2015-03-16", - "version.iri": "http://purl.obolibrary.org/obo/idomal/2015-03-16/idomal.owl" - }, - "ontobee": { - "library": "Library", - "name": "Malaria Ontology", - "prefix": "IDOMAL" - }, - "pattern": "^\\d{7}$" - }, - "idoo": { - "mappings": { - "miriam": "idoo", - "n2t": "idoo" - }, - "miriam": { - "deprecated": false, - "description": "Identifiers.org Ontology", - "homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology", - "id": "00000683", - "name": "Identifiers.org Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9a-zA-Z]+$", - "prefix": "idoo", - "sampleId": "DataCollection", - "uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1" - }, - "n2t": { - "description": "Identifiers.org Ontology", - "example": "DataCollection", - "homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology", - "name": "Identifiers.org Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9a-zA-Z]+$", - "prefix": "idoo", - "uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1" - } - }, - "idot": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "IDOT", - "uri_format": "http://identifiers.org/idot/$1" - }, - "homepage": "http://biomodels.net/vocab/idot.rdf", - "mappings": { - "biocontext": "IDOT", - "miriam": "idot", - "n2t": "idot" - }, - "miriam": { - "deprecated": false, - "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", - "homepage": "https://identifiers.org/", - "id": "00000519", - "name": "Identifiers.org Terms", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z]+$", - "prefix": "idot", - "sampleId": "identifierPattern", - "uri_format": "https://biomodels.net/vocab/idot.rdf#$1" - }, - "n2t": { - "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", - "example": "identifierPattern", - "homepage": "https://identifiers.org/", - "name": "IdoT via biomodels.net", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z]+$", - "prefix": "idot", - "uri_format": "https://biomodels.net/vocab/idot.rdf#$1" - }, - "uri_format": "https://biomodels.net/vocab/idot.rdf#$1" - }, - "idpo": { - "contact": { - "email": "f.quaglia@ibiom.cnr.it", - "github": "federicaquaglia", - "name": "Federica Quaglia", - "orcid": "0000-0002-0341-4888" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.", - "example": "00056", - "homepage": "https://www.disprot.org/ontology", - "name": "Intrinsically Disordered Proteins Ontology", - "pattern": "^\\d{5}$", - "uri_format": "https://www.disprot.org/idpo/IDPO:$1" - }, - "idr": { - "fairsharing": { - "abbreviation": "IDR", - "description": "IDR is a prototype platform for publishing, mining and integrating bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy using the OMERO and Bio-Formats open source software built by the Open Microscopy Environment. Deployed on an OpenStack cloud running on the EMBL-EBI\u2019s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology.", - "id": "2303", - "name": "Image Data Resource", - "prefix": "FAIRsharing.6wf1zw", - "subjects": [ - "Botany", - "Life Science", - "Biomedical Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.6wf1zw", - "miriam": "idr" - }, - "miriam": { - "deprecated": false, - "description": "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created \u201creference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.", - "homepage": "https://idr.openmicroscopy.org", - "id": "00000743", - "name": "Image Data Resource", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]{4}$", - "prefix": "idr", - "sampleId": "0001", - "uri_format": "https://idr.openmicroscopy.org/search/?query=Name:idr$1" - } - }, - "iedb": { - "fairsharing": { - "abbreviation": "IEDB", - "description": "The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB.", - "id": "2346", - "name": "Immune Epitope Database", - "prefix": "FAIRsharing.c886cd", - "subjects": [ - "Bioinformatics", - "Immunology", - "Life Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.c886cd", - "miriam": "iedb" - }, - "miriam": { - "deprecated": false, - "description": "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.", - "homepage": "https://www.lji.org/", - "id": "00000865", - "name": "Immune Epitope Database (IEDB)", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "iedb", - "sampleId": "1038233", - "uri_format": "https://www.iedb.org/reference/$1" - }, - "name": "Immune Epitope Database" - }, - "iev": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "IEV", - "uri_format": "http://purl.obolibrary.org/obo/IEV_$1" - }, - "example": "0000000", - "mappings": { - "biocontext": "IEV", - "obofoundry": "iev", - "prefixcommons": "iev" - }, - "obofoundry": { - "deprecated": true, - "homepage": "http://www.inoh.org", - "name": "Event (INOH pathway ontology)", - "prefix": "iev" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1011", - "description": "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.", - "example": "IEV_0000913", - "homepage": "http://www.inoh.org", - "keywords": [ - "obo", - "pathway", - "structure" - ], - "name": "Event (INOH pathway ontology)", - "pattern": "^IEV_\\d+$", - "prefix": "iev", - "uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1" - } - }, - "igrhcellid": { - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi", - "name": "Integrated Genomic Resources of human Cell Lines for Identification", - "prefix": "IGRhCellID", - "uri_format": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1" - }, - "example": "ACHN", - "mappings": { - "cellosaurus": "IGRhCellID" - } - }, - "igsn": { - "fairsharing": { - "abbreviation": "IGSN", - "description": "IGSN is a globally unique and persistent identifier for material samples. The IGSN registration service will facilitate the discovery, access, and sharing of samples, ensure preservation and access of sample data, aid identification of samples in the literature, and advance the exchange of digital sample data among interoperable data systems.", - "id": "51", - "name": "International GeoSample Number", - "prefix": "FAIRsharing.Yvc76F", - "subjects": [ - "Geochemistry", - "Hydrogeology", - "Environmental Science", - "Geology", - "Earth Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.Yvc76F", - "miriam": "igsn", - "n2t": "igsn" - }, - "miriam": { - "deprecated": false, - "description": "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents.", - "homepage": "http://www.geosamples.org/", - "id": "00000806", - "name": "International Geo Sample Number", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$", - "prefix": "igsn", - "sampleId": "AU124", - "uri_format": "http://igsn.org/$1" - }, - "n2t": { - "example": "SSH000SUA", - "homepage": "http://www.geosamples.org/", - "name": "International Geo Sample Number", - "namespaceEmbeddedInLui": false, - "prefix": "igsn", - "uri_format": "hdl.handle.net/10273/$1" - } - }, - "igsr": { - "cellosaurus": { - "category": "Biological sample resources", - "homepage": "https://www.internationalgenome.org/", - "name": "International Genome Sample Resource", - "prefix": "IGSR", - "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" - }, - "example": "NA06985", - "fairsharing": { - "abbreviation": "IGSR", - "description": "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.", - "id": "2737", - "name": "The International Genome Sample Resource", - "prefix": "FAIRsharing.4Vs9VM", - "subjects": [ - "Genomics", - "Comparative Genomics" - ] - }, - "mappings": { - "cellosaurus": "IGSR", - "fairsharing": "FAIRsharing.4Vs9VM" - } - }, - "ihw": { - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", - "name": "International Histocompatibility Workshop cell lines", - "prefix": "IHW" - }, - "description": "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.", - "example": "IHW09326", - "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", - "mappings": { - "cellosaurus": "IHW" - }, - "name": "International Histocompatibility Workshop cell lines", - "pattern": "^IHW\\d+$" - }, - "illumina.probe": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.", - "example": "ILMN_129894", - "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt", - "name": "Illumina Probe Identifier", - "pattern": "^ILMN_\\d+$", - "references": [ - "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt" - ] - }, - "imanis": { - "cellosaurus": { - "category": "Cell line collections", - "homepage": "https://www.imanislife.com/collections/cell-lines/", - "name": "Imanis Life Sciences cell line products", - "prefix": "Imanis", - "uri_format": "https://www.imanislife.com/?s=$1" - }, - "example": "CL070", - "mappings": { - "cellosaurus": "Imanis" - } - }, - "imdrf": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence.", - "homepage": "http://www.imdrf.org/", - "name": "International Medical Device Regulators Forum", - "no_own_terms": true, - "references": [ - "https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes" - ] - }, - "imex": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "IMEX", - "uri_format": "http://identifiers.org/imex/$1" - }, - "mappings": { - "biocontext": "IMEX", - "miriam": "imex", - "n2t": "imex", - "prefixcommons": "imex" - }, - "miriam": { - "deprecated": false, - "description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.", - "homepage": "https://www.imexconsortium.org/", - "id": "00000122", - "name": "IMEx", - "namespaceEmbeddedInLui": false, - "pattern": "^IM-\\d+(-?)(\\d+?)$", - "prefix": "imex", - "providers": [ - { - "code": "CURATOR_REVIEW", - "description": "IMEx Consortium though Intact", - "homepage": "https://www.ebi.ac.uk/intact/", - "name": "IMEx Consortium though Intact", - "uri_format": "https://imexcentral.org/icentral/imex/rec/$1" - } - ], - "sampleId": "IM-19210-3", - "uri_format": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1" - }, - "n2t": { - "description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.", - "example": "IM-19210-3", - "homepage": "https://www.imexconsortium.org/", - "name": "IMEx Consortium running at EBI", - "namespaceEmbeddedInLui": false, - "pattern": "^IM-\\d+(-?)(\\d+?)$", - "prefix": "imex", - "uri_format": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1" - }, - "name": "International Molecular Exchange", - "prefixcommons": { - "description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.", - "example": "IM-12080-80", - "homepage": "http://disber.net/imexdrupal/", - "keywords": [ - "molecule", - "interaction" - ], - "name": "International Molecular Exchange", - "pattern": "^IM-\\d+(-?)(\\d+?)$", - "prefix": "imex", - "pubmed_ids": [ - "17893861" - ], - "uri_format": "http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1" - } - }, - "img.gene": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "IMG.GENE", - "uri_format": "http://identifiers.org/img.gene/$1" - }, - "mappings": { - "biocontext": "IMG.GENE", - "miriam": "img.gene", - "n2t": "img.gene", - "prefixcommons": "img.gene" - }, - "miriam": { - "deprecated": false, - "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.", - "homepage": "http://img.jgi.doe.gov/", - "id": "00000176", - "name": "Integrated Microbial Genomes Gene", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "img.gene", - "sampleId": "638309541", - "uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1" - }, - "n2t": { - "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. 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Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.", - "example": "RYYVLZVUVIJVGH-UHFFFAOYSA-N", - "homepage": "http://cactus.nci.nih.gov/chemical/structure", - "name": "InChiKey resolver at NCI", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])?", - "prefix": "inchikey", - "uri_format": "http://cactus.nci.nih.gov/chemical/structure/$1/names" - }, - "wikidata": { - "prefix": "P235" - } - }, - "inhand": { - "comment": "This nomenclature is available via email. Truly a disgrace.", - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", - "fairsharing": { - "abbreviation": "INHAND", - "description": "Standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", - "id": "392", - "name": "International Harmonization of Nomenclature and Diagnostic criteria", - "prefix": "FAIRsharing.9gqfpm", - "subjects": [ - "Biomedical Science" - ] - }, - "homepage": "https://www.goreni.org/gr3_nomenclature.php", - "mappings": { - "fairsharing": "FAIRsharing.9gqfpm" - }, - "name": "The International Harmonization of Nomenclature and Diagnostic criteria", - "proprietary": true - }, - "inn": { - "comment": "can not find a place to resolve to", - "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", - "example": "fluticasone", - "homepage": "https://www.who.int/teams/health-product-and-policy-standards/inn", - "name": "International Nonproprietary Names", - "synonyms": [ - "INN_ID" - ], - "uri_format": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1", - "wikidata": { - "prefix": "P2275" - } - }, - "ino": { - "biolink": { - "is_identifiers": false, - "is_obo": true, - "prefix": "INO", - "uri_format": "http://purl.obolibrary.org/obo/INO_$1" - }, - "bioportal": { - "name": "Interaction Network Ontology", - "prefix": "INO" - }, - "example": "0000003", - "fairsharing": { - "abbreviation": "INO", - "description": "The Interaction Network Ontology (INO) aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It models general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies, and includes over 500 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms.", - "id": "891", - "name": "Interaction Network Ontology", - "prefix": "FAIRsharing.mm72as", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biolink": "INO", - "bioportal": "INO", - "fairsharing": "FAIRsharing.mm72as", - "obofoundry": "ino", - "ols": "ino", - "ontobee": "INO" - }, - "obofoundry": { - "contact": "yongqunh@med.umich.edu", - "contact.github": "yongqunh", - "contact.label": "Yongqun Oliver He", - "contact.orcid": "0000-0001-9189-9661", - "deprecated": false, - "description": "An ontology of interactions and interaction networks", - "download.owl": "http://purl.obolibrary.org/obo/ino.owl", - "homepage": "https://github.com/INO-ontology/ino", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Interaction Network Ontology", - "preferredPrefix": "INO", - "prefix": "ino", - "repository": "https://github.com/INO-ontology/ino" - }, - "ols": { - "description": "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.", - "download": "http://purl.obolibrary.org/obo/ino.owl", - "homepage": "https://github.com/INO-ontology/ino", - "name": "INO: Interaction Network Ontology", - "prefix": "ino", - "version": "1.0.112" - }, - "ontobee": { - "library": "Library", - "name": "Interaction Network Ontology", - "prefix": "INO" - }, - "pattern": "^\\d{7}$" - }, - "insdc": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "INSDC", - "uri_format": "http://identifiers.org/insdc/$1" - }, - "mappings": { - "biocontext": "INSDC", - "miriam": "insdc", - "n2t": "insdc", - "prefixcommons": "insdc" - }, - "miriam": { - "deprecated": false, - "description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.", - "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", - "id": "00000029", - "name": "Nucleotide Sequence Database", - "namespaceEmbeddedInLui": false, - "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", - "prefix": "insdc", - "providers": [ - { - "code": "CURATOR_REVIEW", - "description": "INSDC through DDBJ", - "homepage": "http://www.ddbj.nig.ac.jp/", - "name": "INSDC through DDBJ", - "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1" - }, - { - "code": "ebi", - "description": "INSDC through European Nucleotide Archive (ENA)", - "homepage": "https://www.ebi.ac.uk/ena/", - "name": "INSDC through European Nucleotide Archive (ENA)", - "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" - }, - { - "code": "ncbi", - "description": "INSDC through Nucleotide database at NCBI", - "homepage": "https://www.ncbi.nlm.nih.gov/nuccore/", - "name": "INSDC through Nucleotide database at NCBI", - "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" - } - ], - "sampleId": "X58356", - "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" - }, - "n2t": { - "description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.", - "example": "X58356", - "homepage": "https://www.ncbi.nlm.nih.gov/nuccore/", - "name": "INSDC through Nucleotide database at NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", - "prefix": "insdc", - "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" - }, - "prefixcommons": { - "description": "The International Nucleotide Sequence Databases (INSD) have been developed and maintained collaboratively between DDBJ, EMBL, and GenBank for over 18 years.", - "example": "X58356", - "homepage": "http://www.insdc.org/", - "keywords": [ - "DNA" - ], - "name": "International Nucleotide Sequence Database Collaboration (GenBank, EMBL, DDBJ)", - "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", - "prefix": "insdc", - "pubmed_ids": [ - "17148479", - "17202161", - "2326192", - "12436968" - ] - } - }, - "insdc.cds": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "INSDC.CDS", - "uri_format": "http://identifiers.org/insdc.cds/$1" - }, - "has_canonical": "ncbiprotein", - "mappings": { - "biocontext": "INSDC.CDS", - "miriam": "insdc.cds", - "n2t": "insdc.cds" - }, - "miriam": { - "deprecated": false, - "description": "The coding sequence or protein identifiers as maintained in INSDC.", - "homepage": "http://getentry.ddbj.nig.ac.jp", - "id": "00000606", - "name": "INSDC CDS", - "namespaceEmbeddedInLui": false, - "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", - "prefix": "insdc.cds", - "providers": [ - { - "code": "CURATOR_REVIEW", - "description": "INSDC CDS through ENA", - "homepage": "https://www.ebi.ac.uk/ena", - "name": "INSDC CDS through ENA", - "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" - }, - { - "code": "CURATOR_REVIEW", - "description": "INSDC CDS through NCBI", - "homepage": "https://www.ncbi.nlm.nih.gov/protein/", - "name": "INSDC CDS through NCBI", - "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" - } - ], - "sampleId": "AAA35559", - "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1" - }, - "n2t": { - "description": "The coding sequence or protein identifiers as maintained in INSDC.", - "example": "AAA35559", - "homepage": "https://www.ncbi.nlm.nih.gov/protein/", - "name": "INSDC CDS through NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", - "prefix": "insdc.cds", - "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" - } - }, - "insdc.gca": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "INSDC.GCA", - "uri_format": "http://identifiers.org/insdc.gca/$1" - }, - "mappings": { - "biocontext": "INSDC.GCA", - "miriam": "insdc.gca", - "n2t": "insdc.gca" - }, - "miriam": { - "deprecated": false, - "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. 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The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.", - "example": "GCA_000155495.1", - "homepage": "https://www.ncbi.nlm.nih.gov/assembly/", - "name": "Genome assembly database NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^GCA_[0-9]{9}\\.[0-9]$", - "prefix": "insdc.gca", - "uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1" - } - }, - "insdc.run": { - "comment": "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --", - "contributor": { - "email": "cjmungall@lbl.gov", - "github": "cmungall", - "name": "Chris Mungall", - "orcid": "0000-0002-6601-2165" - }, - "description": "An experimental run, served thrugh the ENA", - "example": "ERR436051", - "has_canonical": "ena.embl", - "homepage": "https://www.insdc.org/", - "name": "International Nucleotide Sequence Database Collaboration (INSDC) Run", - "pattern": "^(E|D|S)RR[0-9]{6,}$", - "reviewer": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1" - }, - "insdc.sra": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "INSDC.SRA", - "uri_format": "http://identifiers.org/insdc.sra/$1" - }, - "fairsharing": { - "abbreviation": "SRA", - "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", - "id": "1978", - "name": "Sequence Read Archive", - "prefix": "FAIRsharing.g7t2hv", - "subjects": [ - "Virology", - "Life Science", - "Epidemiology" - ] - }, - "mappings": { - "biocontext": "INSDC.SRA", - "fairsharing": "FAIRsharing.g7t2hv", - "miriam": "insdc.sra", - "n2t": "insdc.sra" - }, - "miriam": { - "deprecated": false, - "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", - "homepage": "https://www.ncbi.nlm.nih.gov/sra", - "id": "00000243", - "name": "Sequence Read Archive", - "namespaceEmbeddedInLui": false, - "pattern": "^[SED]R[APRSXZ]\\d+$", - "prefix": "insdc.sra", - "providers": [ - { - "code": "ebi", - "description": "European Nucleotide Archive (ENA)", - "homepage": "https://www.ebi.ac.uk/ena", - "name": "European Nucleotide Archive (ENA)", - "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" - }, - { - "code": "ddbj", - "description": "DDBJ Sequence Read Archive (DRA)", - "homepage": "http://trace.ddbj.nig.ac.jp/dra/", - "name": "DDBJ Sequence Read Archive (DRA)", - "uri_format": "http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1" - } - ], - "sampleId": "SRX000007", - "uri_format": "https://www.ncbi.nlm.nih.gov/sra/$1" - }, - "n2t": { - "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", - "example": "SRX000007", - "homepage": "https://www.ncbi.nlm.nih.gov/sra", - "name": "Sequence Read Archive at NCBI", - "namespaceEmbeddedInLui": false, - "pattern": "^[SED]R[APRSXZ]\\d+$", - "prefix": "insdc.sra", - "uri_format": "https://www.ncbi.nlm.nih.gov/sra/$1" - } - }, - "intact": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "INTACT", - "uri_format": "http://identifiers.org/intact/$1" - }, - "fairsharing": { - "abbreviation": "IntAct", - "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.", - "id": "1599", - "name": "IntAct molecular interaction database", - "prefix": "FAIRsharing.d05nwx", - "subjects": [ - "Biology" - ] - }, - "go": { - "homepage": "https://www.ebi.ac.uk/intact/", - "name": "IntAct protein interaction database", - "prefix": "IntAct" - }, - "mappings": { - "biocontext": "INTACT", - "fairsharing": "FAIRsharing.d05nwx", - "go": "IntAct", - "miriam": "intact", - "n2t": "intact", - "prefixcommons": "intact", - "uniprot": "IntAct" - }, - "miriam": { - "deprecated": false, - "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.", - "homepage": "https://www.ebi.ac.uk/intact/", - "id": "00000010", - "name": "IntAct", - "namespaceEmbeddedInLui": false, - "pattern": "^EBI\\-[0-9]+$", - "prefix": "intact", - "sampleId": "EBI-2307691", - "uri_format": "https://www.ebi.ac.uk/intact/interaction/$1" - }, - "n2t": { - "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.", - "example": "EBI-2307691", - "homepage": "https://www.ebi.ac.uk/intact/", - "name": "IntAct at EBI", - "namespaceEmbeddedInLui": false, - "pattern": "^EBI\\-[0-9]+$", - "prefix": "intact", - "uri_format": "https://www.ebi.ac.uk/intact/interaction/$1" - }, - "prefixcommons": { - "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. 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This collection references interactor molecules.", - "homepage": "https://www.ebi.ac.uk/intact/", - "id": "00000427", - "name": "IntAct Molecule", - "namespaceEmbeddedInLui": false, - "pattern": "^EBI\\-[0-9]+$", - "prefix": "intact.molecule", - "sampleId": "EBI-366083", - "uri_format": "https://www.ebi.ac.uk/intact/molecule/$1" - }, - "n2t": { - "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. 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Final content review from NeuroLex is still ongoing.", - "id": "1118", - "name": "InterLex", - "prefix": "FAIRsharing.67sssf", - "subjects": [ - "Anatomy", - "Neurobiology", - "Biomedical Science" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.67sssf", - "miriam": "ilx" - }, - "miriam": { - "deprecated": false, - "description": "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. 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"kegg.dgroup": { - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "KEGG.DGROUP", - "uri_format": "http://www.kegg.jp/entry/$1" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. 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It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.", - "homepage": "https://www.genome.jp/kegg/glycan/", - "id": "00000026", - "name": "KEGG Glycan", - "namespaceEmbeddedInLui": false, - "pattern": "^G\\d+$", - "prefix": "kegg.glycan", - "sampleId": "G00123", - "uri_format": "https://www.kegg.jp/entry/$1" - }, - "n2t": { - "description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. 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It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.", - "example": "G00123", - "homepage": "http://www.genome.jp/kegg/glycan/", - "keywords": [ - "small molecule" - ], - "name": "KEGG Glycan", - "pattern": "^G\\d+$", - "prefix": "kegg.glycan", - "pubmed_ids": [ - "16014746" - ], - "uri_format": "http://www.genome.jp/dbget-bin/www_bget?gl:$1" - } - }, - "kegg.ligand": { - "comment": "This database has been discontinued by KEGG. 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Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.", - "example": "D00001", - "homepage": "http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en", - "name": "LigandBox at", - "namespaceEmbeddedInLui": false, - "pattern": "^D\\d{5}", - "prefix": "ligandbox", - "uri_format": "http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$1" - } - }, - "ligandexpo": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LIGANDEXPO", - "uri_format": "http://identifiers.org/ligandexpo/$1" - }, - "fairsharing": { - "abbreviation": "Ligand Expo", - "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.", - "id": "2043", - "name": "Ligand Expo", - "prefix": "FAIRsharing.2ma4gq", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "LIGANDEXPO", - "fairsharing": "FAIRsharing.2ma4gq", - "miriam": "ligandexpo", - "n2t": "ligandexpo", - "prefixcommons": "ligandexpo" - }, - "miriam": { - "deprecated": false, - "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.", - "homepage": "http://ligand-depot.rutgers.edu/index.html", - "id": "00000062", - "name": "Ligand Expo", - "namespaceEmbeddedInLui": false, - "pattern": "^(\\w){3}$", - "prefix": "ligandexpo", - "providers": [ - { - "code": "CURATOR_REVIEW", - "description": "Ligand Expo at Rutgers", - "homepage": "http://ligand-expo.rcsb.org/", - "name": "Ligand Expo at Rutgers", - "uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" - } - ], - "sampleId": "ABC", - "uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" - }, - "n2t": { - "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.", - "example": "ABC", - "homepage": "http://ligand-expo.rcsb.org/", - "name": "Ligand Expo at Rutgers", - "namespaceEmbeddedInLui": false, - "pattern": "^(\\w){3}$", - "prefix": "ligandexpo", - "uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" - }, - "prefixcommons": { - "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.", - "example": "ABC", - "homepage": "http://ligand-depot.rutgers.edu/", - "keywords": [ - "interaction", - "structure", - "protein", - "chemical", - "nucleic acid" - ], - "name": "Ligand Expo", - "pattern": "^(\\w){3}$", - "prefix": "ligandexpo", - "pubmed_ids": [ - "15059838" - ], - "uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" - } - }, - "ligea": { - "cellosaurus": { - "category": "Polymorphism and mutation databases", - "homepage": "http://hpc-bioinformatics.cineca.it/fusion/main", - "name": "Cancer cell LInes GEne fusions portAl", - "prefix": "LiGeA", - "uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1" - }, - "comment": "This might just be a provider for CCLE", - "example": "CCLE_867", - "mappings": { - "cellosaurus": "LiGeA" - } - }, - "limore": { - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "https://www.picb.ac.cn/limore/home", - "name": "Liver Cancer Model Repository", - "prefix": "LIMORE", - "uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1" - }, - "example": "Li7", - "mappings": { - "cellosaurus": "LIMORE" - } - }, - "lincs.cell": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LINCS.CELL", - "uri_format": "http://identifiers.org/lincs.cell/$1" - }, - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "http://lincsportal.ccs.miami.edu/cells/", - "name": "LINCS Data Portal", - "prefix": "LINCS_LDP", - "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" - }, - "mappings": { - "biocontext": "LINCS.CELL", - "cellosaurus": "LINCS_LDP", - "miriam": "lincs.cell", - "n2t": "lincs.cell" - }, - "miriam": { - "deprecated": false, - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", - "homepage": "http://lincsportal.ccs.miami.edu/cells/", - "id": "00000544", - "name": "LINCS Cell", - "namespaceEmbeddedInLui": false, - "pattern": "(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)", - "prefix": "lincs.cell", - "sampleId": "LCL-2085", - "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" - }, - "n2t": { - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", - "example": "LCL-2085", - "homepage": "http://lincsportal.ccs.miami.edu/cells/", - "name": "LINCS Portal", - "namespaceEmbeddedInLui": false, - "pattern": "(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)", - "prefix": "lincs.cell", - "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" - }, - "pattern": "^(LCL|LDC|ES|LSC|LPC)-\\d+$", - "synonyms": [ - "LINCS_LDP" - ] - }, - "lincs.data": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LINCS.DATA", - "uri_format": "http://identifiers.org/lincs.data/$1" - }, - "mappings": { - "biocontext": "LINCS.DATA", - "miriam": "lincs.data", - "n2t": "lincs.data" - }, - "miriam": { - "deprecated": false, - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).", - "homepage": "http://lincsportal.ccs.miami.edu/datasets/", - "id": "00000588", - "name": "LINCS Data", - "namespaceEmbeddedInLui": false, - "pattern": "^[EL]D[SG]-\\d+$", - "prefix": "lincs.data", - "providers": [ - { - "code": "omicsdi", - "description": "Lincs through OmicsDI", - "homepage": "https://www.omicsdi.org/", - "name": "Lincs through OmicsDI", - "uri_format": "https://www.omicsdi.org/dataset/lincs/$1" - } - ], - "sampleId": "LDS-1110", - "uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1" - }, - "n2t": { - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).", - "example": "LDS-1110", - "homepage": "http://lincsportal.ccs.miami.edu/datasets/", - "name": "LINCS Data at University of Miami", - "namespaceEmbeddedInLui": false, - "pattern": "^[EL]D[SG]-\\d+$", - "prefix": "lincs.data", - "uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1" - } - }, - "lincs.protein": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LINCS.PROTEIN", - "uri_format": "http://identifiers.org/lincs.protein/$1" - }, - "mappings": { - "biocontext": "LINCS.PROTEIN", - "miriam": "lincs.protein", - "n2t": "lincs.protein" - }, - "miriam": { - "deprecated": false, - "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.", - "homepage": "http://lincs.hms.harvard.edu/db/proteins/", - "id": "00000545", - "name": "LINCS Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "lincs.protein", - "sampleId": "200282", - "uri_format": "http://lincs.hms.harvard.edu/db/proteins/$1/" - }, - "n2t": { - "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.", - "example": "200282", - "homepage": "http://lincs.hms.harvard.edu/db/proteins/", - "name": "LINCS Protein at Harvard Medical School", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "lincs.protein", - "uri_format": "http://lincs.hms.harvard.edu/db/proteins/$1/" - }, - "uri_format": "https://lincs.hms.harvard.edu/db/proteins/$1" - }, - "lincs.smallmolecule": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LINCS.SMALLMOLECULE", - "uri_format": "http://identifiers.org/lincs.smallmolecule/$1" - }, - "mappings": { - "biocontext": "LINCS.SMALLMOLECULE", - "miriam": "lincs.smallmolecule", - "n2t": "lincs.smallmolecule" - }, - "miriam": { - "deprecated": false, - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", - "homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/", - "id": "00000546", - "name": "LINCS Small Molecule", - "namespaceEmbeddedInLui": false, - "pattern": "^LSM-\\d+$", - "prefix": "lincs.smallmolecule", - "sampleId": "LSM-6306", - "uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1" - }, - "n2t": { - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", - "example": "LSM-6306", - "homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/", - "name": "LINCS Portal", - "namespaceEmbeddedInLui": false, - "pattern": "^LSM-\\d+$", - "prefix": "lincs.smallmolecule", - "uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1" - }, - "synonyms": [ - "lincs" - ] - }, - "linguist": { - "homepage": "https://github.com/github/linguist", - "mappings": { - "miriam": "linguist" - }, - "miriam": { - "deprecated": false, - "description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.", - "homepage": "https://github.com/", - "id": "00000849", - "name": "Linguist", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-zA-Z0-9 +#'*]+$", - "prefix": "linguist", - "sampleId": "Python", - "uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1" - }, - "repository": "https://github.com/github/linguist" - }, - "lipidbank": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LIPIDBANK", - "uri_format": "http://identifiers.org/lipidbank/$1" - }, - "fairsharing": { - "abbreviation": "LipidBank", - "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", - "id": "2111", - "name": "LipidBank", - "prefix": "FAIRsharing.bdn9br", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "LIPIDBANK", - "fairsharing": "FAIRsharing.bdn9br", - "miriam": "lipidbank", - "n2t": "lipidbank", - "prefixcommons": "lipidbank" - }, - "miriam": { - "deprecated": false, - "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", - "homepage": "http://lipidbank.jp/index.html", - "id": "00000115", - "name": "LipidBank", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+\\d+$", - "prefix": "lipidbank", - "sampleId": "BBA0001", - "uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1" - }, - "n2t": { - "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", - "example": "BBA0001", - "homepage": "http://lipidbank.jp/index.html", - "name": "LipidBank the Lipid database", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+\\d+$", - "prefix": "lipidbank", - "uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1" - }, - "prefixcommons": { - "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", - "example": "BBA0001", - "homepage": "http://lipidbank.jp/index.html", - "keywords": [ - "lipid", - "molecule", - "structure" - ], - "name": "LipidBank", - "pattern": "^\\w+\\d+$", - "prefix": "lipidbank", - "pubmed_ids": [ - "12058481" - ], - "uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1" - } - }, - "lipidmaps": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LIPIDMAPS", - "uri_format": "http://identifiers.org/lipidmaps/$1" - }, - "cheminf": { - "description": "Identifier used by the LipidMaps database, http://www.lipidmaps.org/.", - "name": "LipidMaps", - "obsolete": false, - "prefix": "000564" - }, - "fairsharing": { - "abbreviation": "LIPID MAPS", - "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", - "id": "2090", - "name": "LIPID MAPS", - "prefix": "FAIRsharing.cpneh8", - "subjects": [ - "Endocrinology", - "Life Science", - "Biomedical Science", - "Systems Biology" - ] - }, - "mappings": { - "biocontext": "LIPIDMAPS", - "cheminf": "000564", - "fairsharing": "FAIRsharing.cpneh8", - "miriam": "lipidmaps", - "n2t": "lipidmaps", - "prefixcommons": "lipidmaps", - "scholia": "lipidmaps" - }, - "miriam": { - "deprecated": false, - "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", - "homepage": "http://www.lipidmaps.org", - "id": "00000052", - "name": "LIPID MAPS", - "namespaceEmbeddedInLui": false, - "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", - "prefix": "lipidmaps", - "providers": [ - { - "code": "scholia", - "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", - "homepage": "https://scholia.toolforge.org/", - "name": "Scholia", - "uri_format": "https://scholia.toolforge.org/lipidmaps/$1" - } - ], - "sampleId": "LMPR0102010012", - "uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1" - }, - "n2t": { - "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", - "example": "LMPR0102010012", - "homepage": "http://www.lipidmaps.org", - "name": "Department of Bioengineering and the San Diego Supercomputer Center", - "namespaceEmbeddedInLui": false, - "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", - "prefix": "lipidmaps", - "uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1" - }, - "prefixcommons": { - "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", - "example": "LMPR0102010012", - "homepage": "http://www.lipidmaps.org", - "keywords": [ - "lipid", - "structure", - "taxonomy" - ], - "name": "LIPID MAPS", - "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", - "prefix": "lipidmaps", - "pubmed_ids": [ - "17098933", - "15722563" - ], - "uri_format": "http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=$1" - }, - "synonyms": [ - "LIPID MAPS", - "LIPID_MAPS_class", - "LIPID_MAPS_instance" - ], - "wikidata": { - "prefix": "P2063" - } - }, - "lipro": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "LIPRO", - "uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1" - }, - "bioportal": { - "name": "Lipid Ontology", - "prefix": "LIPRO" - }, - "mappings": { - "biocontext": "LIPRO", - "bioportal": "LIPRO", - "obofoundry": "lipro" - }, - "obofoundry": { - "contact": "bakerc@unb.ca", - "contact.label": "Christipher Baker", - "deprecated": true, - "description": "An ontology representation of the LIPIDMAPS nomenclature classification.", - "name": "Lipid Ontology", - "prefix": "lipro" - } - }, - "lncipedia": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "A comprehensive compendium of human long non-coding RNAs", - "example": "SNHG3", - "fairsharing": { - "abbreviation": "LNCipedia", - "description": "LNCipedia is a database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria.", - "id": "2647", - "name": "LNCipedia", - "prefix": "FAIRsharing.84c1a7", - "subjects": [ - "Life Science" - ] - }, - "homepage": "https://lncipedia.org", - "mappings": { - "fairsharing": "FAIRsharing.84c1a7" - }, - "name": "LNCipedia" - }, - "loggerhead": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "LOGGERHEAD", - "uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1" - }, - "mappings": { - "biocontext": "LOGGERHEAD", - "obofoundry": "loggerhead" - }, - "obofoundry": { - "contact": "peteremidford@yahoo.com", - "contact.label": "Peter Midford", - "contact.orcid": "0000-0001-6512-3296", - "deprecated": true, - "homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html", - "name": "Loggerhead nesting", - "prefix": "loggerhead" - } - }, - "loinc": { - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "LOINC", - "uri_format": "http://loinc.org/rdf/$1" - }, - "bioportal": { - "name": "Logical Observation Identifier Names and Codes", - "prefix": "LOINC" - }, - "description": "The international standard for identifying health measurements, observations, and documents.", - "example": "LL379-9", - "fairsharing": { - "abbreviation": "LOINC", - "description": "LOINC is a common language (set of identifiers, names, and codes) for clinical and laboratory observations. LOINC is a catalog of measurements, including laboratory tests, clinical measures like vital signs and anthropomorphic measures, standardized survey instruments, and more. LOINC enables the exchange and aggregation of clinical results for care delivery, outcomes management, and research by providing a set of universal codes and structured names to unambiguously identify things you can measure or observe.", - "id": "2", - "name": "Logical Observation Identifier Names and Codes", - "prefix": "FAIRsharing.2mk2zb", - "subjects": [ - "Life Science", - "Biomedical Science", - "Preclinical Studies" - ] - }, - "homepage": "https://loinc.org/", - "mappings": { - "biolink": "LOINC", - "bioportal": "LOINC", - "fairsharing": "FAIRsharing.2mk2zb" - }, - "name": "Logical Observation Identifiers Names and Codes", - "synonyms": [ - "LNC" - ], - "uri_format": "https://loinc.org/$1" - }, - "lonza": { - "cellosaurus": { - "category": "Cell line databases/resources", - "homepage": "https://knowledge.lonza.com", - "name": "Lonza Cell and Transfection Database", - "prefix": "Lonza", - "uri_format": "https://knowledge.lonza.com/cell?id=$1" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Contains information about cells and data sheets related to transfection.", - "example": "968", - "homepage": "https://knowledge.lonza.com", - "mappings": { - "cellosaurus": "Lonza" - }, - "name": "Lonza", - "pattern": "^\\d+$", - "uri_format": "https://knowledge.lonza.com/cell?id=$1" - }, - "lotus": { - "comment": "IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case.", - "contact": { - "email": "adriano.rutz@ik.me", - "github": "adafede", - "name": "Adriano Rutz", - "orcid": "0000-0003-0443-9902" - }, - "contributor": { - "github": "adafede", - "name": "Adriano Rutz", - "orcid": "0000-0003-0443-9902" - }, - "description": "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts\u2019s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry.", - "example": "LTS0004651", - "homepage": "https://lotus.naturalproducts.net", - "name": "LOTUS Initiative for Open Natural Products Research", - "pattern": "^LTS\\d{7}$", - "reviewer": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "uri_format": "https://lotus.naturalproducts.net/compound/lotus_id/$1", - "wikidata": { - "database": "Q104225190" - } - }, - "lpt": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "LPT", - "uri_format": "http://purl.obolibrary.org/obo/LPT_$1" - }, - "bioportal": { - "name": "Livestock Product Trait Ontology", - "prefix": "LPT" - }, - "contact": { - "email": "caripark@iastate.edu", - "github": "caripark", - "name": "Carissa Park", - "orcid": "0000-0002-2346-5201" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.", - "download_obo": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo", - "download_owl": "https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl", - "example": "0000001", - "fairsharing": { - "abbreviation": "LPT", - "description": "The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.", - "id": "739", - "name": "Livestock Product Trait Ontology", - "prefix": "FAIRsharing.g78mbm", - "subjects": [] - }, - "homepage": "https://github.com/AnimalGenome/livestock-product-trait-ontology", - "mappings": { - "biocontext": "LPT", - "bioportal": "LPT", - "fairsharing": "FAIRsharing.g78mbm" - }, - "name": "Livestock Product Trait Ontology", - "pattern": "^\\d+$", - "repository": "https://github.com/AnimalGenome/livestock-product-trait-ontology" - }, - "lrg": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "LRG", - "uri_format": "http://identifiers.org/lrg/$1" - }, - "mappings": { - "biocontext": "LRG", - "miriam": "lrg", - "n2t": "lrg" - }, - "miriam": { - "deprecated": false, - "description": "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI.", - "homepage": "http://www.lrg-sequence.org/", - "id": "00000376", - "name": "Locus Reference Genomic", - "namespaceEmbeddedInLui": false, - "pattern": "^LRG_\\d+$", - "prefix": "lrg", - "providers": [ - { - "code": "CURATOR_REVIEW", - "description": "Locus Reference Genomic through Ensembl", - "homepage": "http://www.ensembl.org/", - "name": "Locus Reference Genomic through Ensembl", - "uri_format": "http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" - }, - { - "code": "CURATOR_REVIEW", - "description": "Locus Reference Genomic through Ensembl mirror (asia)", - "homepage": "http://asia.ensembl.org/", - "name": "Locus Reference Genomic through Ensembl mirror (asia)", - "uri_format": "http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" - }, - { - "code": "CURATOR_REVIEW", - "description": "Locus Reference Genomic through Ensembl mirror (US west)", - "homepage": "http://uswest.ensembl.org/", - "name": "Locus Reference Genomic through Ensembl mirror (US west)", - "uri_format": "http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" - }, - { - "code": "CURATOR_REVIEW", - "description": "Locus Reference Genomic through Ensembl mirror (US east)", - "homepage": "http://useast.ensembl.org/", - "name": "Locus Reference Genomic through Ensembl mirror (US east)", - "uri_format": "http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" - } - ], - "sampleId": "LRG_1", - "uri_format": "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml" - }, - "n2t": { - "description": "Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI).", - "example": "LRG_1", - "homepage": "http://uswest.ensembl.org/", - "name": "Locus Reference Genomic through Ensembl mirror (US west)", - "namespaceEmbeddedInLui": false, - "pattern": "^LRG_\\d+$", - "prefix": "lrg", - "uri_format": "http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" - } - }, - "lspci": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)", - "example": "1", - "homepage": "https://labsyspharm.github.io/lspci/", - "name": "Laboratory of Systems Pharmacology Compound", - "pattern": "^\\d+$", - "uri_format": "https://labsyspharm.github.io/lspci/$1" - }, - "lter": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Ecological terms", - "example": "182", - "homepage": "https://vocab.lternet.edu/vocab/vocab/index.php", - "name": "Long Term Ecological Research Controlled Vocabulary", - "pattern": "^\\d+$", - "uri_format": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1" - }, - "ma": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MA", - "uri_format": "http://purl.obolibrary.org/obo/MA_$1" - }, - "bioportal": { - "name": "Mouse Adult Gross Anatomy Ontology", - "prefix": "MA" - }, - "fairsharing": { - "abbreviation": "MA", - "description": "The Mouse Adult Gross Anatomy ontology also has aliases of 'Mouse Anatomy' or 'Mouse anatomical entity'. The resource is a standard, providing a structured vocabulary for the adult anatomy of the mouse. This ontology is part of the Gene Expression Database (GDX) Project of the Jackson Laboratory.", - "id": "13", - "name": "Mouse Adult Gross Anatomy Ontology", - "prefix": "FAIRsharing.pdwqcr", - "subjects": [ - "Anatomy", - "Life Science" - ] - }, - "go": { - "description": "Adult Mouse Anatomical Dictionary; part of Gene Expression Database", - "homepage": "http://www.informatics.jax.org/", - "name": "Adult Mouse Anatomical Dictionary", - "prefix": "MA", - "uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1" - }, - "mappings": { - "biocontext": "MA", - "bioportal": "MA", - "fairsharing": "FAIRsharing.pdwqcr", - "go": "MA", - "miriam": "ma", - "n2t": "ma", - "obofoundry": "ma", - "ols": "ma", - "ontobee": "MA", - "prefixcommons": "ma" - }, - "miriam": { - "deprecated": false, - "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)", - "homepage": "http://www.informatics.jax.org/", - "id": "00000445", - "name": "Mouse Adult Gross Anatomy", - "namespaceEmbeddedInLui": true, - "pattern": "^MA:\\d+$", - "prefix": "ma", - "sampleId": "0002502", - "uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1" - }, - "n2t": { - "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)", - "example": "0002502", - "homepage": "http://www.informatics.jax.org/", - "name": "Mouse Adult Gross Anatomy at The Jackson Laboratory", - "namespaceEmbeddedInLui": true, - "pattern": "^MA:\\d+$", - "prefix": "ma", - "uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1" - }, - "obofoundry": { - "contact": "Terry.Hayamizu@jax.org", - "contact.github": "tfhayamizu", - "contact.label": "Terry Hayamizu", - "contact.orcid": "0000-0002-0956-8634", - "deprecated": false, - "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).", - "download.obo": "http://purl.obolibrary.org/obo/ma.obo", - "download.owl": "http://purl.obolibrary.org/obo/ma.owl", - "homepage": "https://github.com/obophenotype/mouse-anatomy-ontology", - "license": "CC BY 4.0", - "license.url": "https://creativecommons.org/licenses/by/4.0/", - "name": "Mouse adult gross anatomy", - "preferredPrefix": "MA", - "prefix": "ma", - "repository": "https://github.com/obophenotype/mouse-anatomy-ontology" - }, - "ols": { - "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).", - "download": "http://purl.obolibrary.org/obo/ma.owl", - "homepage": "https://github.com/obophenotype/mouse-anatomy-ontology", - "name": "Mouse adult gross anatomy", - "prefix": "ma", - "version": "2017-02-07", - "version.iri": "http://purl.obolibrary.org/obo/ma/releases/2017-02-07/ma.owl" - }, - "ontobee": { - "library": "Library", - "name": "Mouse adult gross anatomy", - "prefix": "MA" - }, - "pattern": "^\\d+$", - "prefixcommons": { - "bioportal": "1000", - "description": "A structured controlled vocabulary of the adult anatomy of the mouse (Mus).", - "example": "MA:0000021", - "homepage": "http://www.informatics.jax.org/searches/AMA_form.shtml", - "keywords": [ - "obo", - "anatomy", - "mouse" - ], - "name": "Mouse adult gross anatomy", - "pattern": "^MA:\\d+$", - "prefix": "ma" - } - }, - "macie": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MACIE", - "uri_format": "http://identifiers.org/macie/$1" - }, - "fairsharing": { - "abbreviation": "MACiE", - "description": "MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. The database contains the reaction mechanisms for 100 individual enzymes; this includes the overall reactions and the multiple steps that constitute them.", - "id": "1602", - "name": "Mechanism, Annotation and Classification in Enzymes", - "prefix": "FAIRsharing.7xkx69", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "MACIE", - "fairsharing": "FAIRsharing.7xkx69", - "miriam": "macie", - "n2t": "macie", - "prefixcommons": "macie" - }, - "miriam": { - "deprecated": false, - "description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.", - "homepage": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html", - "id": "00000077", - "name": "MACiE", - "namespaceEmbeddedInLui": false, - "pattern": "^M\\d{4}$", - "prefix": "macie", - "sampleId": "M0001", - "uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1" - }, - "n2t": { - "description": "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved.", - "example": "M0001", - "homepage": "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html", - "name": "MACiE database of mechanisms, annotation and classification in enzymes", - "namespaceEmbeddedInLui": false, - "pattern": "^M\\d{4}$", - "prefix": "macie", - "uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1" - }, - "name": "Mechanism, Annotation and Classification in Enzymes", - "prefixcommons": { - "description": "MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. 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] - }, - "go": { - "homepage": "https://www.maizegdb.org/", - "name": "MaizeGDB", - "prefix": "MaizeGDB_Locus", - "uri_format": "https://www.maizegdb.org/gene_center/gene/$1" - }, - "mappings": { - "biocontext": "MAIZEGDB.LOCUS", - "fairsharing": "FAIRsharing.aq280w", - "go": "MaizeGDB_Locus", - "miriam": "maizegdb.locus", - "n2t": "maizegdb.locus", - "ncbi": "MaizeGDB", - "prefixcommons": "maizegdb", - "uniprot": "MaizeGDB" - }, - "miriam": { - "deprecated": false, - "description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.", - "homepage": "http://www.maizegdb.org/", - "id": "00000177", - "name": "MaizeGDB Locus", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "maizegdb.locus", - "sampleId": "25011", - "uri_format": "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1" - }, - "n2t": { - "description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.", - 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"comment": "Replacement for MaizeDB", - "identifier": "58", - "link_is_explicit": "true", - "name": "Maize Genetics and Genomics Database", - "prefix": "MaizeGDB", - "uri_format": "https://www.maizegdb.org/data_center/gene_product?id=$1" - } - }, - "mamo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MAMO", - "uri_format": "http://purl.obolibrary.org/obo/MAMO_$1" - }, - "bioportal": { - "name": "Mathematical Modelling Ontology", - "prefix": "MAMO" - }, - "example": "0000026", - "fairsharing": { - "abbreviation": "MAMO", - "description": "Classification of the types of mathematical models used mostly in the life sciences, the types of variables, the types of readout and other relevant features.", - "id": "178", - "name": "Mathematical Modelling Ontology", - "prefix": "FAIRsharing.kbz5jh", - "subjects": [ - "Mathematics", - "Computational Biology", - "Systems Biology" - ] - }, - "mappings": { - "biocontext": "MAMO", - "bioportal": "MAMO", - "fairsharing": "FAIRsharing.kbz5jh", - "miriam": "mamo", - "n2t": "mamo", - "obofoundry": "mamo", - "ols": "mamo", - "ontobee": "MAMO" - }, - "miriam": { - "deprecated": false, - "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", - "homepage": "http://bioportal.bioontology.org/ontologies/MAMO", - "id": "00000517", - "name": "Mathematical Modelling Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^MAMO_\\d{7}$", - "prefix": "mamo", - "sampleId": "MAMO_0000026", - "uri_format": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1" - }, - "n2t": { - "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", - "example": "MAMO_0000026", - "homepage": "http://bioportal.bioontology.org/ontologies/MAMO", - "name": "MAMO through BioPortal", - "namespaceEmbeddedInLui": false, - "pattern": "^MAMO_\\d{7}$", - "prefix": "mamo", - "uri_format": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1" - }, - "obofoundry": { - "contact": "nicolas@ascistance.co.uk", - "contact.github": "gambardella", - "contact.label": "Nicolas Gambardella", - "contact.orcid": "0000-0002-6309-7327", - "deprecated": false, - "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", - "download.owl": "http://purl.obolibrary.org/obo/mamo.owl", - "homepage": "http://sourceforge.net/p/mamo-ontology/wiki/Home/", - "license": "Artistic License 2.0", - "license.url": "http://opensource.org/licenses/Artistic-2.0", - "name": "Mathematical modeling ontology", - "preferredPrefix": "MAMO", - "prefix": "mamo", - "repository": "http://sourceforge.net/p/mamo-ontology" - }, - "ols": { - "download": "http://purl.obolibrary.org/obo/mamo.owl", - "name": "Mathematical Modelling Ontology", - "prefix": "mamo", - "version": "2020-08-24" - }, - "ontobee": { - "library": "Library", - "name": "Mathematical modeling ontology", - "prefix": "MAMO" - }, - "pattern": "^\\d{7}$", - "uri_format": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1" - }, - "mao": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MAO", - "uri_format": "http://purl.obolibrary.org/obo/MAO_$1" - }, - "mappings": { - "biocontext": "MAO", - "obofoundry": "mao", - "prefixcommons": "mao" - }, - "obofoundry": { - "contact": "julie@igbmc.u-strasbg.fr", - "contact.label": "Julie Thompson", - "deprecated": true, - "homepage": "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html", - "name": "Multiple alignment", - "prefix": "mao" - }, - "prefixcommons": { - "bioportal": "1026", - "description": "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.", - 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In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", - "example": "ERP004492", - "homepage": "https://www.ebi.ac.uk/metagenomics", - "name": "MGnify Project", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z]+[0-9]+$", - "prefix": "mgnify.proj", - "uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1" - } - }, - "mgnify.samp": { - "mappings": { - "miriam": "mgnify.samp", - "n2t": "mgnify.samp" - }, - "miriam": { - "deprecated": false, - "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", - "homepage": "https://www.ebi.ac.uk/metagenomics", - "id": "00000510", - "name": "MGnify Sample", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z]+[0-9]+$", - "prefix": "mgnify.samp", - "sampleId": "SRS086444", - "uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1" - }, - "n2t": { - "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", - "example": "SRS086444", - "homepage": "https://www.ebi.ac.uk/metagenomics", - "name": "MGnify Sample", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z]+[0-9]+$", - "prefix": "mgnify.samp", - "uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1" - } - }, - "mi": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MI", - "uri_format": "http://purl.obolibrary.org/obo/MI_$1" - }, - "biolink": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MI", - "uri_format": "http://purl.obolibrary.org/obo/MI_$1" - }, - "bioportal": { - "name": "Molecular Interactions", - "prefix": "MI" - }, - "example": "0058", - "go": { - "homepage": "http://www.psidev.info/", - "name": "Proteomic Standard Initiative for Molecular Interaction", - "prefix": "PSI-MI", - "synonyms": [ - "MI" - ] - }, - "mappings": { - "biocontext": "MI", - "biolink": "MI", - "bioportal": "MI", - "go": "PSI-MI", - "miriam": "mi", - "n2t": "psimi", - "obofoundry": "mi", - "ols": "mi", - "ontobee": "MI", - "prefixcommons": "psi.mi" - }, - "miriam": { - "deprecated": false, - "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/mi", - "id": "00000109", - "name": "Molecular Interactions Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^MI:\\d{4}$", - "prefix": "mi", - "sampleId": "0308", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1" - }, - "n2t": { - "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", - "example": "0308", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/mi", - "name": "Molecular Interactions Ontology through OLS", - "namespaceEmbeddedInLui": true, - "pattern": "^MI:\\d{4}$", - "prefix": "psimi", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1" - }, - "obofoundry": { - "contact": "pporras@ebi.ac.uk", - "contact.github": "pporrasebi", - "contact.label": "Pablo Porras Mill\u00e1n", - "contact.orcid": "0000-0002-8429-8793", - "deprecated": false, - "description": "A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions.", - "download.obo": "http://purl.obolibrary.org/obo/mi.obo", - "download.owl": "http://purl.obolibrary.org/obo/mi.owl", - "homepage": "https://github.com/HUPO-PSI/psi-mi-CV", - "license": "CC BY 4.0", - "license.url": "https://creativecommons.org/licenses/by/4.0/", - "name": "Molecular Interactions Controlled Vocabulary", - "preferredPrefix": "MI", - "prefix": "mi", - "repository": "https://github.com/HUPO-PSI/psi-mi-CV" - }, - "ols": { - "download": "https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo", - "name": "mi", - "prefix": "mi", - "version.iri": "http://purl.obolibrary.org/obo/mi/releases/2020-04-13/mi.owl" - }, - "ontobee": { - "library": "Library", - "name": "Molecular Interactions Controlled Vocabulary", - "prefix": "MI" - }, - "pattern": "^\\d{4}$", - "prefixcommons": { - "bioportal": "1040", - "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", - "example": "MI:0308", - "homepage": "http://psidev.sf.net", - "keywords": [ - "obo", - "interaction", - "molecule" - ], - "name": "Proteomic Standard Initiative for Molecular Interaction", - "pattern": "^MI:\\d{4}$", - "prefix": "psi.mi", - "pubmed_ids": [ - "14755292" - ] - }, - "synonyms": [ - "PSI-MI" - ] - }, - "miaa": { - "comment": "same as MAT", - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "deprecated": true, - "name": "Minimal Information About Anatomy ontology", - "references": [ - "https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf" - ] - }, - "miapa": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MIAPA", - "uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1" - }, - "bioportal": { - "name": "MIAPA Ontology", - "prefix": "MIAPA" - }, - "example": "0000010", - "fairsharing": { - "abbreviation": "MIAPA", - "description": "The MIAPA (minimum information about a phylogenetic analysis) checklist details the list of metadata necessary for researchers to evaluate or reuse a published phylogeny.", - "id": "94", - "name": "Minimal Information About a Phylogenetic Analysis", - "prefix": "FAIRsharing.ca48xs", - "subjects": [ - "Phylogeny", - "Phylogenetics", - "Life Science" - ] - }, - "mappings": { - "biocontext": "MIAPA", - "bioportal": "MIAPA", - "fairsharing": "FAIRsharing.ca48xs", - "obofoundry": "miapa", - "ols": "miapa", - "ontobee": "MIAPA" - }, - "name": "Minimum Anformation About a Phylogenetic Analysis Ontology", - "obofoundry": { - "contact": "hilmar.lapp@duke.edu", - "contact.github": "hlapp", - "contact.label": "Hilmar Lapp", - "contact.orcid": "0000-0001-9107-0714", - "deprecated": false, - "description": "An application ontology to formalize annotation of phylogenetic data.", - "download.owl": "http://purl.obolibrary.org/obo/miapa.owl", - "homepage": "http://www.evoio.org/wiki/MIAPA", - "license": "CC0 1.0", - "license.url": "http://creativecommons.org/publicdomain/zero/1.0/", - "name": "MIAPA Ontology", - "preferredPrefix": "MIAPA", - "prefix": "miapa", - "repository": "https://github.com/evoinfo/miapa" - }, - "ols": { - "description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.", - "download": "http://purl.obolibrary.org/obo/miapa.owl", - "homepage": "http://www.evoio.org/wiki/MIAPA", - "name": "Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology", - "prefix": "miapa", - "version": "2017-05-09", - "version.iri": "http://purl.obolibrary.org/obo/miapa/2013-02-01/miapa.owl" - }, - "ontobee": { - "library": "Library", - "name": "MIAPA Ontology", - "prefix": "MIAPA" - }, - "pattern": "^\\d{7}$" - }, - "micro": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MICRO", - "uri_format": "http://purl.obolibrary.org/obo/MICRO_$1" - }, - "example": "0002999", - "fairsharing": { - "abbreviation": "MicrO", - "description": "MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource.", - "id": "1150", - "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", - "prefix": "FAIRsharing.brhpb0", - "subjects": [ - "Bioinformatics", - "Microbiology" - ] - }, - "mappings": { - "biocontext": "MICRO", - "fairsharing": "FAIRsharing.brhpb0", - "obofoundry": "micro", - "ols": "micro", - "ontobee": "MicrO" - }, - "obofoundry": { - "appears_in": [ - "mco" - ], - "contact": "carrine.blank@umontana.edu", - "contact.github": "carrineblank", - "contact.label": "Carrine Blank", - "contact.orcid": "0000-0002-2100-6351", - "deprecated": false, - "description": "An ontology of prokaryotic phenotypic and metabolic characters", - "download.owl": "http://purl.obolibrary.org/obo/micro.owl", - "homepage": "https://github.com/carrineblank/MicrO", - "license": "CC BY 2.0", - "license.url": "https://creativecommons.org/licenses/by/2.0/", - "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", - "preferredPrefix": "MICRO", - "prefix": "micro", - "repository": "https://github.com/carrineblank/MicrO" - }, - "ols": { - "description": "An ontology of prokaryotic phenotypic and metabolic characters", - "download": "http://purl.obolibrary.org/obo/micro.owl", - "homepage": "https://github.com/carrineblank/MicrO", - "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", - "prefix": "micro", - "version": "1.5.1" - }, - "ontobee": { - "library": "Library", - "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", - "prefix": "MicrO" - }, - "pattern": "^\\d{7}$" - }, - "microscope": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MICROSCOPE", - "uri_format": "http://identifiers.org/microscope/$1" - }, - "fairsharing": { - "abbreviation": "MicroScope", - "description": "MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and metabolic analysis specific to each genome.", - "id": "2390", - "name": "Microbial Genome Annotation & Analysis Platform", - "prefix": "FAIRsharing.3t5qc3", - "subjects": [ - "Life Science", - "Comparative Genomics" - ] - }, - "mappings": { - "biocontext": "MICROSCOPE", - "fairsharing": "FAIRsharing.3t5qc3", - "miriam": "microscope", - "n2t": "microscope" - }, - "miriam": { - "deprecated": false, - "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", - "homepage": "http://www.genoscope.cns.fr/agc/microscope", - "id": "00000631", - "name": "MicroScope", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "microscope", - "sampleId": "5601141", - "uri_format": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1" - }, - "n2t": { - "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", - "example": "5601141", - "homepage": "http://www.genoscope.cns.fr/agc/microscope", - "name": "MicroScope", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "microscope", - "uri_format": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1" - } - }, - "microsporidia": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MICROSPORIDIA", - "uri_format": "http://identifiers.org/microsporidia/$1" - }, - "mappings": { - "biocontext": "MICROSPORIDIA", - "miriam": "microsporidia", - "n2t": "microsporidia", - "prefixcommons": "microsporidia" - }, - "miriam": { - "deprecated": false, - "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", - "homepage": "http://microsporidiadb.org/micro/", - "id": "00000152", - "name": "MicrosporidiaDB", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "microsporidia", - "sampleId": "ECU03_0820i", - "uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" - }, - "n2t": { - "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", - "example": "ECU03_0820i", - "homepage": "http://microsporidiadb.org/micro/", - "name": "MicrosporidiaDB at EuPathDB", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+$", - "prefix": "microsporidia", - "uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" - }, - "prefixcommons": { - "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", - "example": "ECU03_0820i", - "homepage": "http://microsporidiadb.org/micro/", - "keywords": [ - "eukaryotic", - "genome" - ], - "name": "MicrosporidiaDB", - "pattern": "^\\w+$", - "prefix": "microsporidia", - "pubmed_ids": [ - "19914931" - ], - "uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" - } - }, - "millipore": { - "cellosaurus": { - "category": "Cell line collections", - "homepage": "https://www.merckmillipore.com/", - "name": "Merck Millipore (EMD Millipore)", - "prefix": "Millipore", - "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" - }, - "example": "SCC111", - "mappings": { - "cellosaurus": "Millipore" - } - }, - "mimodb": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MIMODB", - "uri_format": "http://identifiers.org/mimodb/$1" - }, - "fairsharing": { - "abbreviation": "MimoDB", - "description": "Mimotope database, active site-mimicking peptides selected from phage-display libraries. It is a database which stores information on peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues, organs, and even entire organisms through phage display technology. Besides the peptide sequences, other information such as the corresponding target, template, library, and structures are also stored. All entries are manually extracted from published peer review articles and other public data sources such as Uniprot, GenBank and PDBSum.", - "id": "1606", - "name": "Mimotope Database", - "prefix": "FAIRsharing.bv0zjz", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "MIMODB", - "fairsharing": "FAIRsharing.bv0zjz", - "miriam": "mimodb", - "n2t": "mimodb", - "prefixcommons": "mimodb" - }, - "miriam": { - "deprecated": false, - "description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.", - "homepage": "http://immunet.cn/bdb/", - "id": "00000251", - "name": "MimoDB", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "mimodb", - "sampleId": "1", - "uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1" - }, - "n2t": { - "description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.", - "example": "1", - "homepage": "http://immunet.cn/bdb/", - "name": "BDB at University of Electronic Science and Technology of China", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "mimodb", - "uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1" - }, - "prefixcommons": { - "description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. 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It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.", - "download": "http://purl.obolibrary.org/obo/mop.owl", - "homepage": "https://github.com/rsc-ontologies/rxno", - "name": "MOP", - "prefix": "mop", - "version": "2022-02-01", - "version.iri": "http://purl.obolibrary.org/obo/mop/releases/2022-02-01/mop.owl" - }, - "ontobee": { - "library": "Library", - "name": "Molecular Process Ontology", - "prefix": "MOP" - }, - "pattern": "^\\d{7}$" - }, - "morpheus": { - "mappings": { - "miriam": "morpheus" - }, - "miriam": { - "deprecated": false, - "description": "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n", - "homepage": "https://morpheus.gitlab.io/", - "id": "00000725", - "name": "Morpheus model repository", - "namespaceEmbeddedInLui": false, - "pattern": "^M[0-9]{4,}$", - "prefix": "morpheus", - "sampleId": "M0001", - "uri_format": "https://morpheus.gitlab.io/models/$1" - } - }, - "mp": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MP", - "uri_format": "http://purl.obolibrary.org/obo/MP_$1" - }, - "bioportal": { - "name": "Mammalian Phenotype Ontology", - "prefix": "MP" - }, - "fairsharing": { - "abbreviation": "MP", - "description": "The observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan.", - "id": "75", - "name": "Mammalian Phenotype Ontology", - "prefix": "FAIRsharing.kg1x4z", - "subjects": [ - "Developmental Biology", - "Life Science", - "Physiology" - ] - }, - "mappings": { - "biocontext": "MP", - "bioportal": "MP", - "fairsharing": "FAIRsharing.kg1x4z", - "miriam": "mp", - "n2t": "mp", - "obofoundry": "mp", - "ols": "mp", - "ontobee": "MP", - "prefixcommons": "mp" - }, - "miriam": { - "deprecated": false, - "description": "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.", - "homepage": "http://www.informatics.jax.org/", - "id": "00000580", - "name": "Mammalian Phenotype Ontology", - "namespaceEmbeddedInLui": true, - "pattern": "^MP:\\d{7}$", - "prefix": "mp", - "sampleId": "0005452", - "uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1" - }, - "n2t": { - "description": "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. 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Smith, Susan M. Bello, Anna, Anagnostopoulos, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org, Susan.Bello@jax.org or to GitHub tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330.", - "download": "http://purl.obolibrary.org/obo/mp.owl", - "homepage": "http://www.informatics.jax.org/searches/MP_form.shtml", - "name": "The Mammalian Phenotype Ontology", - "prefix": "mp", - "version.iri": "http://purl.obolibrary.org/obo/mp/releases/2022-04-21" - }, - "ontobee": { - "library": "Library", - "name": "Mammalian Phenotype Ontology", - "prefix": "MP" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1025", - "description": "The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data.", - "example": "MP:0000001", - "homepage": "http://www.informatics.jax.org/searches/MP_form.shtml", - "keywords": [ - "obo", - "phenotype", - "mammalian" - ], - "name": "Mammalian phenotype", - "pattern": "^MP:\\d+$", - "prefix": "mp", - "uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=$1" - } - }, - "mpath": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MPATH", - "uri_format": "http://purl.obolibrary.org/obo/MPATH_$1" - }, - "bioportal": { - "name": "Mouse Pathology Ontology", - "prefix": "MPATH" - }, - "download_obo": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo", - "example": "728", - "fairsharing": { - "abbreviation": "MPATH", - "description": "Mouse PATHology (MPATH) ontology is a structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes. 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The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource.", - "id": "1937", - "name": "Microbial Protein Interaction Database", - "prefix": "FAIRsharing.eyjkws", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "MPID", - "fairsharing": "FAIRsharing.eyjkws", - "miriam": "mpid", - "n2t": "mpid" - }, - "miriam": { - "deprecated": false, - "description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.", - "homepage": "http://www.jcvi.org/mpidb/about.php", - "id": "00000124", - "name": "Microbial Protein Interaction Database", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "mpid", - "providers": [ - { - "code": "ebi", - "description": "Microbial Protein Interaction Database subset through IntAct", - "homepage": "https://www.ebi.ac.uk/intact/", - "name": "Microbial Protein Interaction Database subset through IntAct", - "uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1" - } - ], - "sampleId": "172", - "uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1" - }, - "n2t": { - "description": "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.", - "example": "172", - "homepage": "http://www.jcvi.org/mpidb/about.php", - "name": "Microbial Protein Interaction Database", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "mpid", - "uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1" - }, - "synonyms": [ - "mpidb" - ] - }, - "mpio": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MPIO", - "uri_format": "http://purl.obolibrary.org/obo/MPIO_$1" - }, - "bioportal": { - "name": "Minimum PDDI Information Ontology", - "prefix": "MPIO" - }, - "example": "0000004", - "mappings": { - "biocontext": "MPIO", - "bioportal": "MPIO", - "obofoundry": "mpio", - "ols": "mpio", - "ontobee": "MPIO" - }, - "obofoundry": { - "contact": "mbrochhausen@uams.edu", - "contact.github": "mbrochhausen", - "contact.label": "Mathias Brochhausen", - "contact.orcid": "0000-0003-1834-3856", - "deprecated": false, - "description": "An ontology of minimum information regarding potential drug-drug interaction information.", - "download.owl": "http://purl.obolibrary.org/obo/mpio.owl", - "homepage": "https://github.com/MPIO-Developers/MPIO", - "license": "CC BY 4.0", - "license.url": "http://creativecommons.org/licenses/by/4.0/", - "name": "Minimum PDDI Information Ontology", - "preferredPrefix": "MPIO", - "prefix": "mpio", - "repository": "https://github.com/MPIO-Developers/MPIO" - }, - "ols": { - "description": "An ontology of minimum information regarding potential drug-drug interaction information.", - "download": "http://purl.obolibrary.org/obo/mpio.owl", - "homepage": "https://github.com/MPIO-Developers/MPIO", - "name": "Minimum PDDI Information Ontology", - "prefix": "mpio", - "version": "2019-01-30", - "version.iri": "http://purl.obolibrary.org/obo/mpio/release/2019-01-30/mpio.owl" - }, - "ontobee": { - "library": "Library", - "name": "Minimum PDDI Information Ontology", - "prefix": "MPIO" - }, - "pattern": "^\\d{7}$" - }, - "mro": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MRO", - "uri_format": "http://purl.obolibrary.org/obo/MRO_$1" - }, - "bioportal": { - "name": "Defen", - "prefix": "MRO" - }, - "example": "0000634", - "fairsharing": { - "abbreviation": "MRO", - "description": "MHC molecules form a highly diverse family of proteins that play a key role in cellular immune recognition. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology (MaHCO) and created MRO to represent MHC molecules as they relate to immunological experiments. MRO models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multichain proteins, and establishes evidence codes for MHC restriction.", - "id": "849", - "name": "MHC Restriction Ontology", - "prefix": "FAIRsharing.k893xa", - "subjects": [ - "Immunology" - ] - }, - "mappings": { - "biocontext": "MRO", - "bioportal": "MRO", - "fairsharing": "FAIRsharing.k893xa", - "obofoundry": "mro", - "ols": "mro", - "ontobee": "MRO" - }, - "obofoundry": { - "contact": "bpeters@lji.org", - "contact.github": "bpeters42", - "contact.label": "Bjoern Peters", - "contact.orcid": "0000-0002-8457-6693", - "deprecated": false, - "description": "An ontology for Major Histocompatibility Complex (MHC) restriction in experiments", - "download.owl": "http://purl.obolibrary.org/obo/mro.owl", - "homepage": "https://github.com/IEDB/MRO", - "license": "CC BY 3.0", - "license.url": "https://creativecommons.org/licenses/by/3.0/", - "name": "MHC Restriction Ontology", - "preferredPrefix": "MRO", - "prefix": "mro", - "repository": "https://github.com/IEDB/MRO" - }, - "ols": { - "description": "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.", - "download": "http://purl.obolibrary.org/obo/mro.owl", - "homepage": "https://github.com/IEDB/MRO", - "name": "MHC Restriction Ontology", - "prefix": "mro", - "version": "2022-03-14", - "version.iri": "http://purl.obolibrary.org/obo/mro/2022-03-14/mro.owl" - }, - "ontobee": { - "library": "Library", - "name": "MHC Restriction Ontology", - "prefix": "MRO" - }, - "pattern": "^\\d{7}$" - }, - "ms": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "MS", - "uri_format": "http://purl.obolibrary.org/obo/MS_$1" - }, - "bioportal": { - "name": "Mass Spectrometry Ontology", - "prefix": "MS" - }, - "example": "1000560", - "mappings": { - "biocontext": "MS", - "bioportal": "MS", - "miriam": "ms", - "n2t": "ms", - "obofoundry": "ms", - "ols": "ms", - "ontobee": "MS" - }, - "miriam": { - "deprecated": false, - "description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/ms", - "id": "00000590", - "name": "Mass Spectrometry Controlled Vocabulary", - "namespaceEmbeddedInLui": true, - "pattern": "^MS:\\d{7}$", - "prefix": "ms", - "sampleId": "1000001", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1" - }, - "n2t": { - "description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.", - "example": "1000001", - "homepage": "https://bioportal.bioontology.org/ontologies/MS", - "name": "Mass Spectrometry Controlled Vocabulary through BioPortal", - "namespaceEmbeddedInLui": true, - "pattern": "^MS:\\d{7}$", - "prefix": "ms", - "uri_format": "http://purl.bioontology.org/ontology/MS/MS:$1" - }, - "obofoundry": { - "contact": "gerhard.mayer@rub.de", - "contact.github": "germa", - "contact.label": "Gerhard Mayer", - "contact.orcid": "0000-0002-1767-2343", - "depends_on": [ - "pato", - "uo" - ], - "deprecated": false, - "description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.", - "download.obo": "http://purl.obolibrary.org/obo/ms.obo", - "download.owl": "http://purl.obolibrary.org/obo/ms.owl", - "homepage": "http://www.psidev.info/groups/controlled-vocabularies", - "license": "CC BY 3.0", - "license.url": "https://creativecommons.org/licenses/by/3.0/", - "name": "Mass spectrometry ontology", - "preferredPrefix": "MS", - "prefix": "ms", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/23482073", - "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary." - } - ], - "repository": "https://github.com/HUPO-PSI/psi-ms-CV" - }, - "ols": { - "contact": "psidev-ms-vocab@lists.sourceforge.net", - "description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.", - "download": "http://purl.obolibrary.org/obo/ms.owl", - "homepage": "http://www.psidev.info/groups/controlled-vocabularies", - "name": "Mass spectrometry ontology", - "prefix": "ms", - "version.iri": "http://purl.obolibrary.org/obo/ms/4.1.86/ms.owl" - }, - "ontobee": { - "library": "Library", - "name": "Mass spectrometry ontology", - "prefix": "MS" - }, - "pattern": "^\\d{7}$" - }, - "msigdb": { - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "MSigDB", - "uri_format": "https://www.gsea-msigdb.org/gsea/msigdb/$1" - }, - "description": "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can", - "example": "NADELLA_PRKAR1A_TARGETS_DN", - "homepage": "https://www.gsea-msigdb.org", - "mappings": { - "biolink": "MSigDB" - }, - "name": "Molecular Signatures Database", - "synonyms": [ - "msig" - ], - "wikidata": { - "paper": "Q34509167" - } - }, - "msio": { - "example": "0000111", - "mappings": { - "ols": "msio" - }, - "name": "Metabolomics Standards Initiative Ontology", - "ols": { - "description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.", - "download": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl", - "homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", - "name": "Metabolomics Standards Initiative Ontology (MSIO)", - "prefix": "msio", - "version": "1.0.1" - }, - "pattern": "^\\d{7}$", - "repository": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO" - }, - "multicellds": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", - "example": "MCDS_S_0000000001", - "fairsharing": { - "abbreviation": "MultiCellDS", - "description": "MultiCellDS (Multicellular data specification), an outgrowth of the earlier MultiCellXML project, aims to create a data standard for sharing multicellular experimental, simulation, and clinical data. Our ultimate goal is to foster a community that develops user-friendly tools that can read, write, and recombine data into better simulations and analyses for multicellular biology and predictive medicine. As part of this effort, we are developing MultiCellDB: a repository for a curated library of digital cell lines and peer-reviewed simulation and experimental data. A novel part of MultiCellDS is the digital cell line: a digital analogue of experimental cell lines that will help to collect biophysical cell line measurements coming from many research groups and make them readily accessible to an ecosystem of compatible computational models. You can learn more about digital cell lines and other core ideas on this page. We are currently preparing a draft of the upcoming MultiCellDS 1.0 specification. After a multiple rounds of comment and review by a multidisciplinary review panel and the general public, we target an October 2016 release of the data specification and software support tools.", - "id": "1542", - "name": "MultiCellular Data Standard", - "prefix": "FAIRsharing.pqzyd5", - "subjects": [ - "Life Science" - ] - }, - "homepage": "http://multicellds.org/MultiCellDB.php", - "mappings": { - "fairsharing": "FAIRsharing.pqzyd5" - }, - "name": "MultiCellDS", - "uri_format": "http://multicellds.org/MultiCellDB/$1" - }, - "multicellds.cell_line": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MULTICELLDS.CELL_LINE", - "uri_format": "http://identifiers.org/multicellds.cell_line/$1" - }, - "mappings": { - "biocontext": "MULTICELLDS.CELL_LINE", - "miriam": "multicellds.cell_line", - "n2t": "multicellds.cell_line" - }, - "miriam": { - "deprecated": false, - "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", - "homepage": "http://multicellds.org/MultiCellDB.php", - "id": "00000584", - "name": "MultiCellDS Digital Cell Line", - "namespaceEmbeddedInLui": false, - "pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$", - "prefix": "multicellds.cell_line", - "sampleId": "MCDS_L_0000000001", - "uri_format": "http://multicellds.org/MultiCellDB/$1" - }, - "n2t": { - "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", - "example": "MCDS_L_0000000001", - "homepage": "http://multicellds.org/MultiCellDB.php", - "name": "MultiCellDS Digital Cell Line at Keck School of Medicine", - "namespaceEmbeddedInLui": false, - "pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$", - "prefix": "multicellds.cell_line", - "uri_format": "http://multicellds.org/MultiCellDB/$1" - }, - "part_of": "multicellds" - }, - "multicellds.collection": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MULTICELLDS.COLLECTION", - "uri_format": "http://identifiers.org/multicellds.collection/$1" - }, - "mappings": { - "biocontext": "MULTICELLDS.COLLECTION", - "miriam": "multicellds.collection", - "n2t": "multicellds.collection" - }, - "miriam": { - "deprecated": false, - "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).", - "homepage": "http://multicellds.org/MultiCellDB.php", - "id": "00000582", - "name": "MultiCellDS collection", - "namespaceEmbeddedInLui": false, - "pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$", - "prefix": "multicellds.collection", - "sampleId": "MCDS_C_0000000001", - "uri_format": "http://multicellds.org/MultiCellDB/$1" - }, - "n2t": { - "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).", - "example": "MCDS_C_0000000001", - "homepage": "http://multicellds.org/MultiCellDB.php", - "name": "MultiCellDScollection at Keck School of Medicine", - "namespaceEmbeddedInLui": false, - "pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$", - "prefix": "multicellds.collection", - "uri_format": "http://multicellds.org/MultiCellDB/$1" - }, - "part_of": "multicellds" - }, - "multicellds.snapshot": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MULTICELLDS.SNAPSHOT", - "uri_format": "http://identifiers.org/multicellds.snapshot/$1" - }, - "mappings": { - "biocontext": "MULTICELLDS.SNAPSHOT", - "miriam": "multicellds.snapshot", - "n2t": "multicellds.snapshot" - }, - "miriam": { - "deprecated": false, - "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.", - "homepage": "http://multicellds.org/MultiCellDB.php", - "id": "00000583", - "name": "MultiCellDS Digital snapshot", - "namespaceEmbeddedInLui": false, - "pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$", - "prefix": "multicellds.snapshot", - "sampleId": "MCDS_S_0000000001", - "uri_format": "http://multicellds.org/MultiCellDB/$1" - }, - "n2t": { - "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.", - "example": "MCDS_S_0000000001", - "homepage": "http://multicellds.org/MultiCellDB.php", - "name": "MultiCellDS snapshot at Keck School of Medicine", - "namespaceEmbeddedInLui": false, - "pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$", - "prefix": "multicellds.snapshot", - "uri_format": "http://multicellds.org/MultiCellDB/$1" - }, - "part_of": "multicellds" - }, - "mw.project": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MW.PROJECT", - "uri_format": "http://identifiers.org/mw.project/$1" - }, - "mappings": { - "biocontext": "MW.PROJECT", - "miriam": "mw.project", - "n2t": "mw.project" - }, - "miriam": { - "deprecated": false, - "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", - "homepage": "http://www.metabolomicsworkbench.org/", - "id": "00000647", - "name": "Metabolomics Workbench Project", - "namespaceEmbeddedInLui": false, - "pattern": "^PR[0-9]{6}$", - "prefix": "mw.project", - "sampleId": "PR000001", - "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1" - }, - "n2t": { - "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", - "example": "PR000001", - "homepage": "http://www.metabolomicsworkbench.org/", - "name": "Metabolomics Workbench Project", - "namespaceEmbeddedInLui": false, - "pattern": "^PR[0-9]{6}$", - "prefix": "mw.project", - "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1" - } - }, - "mw.study": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MW.STUDY", - "uri_format": "http://identifiers.org/mw.study/$1" - }, - "mappings": { - "biocontext": "MW.STUDY", - "miriam": "mw.study", - "n2t": "mw.study" - }, - "miriam": { - "deprecated": false, - "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", - "homepage": "http://www.metabolomicsworkbench.org/", - "id": "00000646", - "name": "Metabolomics Workbench Study", - "namespaceEmbeddedInLui": false, - "pattern": "^ST[0-9]{6}$", - "prefix": "mw.study", - "providers": [ - { - "code": "omicsdi", - "description": "Metabolomics Workbench Study through OmicsDI", - "homepage": "https://www.omicsdi.org/", - "name": "Metabolomics Workbench Study through OmicsDI", - "uri_format": "https://www.omicsdi.org/dataset/metabolomics_workbench/$1" - } - ], - "sampleId": "ST000900", - "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1" - }, - "n2t": { - "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", - "example": "ST000900", - "homepage": "http://www.metabolomicsworkbench.org/", - "name": "Metabolomics Workbench Study", - "namespaceEmbeddedInLui": false, - "pattern": "^ST[0-9]{6}$", - "prefix": "mw.study", - "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1" - } - }, - "myco.lepra": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MYCO.LEPRA", - "uri_format": "http://identifiers.org/myco.lepra/$1" - }, - "mappings": { - "biocontext": "MYCO.LEPRA", - "miriam": "myco.lepra", - "n2t": "myco.lepra", - "prefixcommons": "myco.lepra" - }, - "miriam": { - "deprecated": false, - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", - "homepage": "http://mycobrowser.epfl.ch/leprosy.html", - "id": "00000217", - "name": "MycoBrowser leprae", - "namespaceEmbeddedInLui": false, - "pattern": "^ML\\w+$", - "prefix": "myco.lepra", - "sampleId": "ML0224", - "uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1" - }, - "n2t": { - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", - "example": "ML0224", - "homepage": "http://mycobrowser.epfl.ch/leprosy.html", - "name": "MycoBrowser leprae at Global Health Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^ML\\w+$", - "prefix": "myco.lepra", - "uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1" - }, - "prefixcommons": { - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", - "example": "ML0224", - "homepage": "http://mycobrowser.epfl.ch/leprosy.html", - "keywords": [ - "genome", - "sequence" - ], - "name": "MycoBrowser leprae", - "pattern": "^ML\\w+$", - "prefix": "myco.lepra", - "uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1" - } - }, - "myco.marinum": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MYCO.MARINUM", - "uri_format": "http://identifiers.org/myco.marinum/$1" - }, - "mappings": { - "biocontext": "MYCO.MARINUM", - "miriam": "myco.marinum", - "n2t": "myco.marinum", - "prefixcommons": "myco.marinum" - }, - "miriam": { - "deprecated": false, - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.", - "homepage": "http://mycobrowser.epfl.ch/marinolist.html", - "id": "00000218", - "name": "MycoBrowser marinum", - "namespaceEmbeddedInLui": false, - "pattern": "^MMAR\\_\\d+$", - "prefix": "myco.marinum", - "sampleId": "MMAR_2462", - "uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1" - }, - "n2t": { - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.", - "example": "MMAR_2462", - "homepage": "http://mycobrowser.epfl.ch/marinolist.html", - "name": "MycoBrowser marinum at Global Health Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^MMAR\\_\\d+$", - "prefix": "myco.marinum", - "uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1" - }, - "prefixcommons": { - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.", - "example": "MMAR_2462", - "homepage": "http://mycobrowser.epfl.ch/marinolist.html", - "keywords": [ - "genome", - "sequence" - ], - "name": "MycoBrowser marinum", - "pattern": "^MMAR\\_\\d+$", - "prefix": "myco.marinum", - "uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1" - } - }, - "myco.smeg": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MYCO.SMEG", - "uri_format": "http://identifiers.org/myco.smeg/$1" - }, - "mappings": { - "biocontext": "MYCO.SMEG", - "miriam": "myco.smeg", - "n2t": "myco.smeg", - "prefixcommons": "myco.smeg" - }, - "miriam": { - "deprecated": false, - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", - "homepage": "http://mycobrowser.epfl.ch/smegmalist.html", - "id": "00000219", - "name": "MycoBrowser smegmatis", - "namespaceEmbeddedInLui": false, - "pattern": "^MSMEG\\w+$", - "prefix": "myco.smeg", - "sampleId": "MSMEG_3769", - "uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1" - }, - "n2t": { - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", - "example": "MSMEG_3769", - "homepage": "http://mycobrowser.epfl.ch/smegmalist.html", - "name": "MycoBrowser smegmatis at Global Health Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^MSMEG\\w+$", - "prefix": "myco.smeg", - "uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1" - }, - "prefixcommons": { - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", - "example": "MSMEG_3769", - "homepage": "http://mycobrowser.epfl.ch/smegmalist.html", - "keywords": [ - "genome", - "sequence" - ], - "name": "MycoBrowser smegmatis", - "pattern": "^MSMEG\\w+$", - "prefix": "myco.smeg", - "uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1" - } - }, - "myco.tuber": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "MYCO.TUBER", - "uri_format": "http://identifiers.org/myco.tuber/$1" - }, - "mappings": { - "biocontext": "MYCO.TUBER", - "miriam": "myco.tuber", - "n2t": "myco.tuber", - "ncbi": "TubercuList", - "prefixcommons": "tuberculist", - "uniprot": "TubercuList" - }, - "miriam": { - "deprecated": false, - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.", - "homepage": "http://tuberculist.epfl.ch/", - "id": "00000216", - "name": "MycoBrowser tuberculosis", - "namespaceEmbeddedInLui": false, - "pattern": "^Rv\\d{4}(A|B|c)?$", - "prefix": "myco.tuber", - "sampleId": "Rv1908c", - "uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1" - }, - "n2t": { - "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. 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OBI fosters clear communication about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more.", - "id": "1488", - "name": "Ontology for Biomedical Investigations", - "prefix": "FAIRsharing.284e1z", - "subjects": [ - "Functional Genomics", - "Life Science", - "Biomedical Science" - ] - }, - "go": { - "homepage": "http://obi-ontology.org/", - "name": "Ontology for Biomedical Investigations", - "prefix": "OBI" - }, - "mappings": { - "biocontext": "OBI", - "bioportal": "OBI", - "fairsharing": "FAIRsharing.284e1z", - "go": "OBI", - "miriam": "obi", - "n2t": "obi", - "obofoundry": "obi", - "ols": "obi", - "ontobee": "OBI", - "prefixcommons": "obi" - }, - "miriam": { - "deprecated": false, - "description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).", - "homepage": "http://www.ontobee.org/", - "id": "00000127", - "name": "Ontology for Biomedical Investigations", - "namespaceEmbeddedInLui": false, - "pattern": "(^OBI:\\d{7}$)|(^OBI_\\d{7}$)", - "prefix": "obi", - "sampleId": "OBI_0000070", - "uri_format": "http://purl.obolibrary.org/obo/$1" - }, - "n2t": { - "description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).", - "example": "OBI_0000070", - "homepage": "http://www.ontobee.org/", - "name": "OBI through Ontobee", - "namespaceEmbeddedInLui": false, - "pattern": "(^OBI:\\d{7}$)|(^OBI_\\d{7}$)", - "prefix": "obi", - "uri_format": "http://purl.obolibrary.org/obo/$1" - }, - "obofoundry": { - "appears_in": [ - "agro", - "foodon", - "hso", - "labo", - "mco", - "one", - "ons", - "rbo", - "scdo" - ], - "contact": "bpeters@lji.org", - "contact.github": "bpeters42", - "contact.label": "Bjoern Peters", - "contact.orcid": "0000-0002-8457-6693", - "deprecated": false, - "description": "An integrated ontology for the description of life-science and clinical investigations", - "download.obo": "http://purl.obolibrary.org/obo/obi.obo", - "download.owl": "http://purl.obolibrary.org/obo/obi.owl", - "homepage": "http://obi-ontology.org", - "license": "CC BY 4.0", - "license.url": "https://creativecommons.org/licenses/by/4.0/", - "name": "Ontology for Biomedical Investigations", - "preferredPrefix": "OBI", - "prefix": "obi", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/27128319", - "title": "The Ontology for Biomedical Investigations" - } - ], - "repository": "https://github.com/obi-ontology/obi" - }, - "ols": { - "description": "The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.", - "download": "http://purl.obolibrary.org/obo/obi.owl", - "homepage": "http://obi-ontology.org", - "name": "Ontology for Biomedical Investigations", - "prefix": "obi", - "version": "2022-01-03", - "version.iri": "http://purl.obolibrary.org/obo/obi/2022-01-03/obi.owl" - }, - "ontobee": { - "library": "Foundry", - "name": "Ontology for Biomedical Investigations", - "prefix": "OBI" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1123", - "description": "The Ontology for Biomedical Investigations (OBI) an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it.", - "example": "OBI_0000011", - "homepage": "http://purl.obolibrary.org/obo/obi", - "keywords": [ - "ontology" - ], - "name": "Ontology for Biomedical Investigations", - "pattern": "^OBI_\\d{7}$", - "prefix": "obi", - "uri_format": "http://purl.obolibrary.org/obo/$1" - }, - "uri_format": "http://purl.obolibrary.org/obo/OBI_$1" - }, - "obib": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OBIB", - "uri_format": "http://purl.obolibrary.org/obo/OBIB_$1" - }, - "bioportal": { - "name": "Ontology for Biobanking", - "prefix": "OBIB" - }, - "example": "0000389", - "fairsharing": { - "abbreviation": "OBIB", - "description": "The ontology for Biobanking (OBIB) is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigations (OBI) using Basic Formal Ontology (BFO) as top ontology and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology.", - "id": "1455", - "name": "Ontology for Biobanking", - "prefix": "FAIRsharing.bxc508", - "subjects": [ - "Health Science" - ] - }, - "mappings": { - "biocontext": "OBIB", - "bioportal": "OBIB", - "fairsharing": "FAIRsharing.bxc508", - "obofoundry": "obib", - "ols": "obib", - "ontobee": "OBIB" - }, - "obofoundry": { - "contact": "jiezheng@pennmedicine.upenn.edu", - "contact.github": "zhengj2007", - "contact.label": "Jie Zheng", - "contact.orcid": "0000-0002-2999-0103", - "deprecated": false, - "description": "An ontology built for annotation and modeling of biobank repository and biobanking administration", - "download.owl": "http://purl.obolibrary.org/obo/obib.owl", - "homepage": "https://github.com/biobanking/biobanking", - "license": "CC BY 4.0", - "license.url": "http://creativecommons.org/licenses/by/4.0/", - "name": "Ontology for Biobanking", - "preferredPrefix": "OBIB", - "prefix": "obib", - "repository": "https://github.com/biobanking/biobanking" - }, - "ols": { - "description": "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.", - "download": "http://purl.obolibrary.org/obo/obib.owl", - "homepage": "https://github.com/biobanking/biobanking", - "name": "Ontology for BIoBanking (OBIB)", - "prefix": "obib", - "version": "2021-11-12", - "version.iri": "http://purl.obolibrary.org/obo/obib/2021-11-12/obib.owl" - }, - "ontobee": { - "library": "Library", - "name": "Ontology for Biobanking", - "prefix": "OBIB" - }, - "pattern": "^\\d{7}$" - }, - "obo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OBO", - "uri_format": "http://purl.obolibrary.org/obo/$1" - }, - "description": "Community development of interoperable ontologies for the biological sciences", - "fairsharing": { - "abbreviation": "OBO", - "description": "The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.", - "id": "2600", - "name": "OBO Foundry", - "prefix": "FAIRsharing.847069", - "subjects": [ - "Ontology and Terminology" - ] - }, - "homepage": "http://www.obofoundry.org/", - "mappings": { - "biocontext": "OBO", - "fairsharing": "FAIRsharing.847069" - }, - "name": "Internal OBO and PyOBO Relations" - }, - "oboformat": { - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "oboformat", - "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Related to the OBO in OWL meta-model", - "example": "alt_id", - "fairsharing": { - "abbreviation": "OBO Format", - "description": "The first part of this specification describes the syntax and structure of OBO Format using BNF. This states how strings of characters in OBOF Files are parsed into abstract OBO documents, and describes constraints on the structure of these documents. The second part of this specification describes the semantics of an OBO document via a mapping to OWL2-DL and community metadata vocabularies.", - "id": "344", - "name": "OBO Format Syntax and Semantics", - "prefix": "FAIRsharing.aa0eat", - "subjects": [ - "Life Science" - ] - }, - "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", - "mappings": { - "biolink": "oboformat", - "fairsharing": "FAIRsharing.aa0eat" - }, - "name": "OBO Format", - "preferred_prefix": "oboFormat", - "repository": "https://github.com/geneontology/go-ontology" - }, - "oboinowl": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "OIO", - "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" - }, - "description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties", - "download_obo": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo", - "example": "hasDbXref", - "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", - "mappings": { - "biocontext": "OIO" - }, - "name": "OBO in OWL", - "preferred_prefix": "oboInOwl", - "repository": "https://github.com/geneontology/go-ontology", - "synonyms": [ - "oio" - ], - "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" - }, - "occ": { - "mappings": { - "miriam": "occ", - "n2t": "occ" - }, - "miriam": { - "deprecated": false, - "description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.", - "homepage": "https://w3id.org/oc/corpus", - "id": "00000693", - "name": "OpenCitations Corpus", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z][a-z]/[0-9]+$", - "prefix": "occ", - "sampleId": "br/1", - "uri_format": "https://w3id.org/oc/corpus/$1" - }, - "n2t": { - "description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.", - "example": "br/1", - "homepage": "https://w3id.org/oc/corpus", - "name": "OpenCitations Corpus", - "namespaceEmbeddedInLui": false, - "pattern": "^[a-z][a-z]/[0-9]+$", - "prefix": "occ", - "uri_format": "https://w3id.org/oc/corpus/$1" - } - }, - "oci": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "OCI", - "uri_format": "http://identifiers.org/oci/$1" - }, - "mappings": { - "biocontext": "OCI", - "miriam": "oci", - "n2t": "oci" - }, - "miriam": { - "deprecated": false, - "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where \u201coci:\u201d is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310\u201301022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.", - "homepage": "http://opencitations.net", - "id": "00000660", - "name": "OCI", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+-[0-9]+$", - "prefix": "oci", - "sampleId": "1-18", - "uri_format": "https://w3id.org/oc/oci/$1" - }, - "n2t": { - "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information. OCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus. OCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312. OCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.", - "example": "1-18", - "homepage": "http://opencitations.net", - "name": "OpenCitations", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+-[0-9]+$", - "prefix": "oci", - "uri_format": "https://w3id.org/oc/oci/$1" - }, - "name": "Open Citation Identifier" - }, - "ocid": { - "banana": "ocid", - "mappings": { - "miriam": "ocid" - }, - "miriam": { - "deprecated": false, - "description": "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.", - "homepage": "https://ontochem.com/", - "id": "00000738", - "name": "Ontology Concept Identifiers", - "namespaceEmbeddedInLui": true, - "pattern": "ocid:[0-9]{12}", - "prefix": "ocid", - "sampleId": "190000021540", - "uri_format": "https://ocid.ontochem.com/prefname?ocid=$1" - }, - "pattern": "^[0-9]{12}$" - }, - "oclc": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "OCLC", - "uri_format": "http://identifiers.org/oclc/$1" - }, - "mappings": { - "biocontext": "OCLC", - "miriam": "oclc", - "n2t": "oclc" - }, - "miriam": { - "deprecated": false, - "description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.", - "homepage": "https://www.oclc.org/en/about.html", - "id": "00000669", - "name": "Online Computer Library Center (OCLC) WorldCat", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "oclc", - "sampleId": "634515043", - "uri_format": "https://www.worldcat.org/oclc/$1" - }, - "n2t": { - "description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.", - "example": "634515043", - "homepage": "https://www.oclc.org/en/about.html", - "name": "Online Computer Library Center (OCLC) WorldCat", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+$", - "prefix": "oclc", - "uri_format": "https://www.worldcat.org/oclc/$1" - }, - "name": "Online Computer Library Center WorldCat" - }, - "odam": { - "mappings": { - "miriam": "odam" - }, - "miriam": { - "deprecated": false, - "description": "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.", - "homepage": "https://metabolome.cgfb.u-bordeaux.fr/", - "id": "00000722", - "name": "Open Data for Access and Mining", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z0-9]+$", - "prefix": "odam", - "sampleId": "frim1", - "uri_format": "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1" - } - }, - "odc.sci": { - "fairsharing": { - "abbreviation": "ODC-SCI", - "description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. There are several challenges for scientific reproducibility and bench-to-bedside translation. For example, only research and data that are published actually get disseminated, a phenomenon known as publication bias. Published research reflects to only a small fraction of all data collected, and data that do not lead to publication are largely ignored, hidden away in filing cabinets and hard drives. This results in an abundance of inaccessible scientific data known as \u201cdark data\u201d. Even when research is disseminated, it is usually in the form of summary reports of aggregated data (e.g. averages across individual subjects) such as scientific articles. The fact that the individual subject-level data are inaccessible further contributes to dark data. The spinal cord injury (SCI) community created the ODC-SCI to mitigate dark data in SCI research. The ODC-SCI also aims to increase transparency with individual-level data, enhance collaboration, facilitate advanced analytics, and conform to increasing mandates by funders and publishers to make data accessible. Members of the ODC-SCI have access to a private digital lab space managed by the PI or multi-PIs for dataset storage and sharing. The PIs can share their labs\u2019 datasets with the registered members of the ODC-SCI community and make their datasets public and citable. The ODC-SCI implements stewardship principles that scientific data be made FAIR (Findable, Accessible, Interoperable and Reusable) and has been widely adopted by the international SCI research community.", - "id": "3307", - "name": "Open Data Commons for Spinal Cord Injury", - "prefix": "FAIRsharing.M6Ruz3", - "subjects": [ - "Neurobiology", - "Neurology", - "Biomedical Science", - "Neuroscience" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.M6Ruz3", - "miriam": "odc.sci" - }, - "miriam": { - "deprecated": false, - "description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.", - "homepage": "https://odc-sci.org", - "id": "00000804", - "name": "Open Data Commons for Spinal Cord Injury", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]*$", - "prefix": "odc.sci", - "sampleId": "602", - "uri_format": "https://odc-sci.org/data/$1" - } - }, - "odc.tbi": { - "mappings": { - "miriam": "odc.tbi" - }, - "miriam": { - "deprecated": false, - "description": "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.", - "homepage": "https://odc-tbi.org", - "id": "00000816", - "name": "Open Data Commons for Traumatic Brain Injury", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]*$", - "prefix": "odc.tbi", - "sampleId": "408", - "uri_format": "https://odc-tbi.org/data/$1" - } - }, - "odor": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "ODOR", - "uri_format": "http://identifiers.org/odor/$1" - }, - "mappings": { - "biocontext": "ODOR", - "miriam": "odor", - "n2t": "odor" - }, - "miriam": { - "deprecated": false, - "description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors", - "homepage": "http://senselab.med.yale.edu/OdorDB", - "id": "00000500", - "name": "Odor Molecules DataBase", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "odor", - "sampleId": "74", - "uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5" - }, - "n2t": { - "description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors", - "example": "74", - "homepage": "http://senselab.med.yale.edu/OdorDB", - "name": "Odor Molecules DataBase at Yale University School of Medicine", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "odor", - "uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5" - } - }, - "ogg": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OGG", - "uri_format": "http://purl.obolibrary.org/obo/OGG_$1" - }, - "bioportal": { - "name": "Ontology of Genes and Genomes", - "prefix": "OGG" - }, - "example": "3000887619", - "fairsharing": { - "abbreviation": "OGG", - "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms. Each gene in OGG has over 10 annotation items, includes gene-associated Gene Ontology (GO) and PubMed article information. OGG has represented genes in human, two viruses, and four bacteria. Additionally, 7 OGG subsets are developed to represent genes and genomes of 7 model systems including mouse, fruit fly, zebrafish, yeast, A. thaliana, C. elegans, and P. falciparum.", - "id": "363", - "name": "Ontology of Genes and Genomes", - "prefix": "FAIRsharing.zmx7nn", - "subjects": [ - "Life Science", - "Biology" - ] - }, - "mappings": { - "biocontext": "OGG", - "bioportal": "OGG", - "fairsharing": "FAIRsharing.zmx7nn", - "obofoundry": "ogg", - "ols": "ogg", - "ontobee": "OGG" - }, - "obofoundry": { - "contact": "yongqunh@med.umich.edu", - "contact.github": "yongqunh", - "contact.label": "Yongqun Oliver He", - "contact.orcid": "0000-0001-9189-9661", - "deprecated": false, - "description": "A formal ontology of genes and genomes of biological organisms.", - "download.owl": "http://purl.obolibrary.org/obo/ogg.owl", - "homepage": "https://bitbucket.org/hegroup/ogg", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "The Ontology of Genes and Genomes", - "preferredPrefix": "OGG", - "prefix": "ogg", - "repository": "https://bitbucket.org/hegroup/ogg" - }, - "ols": { - "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ", - "download": "http://purl.obolibrary.org/obo/ogg.owl", - "homepage": "https://bitbucket.org/hegroup/ogg", - "name": "OGG: Ontology of Genes and Genomes", - "prefix": "ogg", - "version": "1.0.59" - }, - "ontobee": { - "library": "Library", - "name": "The Ontology of Genes and Genomes", - "prefix": "OGG" - }, - "pattern": "^\\d+$" - }, - "ogi": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OGI", - "uri_format": "http://purl.obolibrary.org/obo/OGI_$1" - }, - "bioportal": { - "name": "Ontology for Genetic Interval", - "prefix": "OGI" - }, - "deprecated": true, - "example": "0000019", - "homepage": "https://code.google.com/archive/p/ontology-for-genetic-interval/", - "mappings": { - "biocontext": "OGI", - "bioportal": "OGI", - "obofoundry": "ogi", - "ols": "ogi", - "ontobee": "OGI" - }, - "obofoundry": { - "deprecated": true, - "description": "An ontology that formalizes the genomic element by defining an upper class genetic interval", - "download.owl": "http://purl.obolibrary.org/obo/ogi.owl", - "homepage": "https://code.google.com/p/ontology-for-genetic-interval/", - "name": "Ontology for genetic interval", - "prefix": "ogi" - }, - "ols": { - "description": "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) \u201cGenome, Gene, Interval and Ontology\u201d Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) \u201cFrom Ontology for Genetic Interval(OGI) to Sequence Assembly \u2013 Ontology apply to next generation sequencing\u201d Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) \u201cDNA sequence from below: A Nominalist Approach\u201d Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n", - "download": "http://purl.obolibrary.org/obo/ogi.owl", - "homepage": "https://code.google.com/p/ontology-for-genetic-interval/", - "name": "Ontology for genetic interval", - "prefix": "ogi", - "version": "2.0" - }, - "ontobee": { - "library": "Library", - "name": "Ontology for genetic interval", - "prefix": "OGI" - }, - "pattern": "^\\d{7}$", - "synonyms": [ - "OGI.owl" - ] - }, - "ogms": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OGMS", - "uri_format": "http://purl.obolibrary.org/obo/OGMS_$1" - }, - "bioportal": { - "name": "Ontology for General Medical Science", - "prefix": "OGMS" - }, - "example": "0000031", - "fairsharing": { - "abbreviation": "OGMS", - "description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies.", - "id": "431", - "name": "Ontology for General Medical Science", - "prefix": "FAIRsharing.rvz0m9", - "subjects": [ - "Medicine", - "Biomedical Science" - ] - }, - "mappings": { - "biocontext": "OGMS", - "bioportal": "OGMS", - "fairsharing": "FAIRsharing.rvz0m9", - "obofoundry": "ogms", - "ols": "ogms", - "ontobee": "OGMS" - }, - "obofoundry": { - "appears_in": [ - "labo", - "scdo" - ], - "contact": "baeverma@jcvi.org", - "contact.github": "BAevermann", - "contact.label": "Brian Aevermann", - "contact.orcid": "0000-0003-1346-1327", - "deprecated": false, - "description": "An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities", - "download.owl": "http://purl.obolibrary.org/obo/ogms.owl", - "homepage": "https://github.com/OGMS/ogms", - "license": "CC BY 4.0", - "license.url": "http://creativecommons.org/licenses/by/4.0/", - "name": "Ontology for General Medical Science", - "preferredPrefix": "OGMS", - "prefix": "ogms", - "repository": "https://github.com/OGMS/ogms" - }, - "ols": { - "description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.", - "download": "http://purl.obolibrary.org/obo/ogms.owl", - "homepage": "https://github.com/OGMS/ogms", - "name": "Ontology for General Medical Science", - "prefix": "ogms", - "version": "2021-08-19", - "version.iri": "http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl" - }, - "ontobee": { - "library": "Library", - "name": "Ontology for General Medical Science", - "prefix": "OGMS" - }, - "pattern": "^\\d{7}$", - "synonyms": [ - "ogms/OMRE" - ], - "wikidata": { - "database": "Q4866972" - } - }, - "ogsf": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OGSF", - "uri_format": "http://purl.obolibrary.org/obo/OGSF_$1" - }, - "bioportal": { - "name": "Ontology for Genetic Susceptibility Factor", - "prefix": "OGSF" - }, - "example": "0000025", - "fairsharing": { - "abbreviation": "OGSF", - "description": "Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO 2.0's framework. The ontology is under the domain of genetic epidemiology. OGSF is built from a combination of three ontologies: the Ontology of Geographical Region (OGR), the Ontology of Glucose Metabolism (OGMD), and the Ontology of Genetic Disease Investigations (OGDI).", - "id": "445", - "name": "Ontology for Genetic Susceptibility Factor", - "prefix": "FAIRsharing.egv2cz", - "subjects": [ - "Genetics", - "Biomedical Science", - "Epidemiology" - ] - }, - "mappings": { - "biocontext": "OGSF", - "bioportal": "OGSF", - "fairsharing": "FAIRsharing.egv2cz", - "obofoundry": "ogsf", - "ols": "ogsf", - "ontobee": "OGSF" - }, - "obofoundry": { - "contact": "linikujp@gmail.com", - "contact.github": "linikujp", - "contact.label": "Asiyah Yu Lin", - "contact.orcid": "0000-0002-5379-5359", - "deprecated": false, - "description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.", - "download.owl": "http://purl.obolibrary.org/obo/ogsf.owl", - "homepage": "https://github.com/linikujp/OGSF", - "license": "CC BY 3.0", - "license.url": "https://creativecommons.org/licenses/by/3.0/", - "name": "Ontology of Genetic Susceptibility Factor", - "preferredPrefix": "OGSF", - "prefix": "ogsf", - "repository": "https://github.com/linikujp/OGSF" - }, - "ols": { - "description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.", - "download": "http://purl.obolibrary.org/obo/ogsf.owl", - "homepage": "https://code.google.com/p/ogsf/", - "name": "Ontology of Genetic Susceptibility Factor", - "prefix": "ogsf", - "version": "2.0" - }, - "ontobee": { - "library": "Library", - "name": "Ontology of Genetic Susceptibility Factor", - "prefix": "OGSF" - }, - "pattern": "^\\d{7}$" - }, - "ohd": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OHD", - "uri_format": "http://purl.obolibrary.org/obo/OHD_$1" - }, - "bioportal": { - "name": "The Oral Health and Disease Ontology", - "prefix": "OHD" - }, - "example": "0000006", - "fairsharing": { - "abbreviation": "OHD", - "description": "The Oral Health and Disease Ontology is intended as a BFO and OBO Foundry compliant ontology for the oral health domain. It is currently used to represent the content of dental practice health records and is intended to be further developed for use in translation medicine. It demonstrates a principled split between billing codes as information entities and what the codes are about, such as dental procedures, materials, and patients. OHD is structured using BFO uses terms from OGMS, OBI, IAO and FMA. In addition it uses terms from CARO, OMRSE, NCBITaxon, and a subset of terms from the Current Dental Terminology (CDT) OHD is in early development and subject to change without notice.", - "id": "1453", - "name": "The Oral Health and Disease Ontology", - "prefix": "FAIRsharing.bg7bb6", - "subjects": [] - }, - "mappings": { - "biocontext": "OHD", - "bioportal": "OHD", - "fairsharing": "FAIRsharing.bg7bb6", - "obofoundry": "ohd", - "ols": "ohd", - "ontobee": "OHD" - }, - "obofoundry": { - "contact": "wdduncan@gmail.com", - "contact.github": "wdduncan", - "contact.label": "Bill Duncan", - "contact.orcid": "0000-0001-9625-1899", - "deprecated": false, - "description": "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records.", - "download.owl": "http://purl.obolibrary.org/obo/ohd.owl", - "homepage": "https://purl.obolibrary.org/obo/ohd/home", - "license": "CC BY 4.0", - "license.url": "http://creativecommons.org/licenses/by/4.0/", - "name": "Oral Health and Disease Ontology", - "preferredPrefix": "OHD", - "prefix": "ohd", - "repository": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology" - }, - "ols": { - "description": "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records.", - "download": "http://purl.obolibrary.org/obo/ohd.owl", - "homepage": "https://purl.obolibrary.org/obo/ohd/home", - "name": "Oral Health and Disease Ontology", - "prefix": "ohd", - "version": "2016-06-27", - "version.iri": "http://purl.obolibrary.org/obo/2016-06-27/ohd-inferred.owl" - }, - "ontobee": { - "library": "Library", - "name": "The Oral Health and Disease Ontology", - "prefix": "OHD" - }, - "pattern": "^\\d{7}$" - }, - "ohmi": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OHMI", - "uri_format": "http://purl.obolibrary.org/obo/OHMI_$1" - }, - "bioportal": { - "name": "Ontology of Host-Microbe Interactions", - "prefix": "OHMI" - }, - "example": "0000460", - "fairsharing": { - "abbreviation": "OHMI", - "description": "OHMI is aimed to ontologically represent various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.", - "id": "166", - "name": "Ontology of Host-Microbe Interactions", - "prefix": "FAIRsharing.cz9cnp", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "OHMI", - "bioportal": "OHMI", - "fairsharing": "FAIRsharing.cz9cnp", - "obofoundry": "ohmi", - "ols": "ohmi", - "ontobee": "OHMI" - }, - "obofoundry": { - "contact": "yongqunh@med.umich.edu", - "contact.github": "yongqunh", - "contact.label": "Yongqun Oliver He", - "contact.orcid": "0000-0001-9189-9661", - "deprecated": false, - "description": "The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions.", - "download.owl": "http://purl.obolibrary.org/obo/ohmi.owl", - "homepage": "https://github.com/ohmi-ontology/ohmi", - "license": "CC BY 4.0", - "license.url": "http://creativecommons.org/licenses/by/4.0/", - "name": "Ontology of Host-Microbiome Interactions", - "preferredPrefix": "OHMI", - "prefix": "ohmi", - "repository": "https://github.com/ohmi-ontology/ohmi" - }, - "ols": { - "description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.", - "download": "http://purl.obolibrary.org/obo/ohmi.owl", - "homepage": "https://github.com/ohmi-ontology/ohmi", - "name": "OHMI: Ontology of Host-Microbiome Interactions", - "prefix": "ohmi", - "version": "2019-09-17", - "version.iri": "http://purl.obolibrary.org/obo/ohmi/2019-09-17/ohmi.owl" - }, - "ontobee": { - "library": "Library", - "name": "Ontology of Host-Microbiome Interactions", - "prefix": "OHMI" - }, - "pattern": "^\\d{7}$" - }, - "ohpi": { - "bioportal": { - "name": "Ontology of Host-Pathogen Interactions", - "prefix": "OHPI" - }, - "example": "9001411", - "fairsharing": { - "abbreviation": "OHPI", - "description": "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is also developed to represent manually curated HPI knowledge available in the PHIDIAS resource.", - "id": "1295", - "name": "Ontology of Host-Pathogen Interactions", - "prefix": "FAIRsharing.vxpUJ6", - "subjects": [ - "Bioinformatics", - "Biomedical Science" - ] - }, - "mappings": { - "bioportal": "OHPI", - "fairsharing": "FAIRsharing.vxpUJ6", - "obofoundry": "ohpi", - "ols": "ohpi", - "ontobee": "OHPI" - }, - "obofoundry": { - "contact": "edong@umich.edu", - "contact.github": "e4ong1031", - "contact.label": "Edison Ong", - "contact.orcid": "0000-0002-5159-414X", - "deprecated": false, - "description": "OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource.", - "download.owl": "http://purl.obolibrary.org/obo/ohpi.owl", - "homepage": "https://github.com/OHPI/ohpi", - "license": "CC BY 4.0", - "license.url": "http://creativecommons.org/licenses/by/4.0/", - "name": "Ontology of Host Pathogen Interactions", - "preferredPrefix": "OHPI", - "prefix": "ohpi", - "repository": "https://github.com/OHPI/ohpi" - }, - "ols": { - "description": "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).", - "download": "http://purl.obolibrary.org/obo/ohpi.owl", - "homepage": "https://github.com/OHPI/ohpi", - "name": "OHPI: Ontology of Host-Pathogen Interactions", - "prefix": "ohpi", - "version": "2019-10-02", - "version.iri": "http://purl.obolibrary.org/obo/ohpi/releases/2019-09-30" - }, - "ontobee": { - "library": "Library", - "name": "Ontology of Host Pathogen Interactions", - "prefix": "OHPI" - }, - "pattern": "^\\d+$" - }, - "oid": { - "mappings": { - "miriam": "oid", - "n2t": "oid" - }, - "miriam": { - "deprecated": false, - "description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.", - "homepage": "http://www.oid-info.com/introduction.htm", - "id": "00000673", - "name": "OID Repository", - "namespaceEmbeddedInLui": false, - "pattern": "^[\\d.]+$", - "prefix": "oid", - "sampleId": "2.16.840", - "uri_format": "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display" - }, - "n2t": { - "description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.", - "example": "2.16.840", - "homepage": "http://www.oid-info.com/introduction.htm", - "name": "OID Repository", - "namespaceEmbeddedInLui": false, - "pattern": "^[\\d.]+$", - "prefix": "oid", - "uri_format": "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display" - } - }, - "olatdv": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "OLATDV", - "uri_format": "http://purl.obolibrary.org/obo/OLATDV_$1" - }, - "bioportal": { - "name": "Medaka Developmental Stages", - "prefix": "OLATDV" - }, - "example": "0000210", - "fairsharing": { - "abbreviation": "OlatDv", - "description": "Life cycle stages for Medaka. OlatDv is based on the original medaka stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult stages.", - "id": "600", - "name": "Medaka Stage Ontology", - "prefix": "FAIRsharing.c86z66", - "subjects": [ - "Aquaculture", - "Developmental Biology", - "Life Science" - ] - }, - "mappings": { - "biocontext": "OLATDV", - "bioportal": "OLATDV", - "fairsharing": "FAIRsharing.c86z66", - "obofoundry": "olatdv", - "ols": "olatdv", - "ontobee": "OLATDV" - }, - "obofoundry": { - "contact": "frederic.bastian@unil.ch", - "contact.github": "fbastian", - "contact.label": "Fr\u00e9d\u00e9ric Bastian", - "contact.orcid": "0000-0002-9415-5104", - "deprecated": false, - "description": "Life cycle stages for Medaka", - "download.obo": "http://purl.obolibrary.org/obo/olatdv.obo", - "download.owl": "http://purl.obolibrary.org/obo/olatdv.owl", - "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Medaka Developmental Stages", - "preferredPrefix": "OlatDv", - "prefix": "olatdv", - "repository": "https://github.com/obophenotype/developmental-stage-ontologies" - }, - "ols": { - "description": "Life cycle stages for Medaka", - "download": "http://purl.obolibrary.org/obo/olatdv.owl", - "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv", - "name": "Medaka Developmental Stages", - "prefix": "olatdv", - "version": "2020-03-10", - "version.iri": "http://purl.obolibrary.org/obo/olatdv/releases/2020-03-10/olatdv.owl" - }, - "ontobee": { - "library": "Library", - "name": "Medaka Developmental Stages", - "prefix": "OLATDV" - }, - "pattern": "^\\d{7}$" - }, - "om": { - "bioportal": { - "name": "Ontology of units of Measure", - "prefix": "OM" - }, - "example": "Dimension", - "mappings": { - "bioportal": "OM", - "ols": "om" - }, - "name": "Ontology of units of Measure", - "ols": { - "contact": "hajo.rijgersberg@wur.nl", - "description": "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging", - "download": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf", - "homepage": "https://github.com/HajoRijgersberg/OM", - "name": "Ontology of units of Measure (OM)", - "prefix": "om", - "version": "2.0.35" - }, - "repository": "https://github.com/HajoRijgersberg/OM" - }, - "oma.grp": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "OMA.GRP", - "uri_format": "http://identifiers.org/oma.grp/$1" - }, - "mappings": { - "biocontext": "OMA.GRP", - "miriam": "oma.grp", - "n2t": "oma.grp" - }, - "miriam": { - "deprecated": false, - "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.", - "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", - "id": "00000343", - "name": "OMA Group", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z]+$", - "prefix": "oma.grp", - "sampleId": "LCSCCPN", - "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1" - }, - "n2t": { - "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.", - "example": "LCSCCPN", - "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", - "name": "OMA Group through OMA browser at ETH Zurich", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z]+$", - "prefix": "oma.grp", - "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1" - } - }, - "oma.hog": { - "banana": "HOG", - "example": "0459895", - "mappings": { - "miriam": "oma.hog" - }, - "miriam": { - "deprecated": false, - "description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ", - "homepage": "https://omabrowser.org", - "id": "00000785", - "name": "OMA HOGs", - "namespaceEmbeddedInLui": true, - "pattern": "^HOG:[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", - "prefix": "oma.hog", - "sampleId": "HOG:0459895", - "uri_format": "https://omabrowser.org/oma/hog/resolve/HOG:$1/" - }, - "namespace_in_lui": false, - "pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", - "uri_format": "https://omabrowser.org/oma/hog/HOG:$1" - }, - "oma.protein": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "OMA.PROTEIN", - "uri_format": "http://identifiers.org/oma.protein/$1" - }, - "mappings": { - "biocontext": "OMA.PROTEIN", - "miriam": "oma.protein", - "n2t": "oma.protein" - }, - "miriam": { - "deprecated": false, - "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.", - "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", - "id": "00000342", - "name": "OMA Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Z0-9]{5}\\d+$", - "prefix": "oma.protein", - "sampleId": "HUMAN16963", - "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1" - }, - "n2t": { - "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. 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It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", - "example": "Orphanet_C023", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo", - "name": "ORDO via OLS", - "namespaceEmbeddedInLui": false, - "pattern": "^Orphanet(_|:)C?\\d+$", - "prefix": "orphanet.ordo", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$1" - }, - "ols": { - "description": "The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10).", - "download": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", - "name": "Orphanet Rare Disease Ontology", - "prefix": "ordo", - "version": "4.0", - "version.iri": "http://www.orpha.net/version4.0" - }, - "pattern": "^C?\\d+$", - "synonyms": [ - "ordo" - ], - "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1" - }, - "orth": { - "bioportal": { - "name": "Orthology Ontology", - "prefix": "ORTH" - }, - "contact": { - "email": "jfernand@um.es", - "github": "jesualdotomasfernandezbreis", - "name": "Jesualdo Tom\u00e1s Fern\u00e1ndez-Breis", - "orcid": "0000-0002-7558-2880" - }, - "download_owl": "https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl", - "example": "HomologyRelation", - "fairsharing": { - "abbreviation": "ORTH", - "description": "ORTH ontology is designed to describe sequence homology data such as gene region, gene and protein-centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures in a single terminology.", - "id": "77", - "name": "Orthology Ontology", - "prefix": "FAIRsharing.4877h0", - "subjects": [ - "Comparative Genomics" - ] - }, - "homepage": "https://github.com/qfo/OrthologyOntology", - "mappings": { - "bioportal": "ORTH", - "fairsharing": "FAIRsharing.4877h0", - "ols": "orth" - }, - "ols": { - "description": "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.", - "download": "http://purl.org/net/orth", - "homepage": "http://purl.org/net/orth", - "name": "Orthology Ontology", - "prefix": "orth", - "version": "This ontology is the second version of the orthology ontology first published in 2015 and available at http://purl.bioontology.org/ontology/ORTH .\n@authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov, C. Dessimoz and F. Villiers.", - "version.iri": "http://purl.org/net/orth/2.0" - }, - "repository": "https://github.com/qfo/OrthologyOntology" - }, - "orthodb": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "ORTHODB", - "uri_format": "http://identifiers.org/orthodb/$1" - }, - "fairsharing": { - "abbreviation": "OrthoDB", - "description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. 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Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.", - "example": "117", - "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", - "name": "Oryzabase v4 Gene at National Institute of Genetics (Japan)", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "oryzabase.gene", - "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1" - } - }, - "oryzabase.mutant": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "ORYZABASE.MUTANT", - "uri_format": "http://identifiers.org/oryzabase.mutant/$1" - }, - "mappings": { - "biocontext": "ORYZABASE.MUTANT", - "miriam": "oryzabase.mutant", - "n2t": "oryzabase.mutant" - }, - "miriam": { - "deprecated": false, - "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. 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The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.", - "example": "P00024", - "homepage": "http://www.pantherdb.org/", - "name": "PANTHER Pathway at USC (Los Angeles)", - "namespaceEmbeddedInLui": false, - "pattern": "^P\\d{5}$", - "prefix": "panther.pathway", - "uri_format": "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1" - }, - "part_of": "panther" - }, - "panther.pthcmp": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PANTHER.PTHCMP", - "uri_format": "http://identifiers.org/panther.pthcmp/$1" - }, - "mappings": { - "biocontext": "PANTHER.PTHCMP", - "miriam": "panther.pthcmp", - "n2t": "panther.pthcmp" - }, - "miriam": { - "deprecated": false, - "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", - "homepage": "http://www.pantherdb.org/", - "id": "00000422", - "name": "PANTHER Pathway Component", - "namespaceEmbeddedInLui": false, - "pattern": "^G|P|U|C|S\\d{5}$", - "prefix": "panther.pthcmp", - "sampleId": "P00266", - "uri_format": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1" - }, - "n2t": { - "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", - "example": "P00266", - "homepage": "http://www.pantherdb.org/", - "name": "PANTHER Pathway Component at USC (Los Angeles)", - "namespaceEmbeddedInLui": false, - "pattern": "^G|P|U|C|S\\d{5}$", - "prefix": "panther.pthcmp", - "uri_format": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1" - }, - "part_of": "panther", - "pattern": "^(G|P|U|C|S)\\d{5}$" - }, - "pao": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "PAO", - "uri_format": "http://purl.obolibrary.org/obo/PAO_$1" - }, - "mappings": { - "biocontext": "PAO", - "obofoundry": "pao" - }, - "obofoundry": { - "contact": "jaiswalp@science.oregonstate.edu", - "contact.github": "jaiswalp", - "contact.label": "Pankaj Jaiswal", - "contact.orcid": "0000-0002-1005-8383", - "deprecated": true, - "homepage": "http://www.plantontology.org", - "name": "Plant Anatomy Ontology", - "prefix": "pao" - } - }, - "pass2": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PASS2", - "uri_format": "http://identifiers.org/pass2/$1" - }, - "deprecated": true, - "homepage": "http://caps.ncbs.res.in/pass2", - "mappings": { - "biocontext": "PASS2", - "miriam": "pass2", - "n2t": "pass2", - "prefixcommons": "pass2" - }, - "miriam": { - "deprecated": false, - "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", - "homepage": "http://caps.ncbs.res.in/pass2/", - "id": "00000468", - "name": "PASS2", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pass2", - "sampleId": "46977", - "uri_format": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1" - }, - "n2t": { - "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", - "example": "46977", - "homepage": "http://caps.ncbs.res.in/pass2/", - "name": "PASS2 at National centre for Biological Sciences (India)", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pass2", - "uri_format": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1" - }, - "name": "Protein Alignment organised as Structural Superfamily", - "prefixcommons": { - "description": "PASS2 is an automatic version of the original superfamily alignment database, CAMPASS. The current version contains 628 multi member superfamilies and 566 structure based sequence annotated single member superfamilies. Sequence members for the superfamilies in different genomes have been listed and aligned.", - "example": "47391", - "homepage": "http://www.ncbs.res.in/~faculty/mini/campass/pass2.html", - "keywords": [ - "structure", - "DNA", - "genome", - "classification" - ], - "name": "Protein Alignments organised as Structural Superfamilies", - "pattern": "^\\d+$", - "prefix": "pass2", - "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/campass/pass/pass.cgi?code=$1" - } - }, - "pathbank": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.", - "example": "SMP0000219", - "fairsharing": { - "abbreviation": "PathBank", - "description": "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics, and systems biology. All PathBank pathways include information on the relevant organelles, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures, and protein complex quaternary structures. The database is easily browsed and supports full text, sequence, and chemical structure searching.", - "id": "2831", - "name": "PathBank", - "prefix": "FAIRsharing.3xwMon", - "subjects": [ - "Endocrinology", - "Molecular biology", - "Animal Genetics", - "Cheminformatics", - "Bioinformatics", - "Genetics", - "Proteomics", - "Drug Metabolism", - "Human Genetics", - "Molecular Microbiology", - "Metabolomics", - "Transcriptomics", - "Cell Biology", - "Database Management", - "Microbiology", - "Biology", - "Systems Biology", - "Medical Informatics", - "Plant Genetics" - ] - }, - "homepage": "https://pathbank.org", - "mappings": { - "fairsharing": "FAIRsharing.3xwMon" - }, - "name": "PathBank", - "pattern": "^(SMP|PW)\\d+$", - "uri_format": "https://pathbank.org/view/$1" - }, - "pathwaycommons": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PATHWAYCOMMONS", - "uri_format": "http://identifiers.org/pathwaycommons/$1" - }, - "mappings": { - "biocontext": "PATHWAYCOMMONS", - "miriam": "pathwaycommons", - "n2t": "pathwaycommons", - "prefixcommons": "pathwaycommons", - "uniprot": "PathwayCommons" - }, - "miriam": { - "deprecated": false, - "description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.", - "homepage": "http://www.pathwaycommons.org/pc/", - "id": "00000073", - "name": "Pathway Commons", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pathwaycommons", - "sampleId": "485991", - "uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1" - }, - "n2t": { - "description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.", - "example": "485991", - "homepage": "http://www.pathwaycommons.org/pc/", - "name": "Pathway Commons", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pathwaycommons", - "uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1" - }, - "prefixcommons": { - "description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases", - "example": "485991", - "homepage": "http://www.pathwaycommons.org/pc/", - "keywords": [ - "pathway" - ], - "name": "Pathway Commons", - "pattern": "^\\d+$", - "prefix": "pathwaycommons", - "uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1" - }, - "uniprot": { - "category": "Enzyme and pathway databases", - "identifier": "253", - "link_is_explicit": "true", - "name": "Pathway Commons web resource for biological pathway data", - "prefix": "PathwayCommons", - "uri_format": "http://apps.pathwaycommons.org/search?q=$1" - } - }, - "pato": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "PATO", - "uri_format": "http://purl.obolibrary.org/obo/PATO_$1" - }, - "bioportal": { - "name": "Phenotypic Quality Ontology", - "prefix": "PATO" - }, - "fairsharing": { - "abbreviation": "PATO", - "description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily phenotype annotation. This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes.", - "id": "1287", - "name": "Phenotypic QualiTy Ontology", - "prefix": "FAIRsharing.ezwdhz", - "subjects": [ - "Biodiversity", - "Biology" - ] - }, - "go": { - "homepage": "http://www.obofoundry.org/ontology/pato.html", - "name": "Phenotypic quality ontology", - "prefix": "PATO" - }, - "mappings": { - "biocontext": "PATO", - "bioportal": "PATO", - "fairsharing": "FAIRsharing.ezwdhz", - "go": "PATO", - "miriam": "pato", - "n2t": "pato", - "obofoundry": "pato", - "ols": "pato", - "ontobee": "PATO", - "prefixcommons": "pato" - }, - "miriam": { - "deprecated": false, - "description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.", - "homepage": "https://www.ebi.ac.uk/ols/ontologies/pato", - "id": "00000112", - "name": "PATO", - "namespaceEmbeddedInLui": true, - "pattern": "^PATO:\\d{7}$", - "prefix": "pato", - "sampleId": "0001998", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1" - }, - "n2t": { - "description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.", - "example": "0001998", - "homepage": "http://bioportal.bioontology.org/ontologies/PATO", - "name": "PATO through BioPortal", - "namespaceEmbeddedInLui": true, - "pattern": "^PATO:\\d{7}$", - "prefix": "pato", - "uri_format": "http://purl.bioontology.org/ontology/PATO/PATO:$1" - }, - "obofoundry": { - "appears_in": [ - "agro", - "aism", - "cdno", - "cl", - "colao", - "ecocore", - "ecto", - "fovt", - "lepao", - "mco", - "ms", - "pcl", - "pco", - "phipo", - "planp", - "rbo", - "xpo", - "zp" - ], - "contact": "g.gkoutos@gmail.com", - "contact.github": "gkoutos", - "contact.label": "George Gkoutos", - "contact.orcid": "0000-0002-2061-091X", - "deprecated": false, - "description": "An ontology of phenotypic qualities (properties, attributes or characteristics)", - "download.json": "http://purl.obolibrary.org/obo/pato.json", - "download.obo": "http://purl.obolibrary.org/obo/pato.obo", - "download.owl": "http://purl.obolibrary.org/obo/pato.owl", - "homepage": "https://github.com/pato-ontology/pato/", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Phenotype And Trait Ontology", - "preferredPrefix": "PATO", - "prefix": "pato", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/28387809", - "title": "The anatomy of phenotype ontologies: principles, properties and applications" - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/15642100", - "title": "Using ontologies to describe mouse phenotypes" - } - ], - "repository": "https://github.com/pato-ontology/pato" - }, - "ols": { - "description": "An ontology of phenotypic qualities (properties, attributes or characteristics).", - "download": "http://purl.obolibrary.org/obo/pato.owl", - "homepage": "https://github.com/pato-ontology/pato/", - "name": "PATO - the Phenotype And Trait Ontology", - "prefix": "pato", - "version": "2022-02-20", - "version.iri": "http://purl.obolibrary.org/obo/pato/releases/2022-02-20/pato.owl" - }, - "ontobee": { - "library": "Foundry", - "name": "Phenotype And Trait Ontology", - "prefix": "PATO" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1107", - "description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.", - "example": "PATO:0001998", - "homepage": "http://obofoundry.org/wiki/index.php/PATO:Main_Page", - "keywords": [ - "obo", - "ontology", - "quality", - "phenotype" - ], - "name": "PATO", - "pattern": "^PATO:\\d{7}$", - "prefix": "pato", - "uri_format": "http://www.ebi.ac.uk/ontology-lookup/?termId=$1" - } - }, - "pav": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "pav", - "uri_format": "http://purl.org/pav/$1" - }, - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "pav", - "uri_format": "http://purl.org/pav/$1" - }, - "bioportal": { - "name": "PAV Provenance, Authoring and Versioning", - "prefix": "PAV" - }, - "contributor": { - "github": "matentzn", - "name": "Nico Matentzoglu", - "orcid": "0000-0002-7356-1779" - }, - "contributor_extras": [ - { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - } - ], - "description": "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.", - "example": "authoredBy", - "fairsharing": { - "abbreviation": "PAV", - "description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource.", - "id": "678", - "name": "Provenance, Authoring and Versioning Ontology", - "prefix": "FAIRsharing.nbfwwv", - "subjects": [ - "Data Management", - "Subject Agnostic" - ] - }, - "homepage": "https://pav-ontology.github.io/pav/", - "mappings": { - "biocontext": "pav", - "biolink": "pav", - "bioportal": "PAV", - "fairsharing": "FAIRsharing.nbfwwv" - }, - "name": "Provenance, Authoring, and Versioning Vocabulary", - "pattern": "^[a-z][a-zA-Z]+$", - "reviewer": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "uri_format": "http://purl.org/pav/$1" - }, - "paxdb.organism": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PAXDB.ORGANISM", - "uri_format": "http://identifiers.org/paxdb.organism/$1" - }, - "mappings": { - "biocontext": "PAXDB.ORGANISM", - "miriam": "paxdb.organism", - "n2t": "paxdb.organism" - }, - "miriam": { - "deprecated": false, - "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.", - "homepage": "http://pax-db.org/", - "id": "00000488", - "name": "PaxDb Organism", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "paxdb.organism", - "sampleId": "9606", - "uri_format": "http://pax-db.org/#!species/$1" - }, - "n2t": { - "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.", - "example": "9606", - "homepage": "http://pax-db.org/", - "name": "PaxDb v3 at University of Zurich", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "paxdb.organism", - "uri_format": "http://pax-db.org/#!species/$1" - } - }, - "paxdb.protein": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PAXDB.PROTEIN", - "uri_format": "http://identifiers.org/paxdb.protein/$1" - }, - "mappings": { - "biocontext": "PAXDB.PROTEIN", - "miriam": "paxdb.protein", - "n2t": "paxdb.protein" - }, - "miriam": { - "deprecated": false, - "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.", - "homepage": "http://pax-db.org/", - "id": "00000489", - "name": "PaxDb Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "paxdb.protein", - "sampleId": "977869", - "uri_format": "http://pax-db.org/#!protein/$1" - }, - "n2t": { - "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.", - "example": "977869", - "homepage": "http://pax-db.org/", - "name": "PaxDb v3 at University of Zurich", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "paxdb.protein", - "uri_format": "http://pax-db.org/#!protein/$1" - } - }, - "pazar": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PAZAR", - "uri_format": "http://identifiers.org/pazar/$1" - }, - "fairsharing": { - "abbreviation": "PAZAR", - "description": "PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data.", - "id": "2032", - "name": "PAZAR", - "prefix": "FAIRsharing.33yggg", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "PAZAR", - "fairsharing": "FAIRsharing.33yggg", - "miriam": "pazar", - "n2t": "pazar", - "prefixcommons": "pazar" - }, - "miriam": { - "deprecated": false, - "description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.", - "homepage": "http://www.pazar.info/", - "id": "00000306", - "name": "Pazar Transcription Factor", - "namespaceEmbeddedInLui": false, - "pattern": "^TF\\w+$", - "prefix": "pazar", - "sampleId": "TF0001053", - "uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1" - }, - "n2t": { - "description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.", - "example": "TF0001053", - "homepage": "http://www.pazar.info/", - "name": "Pazar Transcription Factor at University of British Columbia", - "namespaceEmbeddedInLui": false, - "pattern": "^TF\\w+$", - "prefix": "pazar", - "uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1" - }, - "prefixcommons": { - "description": "PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data.", - "example": "TF0000448", - "homepage": "http://www.pazar.info/", - "keywords": [ - "regulation", - "DNA", - "RNA" - ], - "name": "PAZAR", - "pattern": "^TF\\d+$", - "prefix": "pazar", - "uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?searchtab=tfs&ID_list=PAZAR_TF&geneID=$1" - } - }, - "pba": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "A controlled vocabulary to support the study of transcription in the primate brain", - "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo", - "example": "128011350", - "homepage": "https://www.blueprintnhpatlas.org/", - "name": "Primate Brain Atlas", - "pattern": "^\\d+$", - "preferred_prefix": "PBA" - }, - "pcl": { - "bioportal": { - "name": "Provisional Cell Ontology", - "prefix": "PCL" - }, - "example": "0011124", - "mappings": { - "bioportal": "PCL", - "obofoundry": "pcl", - "ols": "pcl" - }, - "obofoundry": { - "contact": "davidos@ebi.ac.uk", - "contact.github": "dosumis", - "contact.label": "David Osumi-Sutherland", - "contact.orcid": "0000-0002-7073-9172", - "depends_on": [ - "bfo", - "chebi", - "cl", - "go", - "nbo", - "ncbitaxon", - "omo", - "pato", - "pr", - "ro", - "so", - "uberon" - ], - "deprecated": false, - "description": "Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties.", - "download.json": "http://purl.obolibrary.org/obo/pcl.json", - "download.obo": "http://purl.obolibrary.org/obo/pcl.obo", - "download.owl": "http://purl.obolibrary.org/obo/pcl.owl", - "homepage": "https://github.com/obophenotype/provisional_cell_ontology", - "license": "CC BY 4.0", - "license.url": "http://creativecommons.org/licenses/by/4.0/", - "name": "Provisional Cell Ontology", - "preferredPrefix": "PCL", - "prefix": "pcl", - "repository": "https://github.com/obophenotype/provisional_cell_ontology" - }, - "ols": { - "description": "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.", - "download": "https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-full.owl", - "name": "Provisional Cell Ontology", - "prefix": "pcl", - "version": "2022-04-27", - "version.iri": "http://purl.obolibrary.org/obo/pcl/releases/2022-04-27/pcl-full.owl" - }, - "pattern": "^\\d{7}$" - }, - "pco": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "PCO", - "uri_format": "http://purl.obolibrary.org/obo/PCO_$1" - }, - "bioportal": { - "name": "Population and Community Ontology", - "prefix": "PCO" - }, - "example": "0000021", - "fairsharing": { - "abbreviation": "PCO", - "description": "Population and Community Ontology (PCO) is an ontology standard for describing the collective and interacting species of any taxa such as humans or plants. PCO has useful application in community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies.", - "id": "1053", - "name": "Population and Community Ontology", - "prefix": "FAIRsharing.vq28qp", - "subjects": [ - "Ecology", - "Biodiversity", - "Community Care", - "Social and Behavioural Science", - "Population Genetics" - ] - }, - "mappings": { - "biocontext": "PCO", - "bioportal": "PCO", - "fairsharing": "FAIRsharing.vq28qp", - "obofoundry": "pco", - "ols": "pco", - "ontobee": "PCO" - }, - "obofoundry": { - "appears_in": [ - "ecocore", - "envo" - ], - "contact": "rlwalls2008@gmail.com", - "contact.github": "ramonawalls", - "contact.label": "Ramona Walls", - "contact.orcid": "0000-0001-8815-0078", - "depends_on": [ - "bfo", - "bfo", - "caro", - "envo", - "go", - "iao", - "ncbitaxon", - "pato", - "ro" - ], - "deprecated": false, - "description": "An ontology about groups of interacting organisms such as populations and communities", - "download.owl": "http://purl.obolibrary.org/obo/pco.owl", - "homepage": "https://github.com/PopulationAndCommunityOntology/pco", - "license": "CC0 1.0", - "license.url": "http://creativecommons.org/publicdomain/zero/1.0/", - "name": "Population and Community Ontology", - "preferredPrefix": "PCO", - "prefix": "pco", - "repository": "https://github.com/PopulationAndCommunityOntology/pco" - }, - "ols": { - "description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.", - "download": "http://purl.obolibrary.org/obo/pco.owl", - "homepage": "https://github.com/PopulationAndCommunityOntology/pco", - "name": "Population and Community Ontology", - "prefix": "pco", - "version": "2021-05-03", - "version.iri": "http://purl.obolibrary.org/obo/pco/releases/2021-05-03/pco.owl" - }, - "ontobee": { - "library": "Library", - "name": "Population and Community Ontology", - "prefix": "PCO" - }, - "pattern": "^\\d{7}$" - }, - "pd_st": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "PD_ST", - "uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1" - }, - "mappings": { - "biocontext": "PD_ST", - "obofoundry": "pd_st" - }, - "obofoundry": { - "contact": "henrich@embl.de", - "contact.label": "Thorsten Heinrich", - "deprecated": true, - "homepage": "http://4dx.embl.de/platy", - "name": "Platynereis stage ontology", - "prefix": "pd_st" - } - }, - "pdb": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "PDB", - "uri_format": "http://www.ebi.ac.uk/pdbsum/$1" - }, - "fairsharing": { - "abbreviation": "wwPDB", - "description": "The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community. 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The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).", - "example": "PR:000000024", - "homepage": "http://pir.georgetown.edu/pro/", - "keywords": [ - "obo", - "protein" - ], - "name": "PRotein Ontology (PRO)", - "pattern": "^PR\\:\\d+$", - "prefix": "pr", - "pubmed_ids": [ - "18047702" - ], - "uri_format": "http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$1" - }, - "synonyms": [ - "PR", - "PRO" - ], - "uniprot": { - "category": "Miscellaneous databases", - "identifier": "181", - "link_is_explicit": "true", - "name": "Protein Ontology", - "prefix": "PRO", - "uri_format": "https://proconsortium.org/app/entry/$1" - }, - "wikidata": { - "database": "Q55118584", - "database.homepage": "http://pir.georgetown.edu/pro", - "database.label": "Protein Ontology", - "homepage": "https://pir.georgetown.edu/pro/pro.shtml", - "name": "PRotein Ontology ID", - "pattern": "PR:\\d*", - "prefix": "P4926", - "uri_format": "https://proconsortium.org/app/entry/$1/" - } - }, - "prefixcommons": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "A registry of life science prefxes", - "example": "ChEBI", - "homepage": "https://prefixcommons.org", - "name": "Prefix Commons", - "uri_format": "https://bioregistry.io/metaregistry/prefixcommons/$1" - }, - "pride": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PRIDE", - "uri_format": "http://identifiers.org/pride/$1" - }, - "cellosaurus": { - "category": "Proteomic databases", - "homepage": "https://www.ebi.ac.uk/pride/archive/", - "name": "PRoteomics IDEntifications archive", - "prefix": "PRIDE", - "uri_format": "https://www.ebi.ac.uk/pride/archive/projects/$1" - }, - "fairsharing": { - "abbreviation": "PRIDE", - "description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.", - "id": "1863", - "name": "PRoteomics IDEntifications database", - "prefix": "FAIRsharing.e1byny", - "subjects": [ - "Proteomics", - "Life Science" - ] - }, - "mappings": { - "biocontext": "PRIDE", - "cellosaurus": "PRIDE", - "fairsharing": "FAIRsharing.e1byny", - "miriam": "pride", - "n2t": "pride", - "ols": "pride", - "prefixcommons": "pride", - "uniprot": "PRIDE" - }, - "miriam": { - "deprecated": false, - "description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. 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This collection references projects.", - "homepage": "https://www.ebi.ac.uk/pride/", - "id": "00000515", - "name": "PRIDE Project", - "namespaceEmbeddedInLui": false, - "pattern": "^P(X|R)D\\d{6}$", - "prefix": "pride.project", - "providers": [ - { - "code": "omicsdi", - "description": "PRIDE Project through OmicsDI", - "homepage": "https://www.omicsdi.org/", - "name": "PRIDE Project through OmicsDI", - "uri_format": "https://www.omicsdi.org/dataset/pride/$1" - } - ], - "sampleId": "PXD000440", - "uri_format": "https://www.ebi.ac.uk/pride/archive/projects/$1" - }, - "n2t": { - "description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. 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Please note that the last release of this database on the PRINTS website was in 2007.", - "id": "2099", - "name": "PRINTS", - "prefix": "FAIRsharing.h8r843", - "subjects": [ - "Structural Biology", - "Biology" - ] - }, - "go": { - "homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/", - "name": "PRINTS compendium of protein fingerprints", - "prefix": "PRINTS", - "uri_format": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1" - }, - "mappings": { - "biocontext": "PRINTS", - "fairsharing": "FAIRsharing.h8r843", - "go": "PRINTS", - "miriam": "prints", - "n2t": "prints", - "uniprot": "PRINTS" - }, - "miriam": { - "deprecated": false, - "description": "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. 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Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.", - "example": "PR00001", - "homepage": "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/", - "name": "PRINTS through SPRINT", - "namespaceEmbeddedInLui": false, - "pattern": "^PR\\d{5}$", - "prefix": "prints", - "uri_format": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off" - }, - "uniprot": { - "category": "Family and domain databases", - "comment": "Replacement for PRINT", - "identifier": "82", - "link_is_explicit": "true", - "name": "Protein Motif fingerprint database; a protein domain database", - "prefix": "PRINTS", - "uri_format": "http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=$1" - } - }, - "probonto": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PROBONTO", - "uri_format": "http://identifiers.org/probonto/$1" - }, - "fairsharing": { - "abbreviation": "ProbOnto", - "description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 150 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. 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Its original registration with MIRIAM uses a subview over the protein to point to peptides, but the identifiers in this semantic space seem to be about proteins.", - "mappings": { - "biocontext": "PROTEOMICSDB.PEPTIDE", - "miriam": "proteomicsdb.peptide", - "n2t": "proteomicsdb.peptide" - }, - "miriam": { - "deprecated": false, - "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. 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Each entry page provides detailed information about this structural motion.", - "homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html", - "id": "00000370", - "name": "PSCDB", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "pscdb", - "sampleId": "051", - "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html" - }, - "n2t": { - "description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. 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This work is not peer-reviewed.", - "download": "http://purl.obolibrary.org/obo/psdo.owl", - "homepage": "https://github.com/Display-Lab/psdo", - "name": "Performance Summary Display Ontology", - "prefix": "psdo", - "version": "1.0.0", - "version.iri": "http://purl.obolibrary.org/obo/2020-12-04/psdo.owl" - }, - "ontobee": { - "library": "Library", - "name": "Performance Summary Display Ontology", - "prefix": "PSDO" - }, - "pattern": "^\\d{7}$" - }, - "pseudogene": { - "bioportal": { - "name": "Pseudogene", - "prefix": "pseudo" - }, - "description": "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.", - "example": "PGOHUM00000289843", - "homepage": "http://www.pseudogene.org", - "mappings": { - "bioportal": "pseudo", - "prefixcommons": "pseudogene" - }, - "name": "PseudoGene", - "prefixcommons": { - "description": "Pseudogene is a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.", - "example": "4", - "homepage": "http://www.pseudogene.org/", - "keywords": [ - "gene" - ], - "name": "PseudoGene", - "pattern": "^\\d+$", - "prefix": "pseudogene", - "uri_format": "http://tables.pseudogene.org/[?species_name]/$1" - }, - "synonyms": [ - "pseudogene.org" - ], - "wikidata": { - "database": "Q7254809" - } - }, - "pseudomonas": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "PSEUDOMONAS", - "uri_format": "http://identifiers.org/pseudomonas/$1" - }, - "mappings": { - "biocontext": "PSEUDOMONAS", - "miriam": "pseudomonas", - "n2t": "pseudomonas" - }, - "miriam": { - "deprecated": false, - "description": "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. 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It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data.", - "example": "101", - "homepage": "http://rebase.neb.com", - "keywords": [ - "enzyme", - "protein", - "structure", - "small molecule", - "genome", - "DNA", - "RNA" - ], - "name": "Restriction enzymes and methylases database", - "pattern": "^\\d+$", - "prefix": "rebase", - "pubmed_ids": [ - "19846593" - ], - "uri_format": "http://rebase.neb.com/rebase/enz/$1.html" - }, - "uniprot": { - "category": "Protein family/group databases", - "identifier": "89", - "link_is_explicit": "true", - "name": "Restriction enzymes and methylases database", - "prefix": "REBASE", - "uri_format": "http://rebase.neb.com/rebase/enz/$1.html" - } - }, - "receptome.family": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.", - "example": "5.1", - "homepage": "http://www.receptome.org", - "name": "Human Plasma Membrane Receptome Families", - "uri_format": "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1" - }, - "refseq": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "RefSeq", - "uri_format": "http://www.ncbi.nlm.nih.gov/refseq/?term=$1" - }, - "fairsharing": { - "abbreviation": "RefSeq", - "description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.", - "id": "1991", - "name": "Reference Sequence Database", - "prefix": "FAIRsharing.4jg0qw", - "subjects": [ - "Genetics", - "Computational Biology", - "Life Science" - ] - }, - "go": { - "homepage": "http://www.ncbi.nlm.nih.gov/RefSeq/", - "name": "RefSeq", - "prefix": "RefSeq" - }, - "has_canonical": "ncbiprotein", - "mappings": { - "biocontext": "RefSeq", - "fairsharing": "FAIRsharing.4jg0qw", - "go": "RefSeq", - "miriam": "refseq", - "n2t": "refseq", - "prefixcommons": "refseq", - "uniprot": "RefSeq" - }, - "miriam": { - "deprecated": false, - "description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.", - "homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/", - "id": "00000039", - "name": "RefSeq", - "namespaceEmbeddedInLui": false, - "pattern": "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ\\_[A-Z]{2,4}\\d+))(\\.\\d+)?$", - "prefix": "refseq", - "sampleId": "NP_012345", - "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" - }, - "n2t": { - "description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.", - "example": "NP_012345", - "homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/", - "name": "The NCBI Reference Sequence database", - "namespaceEmbeddedInLui": false, - "pattern": "^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+|(NZ\\_[A-Z]{4}\\d+))(\\.\\d+)?$", - "prefix": "refseq", - "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" - }, - "name": "Reference Sequence Collection", - "prefixcommons": { - "description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.", - "example": "NP_012345", - "homepage": "http://www.ncbi.nlm.nih.gov/RefSeq/", - "keywords": [ - "protein", - "DNA", - "RNA" - ], - "name": "Reference Sequence Database", - "pattern": "^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\\d+(\\.\\d+)?$", - "prefix": "refseq", - "pubmed_ids": [ - "17130148" - ], - "uri_format": "http://www.ncbi.nlm.nih.gov/nuccore/[?id]" - }, - "synonyms": [ - "REFSEQ_PROT" - ], - "uniprot": { - "category": "Sequence databases", - "identifier": "117", - "link_is_explicit": "true", - "name": "NCBI Reference Sequences", - "prefix": "RefSeq", - "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" - } - }, - "reo": { - "comment": "From James O.: It was an ontology for \"reagents\" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.", - "contact": { - "email": "matt@tislab.org", - "github": "mbrush", - "name": "Matthew Brush" - }, - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied \u201cchemically\u201d in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.", - "download_owl": "https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl", - "example": "0000079", - "homepage": "https://github.com/tis-lab/reagent-ontology", - "mappings": { - "ontobee": "REO" - }, - "name": "Reagent Ontology", - "ontobee": { - "library": "Not Specified/No", - "name": "Reagent Ontology", - "prefix": "REO" - }, - "pattern": "^\\d{7}$", - "references": [ - "https://github.com/obi-ontology/obi/issues/1015", - "https://code.google.com/archive/p/reagent-ontology/", - "https://github.com/obi-ontology/obi/issues/1135" - ], - "repository": "https://github.com/tis-lab/reagent-ontology" - }, - "repeatsdb.protein": { - "mappings": { - "miriam": "repeatsdb.protein" - }, - "miriam": { - "deprecated": false, - "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.", - "homepage": "https://repeatsdb.org/", - "id": "00000792", - "name": "RepeatsDB Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$", - "prefix": "repeatsdb.protein", - "sampleId": "P29894", - "uri_format": "https://repeatsdb.org/protein/$1" - }, - "provides": "uniprot" - }, - "repeatsdb.structure": { - "mappings": { - "miriam": "repeatsdb.structure" - }, - "miriam": { - "deprecated": false, - "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database.", - "homepage": "https://repeatsdb.org/", - "id": "00000764", - "name": "RepeatsDB Structure", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$", - "prefix": "repeatsdb.structure", - "sampleId": "2gc4E", - "uri_format": "https://repeatsdb.org/structure/$1" - } - }, - "reproduceme": { - "bioportal": { - "name": "REPRODUCE-ME", - "prefix": "REPRODUCE-ME" - }, - "example": "MicrobeamManipulation", - "mappings": { - "bioportal": "REPRODUCE-ME", - "ols": "reproduceme" - }, - "ols": { - "contact": "sheeba.samuel@uni-jena.de", - "description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility.", - "download": "https://sheeba-samuel.github.io/REPRODUCE-ME/doc/reproduce-me.xml", - "homepage": "https://w3id.org/reproduceme/research", - "name": "REPRODUCE-ME Ontology", - "prefix": "reproduceme", - "version": "1.1" - } - }, - "resid": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "RESID", - "uri_format": "http://purl.obolibrary.org/obo/RESID_$1" - }, - "go": { - "homepage": "https://proteininformationresource.org/resid/resid.shtml", - "name": "RESID Database of Protein Modifications", - "prefix": "RESID", - "uri_format": "https://proteininformationresource.org/cgi-bin/resid?id=$1" - }, - "mappings": { - "biocontext": "RESID", - "go": "RESID", - "miriam": "resid", - "n2t": "resid", - "obofoundry": "resid", - "prefixcommons": "resid" - }, - "miriam": { - "deprecated": false, - "description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", - "homepage": "http://pir0.georgetown.edu/resid/", - "id": "00000046", - "name": "RESID", - "namespaceEmbeddedInLui": false, - "pattern": "^AA\\d{4}$", - "prefix": "resid", - "sampleId": "AA0001", - "uri_format": "http://pir0.georgetown.edu/cgi-bin/resid?id=$1" - }, - "n2t": { - "description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", - "example": "AA0001", - "homepage": "http://pir0.georgetown.edu/resid/", - "name": "RESID at Georgetown University", - "namespaceEmbeddedInLui": false, - "pattern": "^AA\\d{4}$", - "prefix": "resid", - "uri_format": "http://pir0.georgetown.edu/cgi-bin/resid?id=$1" - }, - "obofoundry": { - "contact": "john.garavelli@ebi.ac.uk", - "contact.label": "John Garavelli", - "deprecated": true, - "description": "For the description of covalent bonds in proteins.", - "homepage": "http://www.ebi.ac.uk/RESID/", - "name": "Protein covalent bond", - "prefix": "resid" - }, - "prefixcommons": { - "description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", - "example": "AA0001", - "homepage": "http://www.ebi.ac.uk/RESID/", - "keywords": [ - "protein", - "small molecule", - "structure" - ], - "name": "RESID Database of Protein Modifications", - "pattern": "^AA\\d{4}$", - "prefix": "resid", - "pubmed_ids": [ - "15174124" - ], - "uri_format": "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$1']" - } - }, - "reto": { - "bioportal": { - "name": "Regulation of Transcription Ontology", - "prefix": "RETO" - }, - "download_obo": "https://www.bio.ntnu.no/ontology/ReTO/reto.obo", - "download_owl": "https://www.bio.ntnu.no/ontology/ReTO/reto.owl", - "fairsharing": { - "abbreviation": "ReTO", - "description": "An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO.", - "id": "263", - "name": "Regulation of Transcription Ontolology", - "prefix": "FAIRsharing.4qyf0f", - "subjects": [ - "Life Science", - "Transcriptomics" - ] - }, - "mappings": { - "bioportal": "RETO", - "fairsharing": "FAIRsharing.4qyf0f", - "ols": "reto" - }, - "no_own_terms": true, - "ols": { - "contact": "vladimir.n.mironov@gmail.com", - "description": "Regulation of Transcription", - "download": "http://www.bio.ntnu.no/ontology/ReTO/reto.rdf", - "homepage": "http://www.semantic-systems-biology.org/apo", - "name": "Regulation of Transcription Ontology", - "prefix": "reto", - "version": "2019-09-17" - } - }, - "rex": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "REX", - "uri_format": "http://purl.obolibrary.org/obo/REX_$1" - }, - "bioportal": { - "name": "Physico-Chemical Process", - "prefix": "REX" - }, - "download_owl": "http://purl.obolibrary.org/obo/rex.owl", - "example": "0000512", - "fairsharing": { - "abbreviation": "REX", - "description": "REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.", - "id": "1085", - "name": "Physico-chemical process", - "prefix": "FAIRsharing.g0a7s0", - "subjects": [ - "Chemistry", - "Life Science" - ] - }, - "homepage": "https://www.ebi.ac.uk/chebi/", - "mappings": { - "biocontext": "REX", - "bioportal": "REX", - "fairsharing": "FAIRsharing.g0a7s0", - "obofoundry": "rex", - "ols": "rex", - "ontobee": "REX", - "prefixcommons": "rex" - }, - "obofoundry": { - "deprecated": true, - "description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.", - "download.owl": "http://purl.obolibrary.org/obo/rex.owl", - "name": "Physico-chemical process", - "prefix": "rex" - }, - "ols": { - "description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.", - "download": "http://purl.obolibrary.org/obo/rex.owl", - "name": "Physico-chemical process", - "prefix": "rex", - "version": "2017-11-19", - "version.iri": "http://purl.obolibrary.org/obo/rex/releases/2017-11-19/rex.owl" - }, - "ontobee": { - "library": "Library", - "name": "Physico-chemical process", - "prefix": "REX" - }, - "part_of": "chebi", - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1043", - "description": "REX is an ontology of physico-chemical processes and includes microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes.", - "example": "REX_0000517", - "homepage": "http://www.ebi.ac.uk/~kirill/REX/", - "keywords": [ - "obo", - "biochemistry" - ], - "name": "Physico-chemical process", - "pattern": "^REX_\\d{8}$", - "prefix": "rex" - } - }, - "rexo": { - "bioportal": { - "name": "Regulation of Gene Expression Ontolology", - "prefix": "REXO" - }, - "download_obo": "https://www.bio.ntnu.no/ontology/ReXO/rexo.obo", - "download_owl": "https://www.bio.ntnu.no/ontology/ReXO/rexo.owl", - "fairsharing": { - "abbreviation": "ReXO", - "description": "An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO.", - "id": "846", - "name": "Regulation of Gene Expression Ontolology", - "prefix": "FAIRsharing.recas1", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "bioportal": "REXO", - "fairsharing": "FAIRsharing.recas1", - "ols": "rexo" - }, - "no_own_terms": true, - "ols": { - "contact": "vladimir.n.mironov@gmail.com", - "description": "Regulation of Gene Expression", - "download": "http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf", - "homepage": "http://www.semantic-systems-biology.org/apo", - "name": "Regulation of Gene Expression Ontology", - "prefix": "rexo", - "version": "2019-04-11" - } - }, - "rfam": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RFAM", - "uri_format": "http://identifiers.org/rfam/$1" - }, - "fairsharing": { - "abbreviation": "Rfam", - "description": "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence.", - "id": "2396", - "name": "Rfam", - "prefix": "FAIRsharing.fex4c8", - "subjects": [ - "Genetics" - ] - }, - "go": { - "homepage": "https://rfam.org", - "name": "Rfam database of RNA families", - "prefix": "Rfam", - "uri_format": "https://rfam.org/family/$1" - }, - "mappings": { - "biocontext": "RFAM", - "fairsharing": "FAIRsharing.fex4c8", - "go": "Rfam", - "miriam": "rfam", - "n2t": "rfam", - "ncbi": "RFAM" - }, - "miriam": { - "deprecated": false, - "description": "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.", - "homepage": "https://rfam.xfam.org/", - "id": "00000409", - "name": "RFAM", - "namespaceEmbeddedInLui": false, - "pattern": "^RF\\d{5}$", - "prefix": "rfam", - "sampleId": "RF00230", - "uri_format": "https://rfam.xfam.org/family/$1" - }, - "n2t": { - "description": "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.", - "example": "RF00230", - "homepage": "https://rfam.xfam.org/", - "name": "Rfam at EMBL-EBI", - "namespaceEmbeddedInLui": false, - "pattern": "^RF\\d{5}$", - "prefix": "rfam", - "uri_format": "https://rfam.xfam.org/family/$1" - }, - "ncbi": { - "example": "RF00230", - "homepage": "http://www.sanger.ac.uk/Software/Rfam/", - "name": "RNA families database of alignments and CMs", - "prefix": "RFAM" - } - }, - "rgd": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "RGD", - "uri_format": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1" - }, - "bioportal": { - "name": "RRB Group D", - "prefix": "RGD" - }, - "cellosaurus": { - "category": "Organism-specific databases", - "homepage": "https://rgd.mcw.edu", - "name": "Rat Genome Database", - "prefix": "RGD", - "uri_format": "https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1" - }, - "example": "7499841", - "fairsharing": { - "abbreviation": "RGD", - "description": "The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. 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Data curation is performed both manually and via an automated pipeline, giving RGD users integrated access to a wide variety of data to support their research.", - "id": "1951", - "name": "Rat Genome Database", - "prefix": "FAIRsharing.pfg82t", - "subjects": [ - "Genomics", - "Comparative Genomics" - ] - }, - "go": { - "homepage": "https://rgd.mcw.edu/", - "name": "Rat Genome Database", - "prefix": "RGD", - "synonyms": [ - "RAD", - "RGDID" - ], - "uri_format": "https://rgd.mcw.edu/rgdweb/search/search.html?term=$1" - }, - "mappings": { - "biocontext": "RGD", - "bioportal": "RGD", - "cellosaurus": "RGD", - "fairsharing": "FAIRsharing.pfg82t", - "go": "RGD", - "miriam": "rgd", - "n2t": "rgd", - "ncbi": "RGD", - "prefixcommons": "rgd", - "uniprot": "RGD", - "wikidata": "P3853" - }, - "miriam": { - "deprecated": false, - "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. 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This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.", - "homepage": "http://rgd.mcw.edu/", - "id": "00000451", - "name": "Rat Genome Database qTL", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "rgd.qtl", - "sampleId": "1354581", - "uri_format": "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1" - }, - "n2t": { - "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. 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This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.", - "homepage": "http://rgd.mcw.edu/", - "id": "00000452", - "name": "Rat Genome Database strain", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "rgd.strain", - "sampleId": "5688061", - "uri_format": "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1" - }, - "n2t": { - "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.", - "example": "5688061", - "homepage": "http://rgd.mcw.edu/", - "name": "Rat Genome Database strain at Medical College of Wisconsin", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "rgd.strain", - "uri_format": "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1" - } - }, - "rhea": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RHEA", - "uri_format": "http://identifiers.org/rhea/$1" - }, - "fairsharing": { - "abbreviation": "Rhea", - "description": "Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. 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All data in Rhea is freely accessible and available for anyone to use.", - "homepage": "https://www.rhea-db.org", - "name": "Rhea, the Annotated Reactions Database", - "prefix": "RHEA", - "uri_format": "https://www.rhea-db.org/rhea/$1" - }, - "mappings": { - "biocontext": "RHEA", - "fairsharing": "FAIRsharing.pn1sr5", - "go": "RHEA", - "miriam": "rhea", - "n2t": "rhea", - "prefixcommons": "rhea" - }, - "miriam": { - "deprecated": false, - "description": " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. 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Rhea is the standard for enzyme and transporter annotation in UniProtKB.", - "homepage": "https://www.rhea-db.org/", - "id": "00000082", - "name": "Rhea", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{5}$", - "prefix": "rhea", - "sampleId": "12345", - "uri_format": "https://www.rhea-db.org/rhea/$1" - }, - "n2t": { - "description": "Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. 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It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed \"spontaneous\".", - "example": "12345", - "homepage": "http://www.ebi.ac.uk/rhea/", - "keywords": [ - "reaction", - "small molecule" - ], - "name": "Reaction database", - "pattern": "^\\d{5}$", - "prefix": "rhea", - "uri_format": "http://www.ebi.ac.uk/rhea//reaction.xhtml?id=$1" - }, - "synonyms": [ - "RHEA" - ], - "uri_format": "https://www.rhea-db.org/rhea/$1", - "wikidata": { - "database": "Q24265951" - } - }, - "ricegap": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RICEGAP", - "uri_format": "http://identifiers.org/ricegap/$1" - }, - "mappings": { - "biocontext": "RICEGAP", - "miriam": "ricegap", - "n2t": "ricegap" - }, - "miriam": { - "deprecated": false, - "description": "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.", - "homepage": "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml", - "id": "00000358", - "name": "Rice Genome Annotation Project", - "namespaceEmbeddedInLui": false, - "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", - "prefix": "ricegap", - "sampleId": "LOC_Os02g13300", - "uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1" - }, - "n2t": { - "description": "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.", - "example": "LOC_Os02g13300", - "homepage": "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml", - "name": "Rice Genome Annotation Project at TIGR", - "namespaceEmbeddedInLui": false, - "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", - "prefix": "ricegap", - "uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1" - } - }, - "ricenetdb.compound": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RICENETDB.COMPOUND", - "uri_format": "http://identifiers.org/ricenetdb.compound/$1" - }, - "mappings": { - "biocontext": "RICENETDB.COMPOUND", - "miriam": "ricenetdb.compound", - "n2t": "ricenetdb.compound" - }, - "miriam": { - "deprecated": false, - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", - "homepage": "http://bis.zju.edu.cn/ricenetdb", - "id": "00000666", - "name": "RiceNetDB Compound", - "namespaceEmbeddedInLui": false, - "pattern": "^OSC\\d{4}$", - "prefix": "ricenetdb.compound", - "sampleId": "OSC1416", - "uri_format": "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1" - }, - "n2t": { - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", - "example": "OSC1416", - "homepage": "http://bis.zju.edu.cn/ricenetdb", - "name": "RiceNetDB Compound", - "namespaceEmbeddedInLui": false, - "pattern": "^OSC\\d{4}$", - "prefix": "ricenetdb.compound", - "uri_format": "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1" - } - }, - "ricenetdb.gene": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RICENETDB.GENE", - "uri_format": "http://identifiers.org/ricenetdb.gene/$1" - }, - "mappings": { - "biocontext": "RICENETDB.GENE", - "miriam": "ricenetdb.gene", - "n2t": "ricenetdb.gene" - }, - "miriam": { - "deprecated": false, - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", - "homepage": "http://bis.zju.edu.cn/ricenetdb/", - "id": "00000664", - "name": "RiceNetDB Gene", - "namespaceEmbeddedInLui": false, - "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$", - "prefix": "ricenetdb.gene", - "sampleId": "LOC_Os01g49190.1", - "uri_format": "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1" - }, - "n2t": { - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", - "example": "LOC_Os01g49190.1", - "homepage": "http://bis.zju.edu.cn/ricenetdb/", - "name": "RiceNetDB", - "namespaceEmbeddedInLui": false, - "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$", - "prefix": "ricenetdb.gene", - "uri_format": "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1" - } - }, - "ricenetdb.mirna": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RICENETDB.MIRNA", - "uri_format": "http://identifiers.org/ricenetdb.miRNA/$1" - }, - "mappings": { - "biocontext": "RICENETDB.MIRNA", - "miriam": "ricenetdb.mirna", - "n2t": "ricenetdb.mirna" - }, - "miriam": { - "deprecated": false, - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. 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It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", - "example": "osa-miR446", - "homepage": "http://bis.zju.edu.cn/ricenetdb", - "name": "RiceNetDB miRNA", - "namespaceEmbeddedInLui": false, - "pattern": "^osa-miR\\d{3,5}[a-z]{0,1}$", - "prefix": "ricenetdb.mirna", - "uri_format": "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1" - } - }, - "ricenetdb.protein": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RICENETDB.PROTEIN", - "uri_format": "http://identifiers.org/ricenetdb.protein/$1" - }, - "mappings": { - "biocontext": "RICENETDB.PROTEIN", - "miriam": "ricenetdb.protein", - "n2t": "ricenetdb.protein" - }, - "miriam": { - "deprecated": false, - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", - "homepage": "http://bis.zju.edu.cn/ricenetdb/", - "id": "00000665", - "name": "RiceNetDB Protein", - "namespaceEmbeddedInLui": false, - "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", - "prefix": "ricenetdb.protein", - "sampleId": "LOC_Os01g49190", - "uri_format": "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1" - }, - "n2t": { - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", - "example": "LOC_Os01g49190", - "homepage": "http://bis.zju.edu.cn/ricenetdb/", - "name": "RiceNetDB", - "namespaceEmbeddedInLui": false, - "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", - "prefix": "ricenetdb.protein", - "uri_format": "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1" - } - }, - "ricenetdb.reaction": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "RICENETDB.REACTION", - "uri_format": "http://identifiers.org/ricenetdb.reaction/$1" - }, - "mappings": { - "biocontext": "RICENETDB.REACTION", - "miriam": "ricenetdb.reaction", - "n2t": "ricenetdb.reaction" - }, - "miriam": { - "deprecated": false, - "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. 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The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.", - "homepage": "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm", - "id": "00000308", - "name": "RNA Modification Database", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{3}$", - "prefix": "rnamods", - "sampleId": "101", - "uri_format": "http://mods.rna.albany.edu/mods/modifications/view/$1" - }, - "n2t": { - "description": "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. 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"homepage": "https://github.com/bgsu-rna/rnao", - "license": "CC0 1.0", - "license.url": "https://creativecommons.org/publicdomain/zero/1.0/", - "name": "RNA ontology", - "prefix": "rnao", - "repository": "https://github.com/BGSU-RNA/rnao" - }, - "ols": { - "description": "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.", - "download": "http://purl.obolibrary.org/obo/rnao.owl", - "homepage": "https://github.com/bgsu-rna/rnao", - "name": "The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data", - "prefix": "rnao", - "version": "2019-04-15" - }, - "ontobee": { - "library": "Library", - "name": "RNA ontology", - "prefix": "RNAO" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1500", - "description": "The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.", - 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"homepage": "http://www.obofoundry.org/ro", - "keywords": [ - "obo", - "relations" - ], - "name": "Relation Ontology", - "pattern": "^\\w+$", - "prefix": "ro", - "pubmed_ids": [ - "15892874" - ] - }, - "synonyms": [ - "RO_proposed_relation", - "obo_rel", - "oborel" - ], - "uri_format": "http://purl.obolibrary.org/obo/RO_$1", - "wikidata": { - "prefix": "P3590" - } - }, - "rouge": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "ROUGE", - "uri_format": "http://identifiers.org/rouge/$1" - }, - "fairsharing": { - "abbreviation": "ROUGE", - "description": "The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). 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It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.", - "homepage": "https://scicrunch.org/resolver", - "id": "00000558", - "name": "RRID", - "namespaceEmbeddedInLui": true, - "pattern": "^RRID:[a-zA-Z]+.+$", - "prefix": "rrid", - "sampleId": "AB_262044", - "uri_format": "https://scicrunch.org/resolver/RRID:$1" - }, - "n2t": { - "description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. 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These RRIDs are aggregated and can be searched through SciCrunch.", - "example": "AB_262044", - "homepage": "https://scicrunch.org/resolver", - "name": "RRID at SciCrunch", - "namespaceEmbeddedInLui": true, - "pattern": "^RRID:[A-Z_a-z-0-9]+$", - "prefix": "rrid", - "uri_format": "https://scicrunch.org/resolver/RRID:$1" - }, - "name": "Research Resource Identification", - "pattern": "^[a-zA-Z]+.+$" - }, - "rs": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "RS", - "uri_format": "http://purl.obolibrary.org/obo/RS_$1" - }, - "bioportal": { - "name": "Rat Strain Ontology", - "prefix": "RS" - }, - "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo", - "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl", - "example": "0001807", - "fairsharing": { - "abbreviation": "RS", - "description": "This ontology defines the hierarchical display of the different rat strains as derived from the parental strains.", - 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} - ], - "repository": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology" - }, - "ols": { - "description": "Ontology of rat strains", - "download": "http://purl.obolibrary.org/obo/rs.owl", - "homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html", - "name": "Rat Strain Ontology", - "prefix": "rs", - "version": "2019-12-13", - "version.iri": "http://purl.obolibrary.org/obo/rs/6.106/rs.owl" - }, - "ontobee": { - "library": "Library", - "name": "Rat Strain Ontology", - "prefix": "RS" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1150", - "description": "This ontology defines the hierarchical display of the different rat strains as derived from the parental strains", - "example": "RS_0000271", - "homepage": "http://rgd.mcw.edu/", - "keywords": [ - "obo" - ], - "name": "Rat Strain Ontology", - "pattern": "^RS_\\d{7}$", - "prefix": "rs", - "uri_format": "http://purl.obolibrary.org/obo/$1" - } - }, - "runbiosimulations": { - "mappings": { - "miriam": "runbiosimulations" - }, - "miriam": { - "deprecated": false, - "description": "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive.", - "homepage": "https://icahn.mssm.edu/", - "id": "00000897", - "name": "runBioSimulations", - "namespaceEmbeddedInLui": false, - "pattern": "[0-9a-z]{24,24}", - "prefix": "runbiosimulations", - "sampleId": "5fde96bdc5f1aa9ff0cce18a", - "uri_format": "https://run.biosimulations.org/simulations/$1" - } - }, - "rxno": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "RXNO", - "uri_format": "http://purl.obolibrary.org/obo/RXNO_$1" - }, - "bioportal": { - "name": "Name Reaction Ontology", - "prefix": "RXNO" - }, - "download_obo": "https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo", - 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"name": "Saccharomyces cerevisiae pathways at SGD.", - "namespaceEmbeddedInLui": false, - "pattern": "^PWY\\w{2}\\-\\d{3}$", - "prefix": "sgd.pathways", - "uri_format": "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1" - }, - "prefixcommons": { - "description": "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD).", - "example": "PWY3O-214", - "homepage": "http://www.yeastgenome.org/", - "keywords": [ - "genome", - "pathway", - "sequence" - ], - "name": "Saccharomyces genome database pathways", - "pattern": "^PWY\\w{2}\\-\\d{3}$", - "prefix": "sgd.pathways", - "pubmed_ids": [ - "14681421" - ], - "uri_format": "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1" - } - }, - "sgn": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "SGN", - "uri_format": "http://identifiers.org/sgn/$1" - }, - "fairsharing": { - "abbreviation": "SGN", - "description": "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.", - "id": "1841", - "name": "Sol Genomics Network", - "prefix": "FAIRsharing.3zqvaf", - "subjects": [ - "Botany", - "Genomics", - "Agriculture", - "Comparative Genomics" - ] - }, - "go": { - "homepage": "https://www.sgn.cornell.edu/", - "name": "Sol Genomics Network", - "prefix": "SGN", - "synonyms": [ - "SGN_gene" - ], - "uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1" - }, - "mappings": { - "biocontext": "SGN", - "fairsharing": "FAIRsharing.3zqvaf", - "go": "SGN", - "miriam": "sgn", - "n2t": "sgn", - "ncbi": "SGN", - "prefixcommons": "sgn" - }, - "miriam": { - "deprecated": false, - "description": "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.", - "homepage": "http://solgenomics.net/", - "id": "00000185", - "name": "Sol Genomics Network", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sgn", - "sampleId": "0001", - "uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1" - }, - "n2t": { - "description": "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.", - "example": "0001", - "homepage": "http://solgenomics.net/", - "name": "Sol Genomics Network at Boyce Thompson Institute for Plant Research", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sgn", - "uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1" - }, - "ncbi": { - "example": "E553090", - "homepage": "http://www.sgn.cornell.edu", - "name": "SOL Genomics Network", - "prefix": "SGN" - }, - "prefixcommons": { - "description": "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant.", - "example": "1", - "homepage": "http://www.sgn.cornell.edu", - "keywords": [ - "pathway", - "small molecule", - "genome", - "plant" - ], - "name": "Sol Genomics Network", - "pattern": "^\\d+$", - "prefix": "sgn", - "pubmed_ids": [ - "20935049" - ], - "uri_format": "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1" - } - }, - "sheepqtldb": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "SHEEPQTLDB", - "uri_format": "http://identifiers.org/sheepqtldb/$1" - }, - "mappings": { - "biocontext": "SHEEPQTLDB", - "miriam": "sheepqtldb", - "n2t": "sheepqtldb", - "prefixcommons": "sheepqtldb" - }, - "miriam": { - "deprecated": false, - "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.", - "homepage": "https://www.animalgenome.org/QTLdb", - "id": "00000507", - "name": "Animal Genome Sheep QTL", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sheepqtldb", - "sampleId": "19803", - "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" - }, - "n2t": { - "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs.", - "example": "19803", - "homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/index", - "name": "Animal QTL Sheep at Iowa State University", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sheepqtldb", - "uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1" - }, - "part_of": "qtldb", - "prefixcommons": { - "description": "This Sheep Quantitative Trait Locus (QTL) database (Sheep QTLdb) has gathered all sheep QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on sheep chromosomes the most feasible location for genes responsible for quantitative trait important to sheep production.", - "example": "66", - "homepage": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/index", - "keywords": [ - "DNA", - "genome" - ], - "name": "Sheep Quantitative Trait Locus database", - "pattern": "^\\d+$", - "prefix": "sheepqtldb", - "uri_format": "http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1" - } - }, - "sibo": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "SIBO", - "uri_format": "http://purl.obolibrary.org/obo/SIBO_$1" - }, - "bioportal": { - "name": "Social Inset Behavior Ontology", - "prefix": "SIBO" - }, - "example": "0000509", - "fairsharing": { - "abbreviation": "SIBO", - "description": "Social behavior in insects.", - "id": "596", - "name": "Social Inset Behavior Ontology", - "prefix": "FAIRsharing.q09hck", - "subjects": [] - }, - "mappings": { - "biocontext": "SIBO", - "bioportal": "SIBO", - "fairsharing": "FAIRsharing.q09hck", - "obofoundry": "sibo", - "ols": "sibo", - "ontobee": "SIBO" - }, - "obofoundry": { - "contact": "cjmungall@lbl.gov", - "contact.label": "Chris Mungall", - "contact.orcid": "0000-0002-6601-2165", - "deprecated": true, - "description": "Social Behavior in insects", - "download.obo": "http://purl.obolibrary.org/obo/sibo.obo", - "download.owl": "http://purl.obolibrary.org/obo/sibo.owl", - "homepage": "https://github.com/obophenotype/sibo", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Social Insect Behavior Ontology", - "preferredPrefix": "SIBO", - "prefix": "sibo", - "repository": "https://github.com/obophenotype/sibo" - }, - "ols": { - "description": "Social Behavior in insects", - "download": "http://purl.obolibrary.org/obo/sibo.owl", - "homepage": "https://github.com/obophenotype/sibo", - "name": "Social Insect Behavior Ontology", - "prefix": "sibo", - "version": "2015-06-15", - "version.iri": "http://purl.obolibrary.org/obo/sibo/releases/2015-06-15/sibo.owl" - }, - "ontobee": { - "library": "Library", - "name": "Social Insect Behavior Ontology", - "prefix": "SIBO" - }, - "pattern": "^\\d{7}$" - }, - "sider.drug": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "SIDER.DRUG", - "uri_format": "http://identifiers.org/sider.drug/$1" - }, - "mappings": { - "biocontext": "SIDER.DRUG", - "miriam": "sider.drug", - "n2t": "sider.drug" - }, - "miriam": { - "deprecated": false, - "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.", - "homepage": "http://sideeffects.embl.de/", - "id": "00000435", - "name": "SIDER Drug", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sider.drug", - "sampleId": "2244", - "uri_format": "http://sideeffects.embl.de/drugs/$1/" - }, - "n2t": { - "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.", - "example": "2244", - "homepage": "http://sideeffects.embl.de/", - "name": "SIDER Drug v2 at EMBL (Heidelberg)", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sider.drug", - "uri_format": "http://sideeffects.embl.de/drugs/$1/" - }, - "uri_format": "http://sideeffects.embl.de/drugs/$1" - }, - "sider.effect": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "SIDER.EFFECT", - "uri_format": "http://identifiers.org/sider.effect/$1" - }, - "mappings": { - "biocontext": "SIDER.EFFECT", - "miriam": "sider.effect", - "n2t": "sider.effect" - }, - "miriam": { - "deprecated": false, - "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.", - "homepage": "http://sideeffects.embl.de/", - "id": "00000436", - "name": "SIDER Side Effect", - "namespaceEmbeddedInLui": false, - "pattern": "^C\\d+$", - "prefix": "sider.effect", - "sampleId": "C0017565", - "uri_format": "http://sideeffects.embl.de/se/$1/" - }, - "n2t": { - "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.", - "example": "C0017565", - "homepage": "http://sideeffects.embl.de/", - "name": "SIDER Side Effect v2 at EMBL (Heidelberg)", - "namespaceEmbeddedInLui": false, - "pattern": "^C\\d+$", - "prefix": "sider.effect", - "uri_format": "http://sideeffects.embl.de/se/$1/" - }, - "provides": "umls", - "uri_format": "http://sideeffects.embl.de/se/$1" - }, - "sigmaaldirch": { - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "description": "Sigma Aldrich is a life sciences supply vendor.", - "example": "HPA000698", - "homepage": "https://www.sigmaaldrich.com", - "name": "Sigma Aldrich", - "uri_format": "https://www.sigmaaldrich.com/US/en/product/sigma/$1" - }, - "signaling-gateway": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "SIGNALING-GATEWAY", - "uri_format": "http://identifiers.org/signaling-gateway/$1" - }, - "mappings": { - "biocontext": "SIGNALING-GATEWAY", - "miriam": "signaling-gateway", - "n2t": "signaling-gateway", - "prefixcommons": "signaling-gateway" - }, - "miriam": { - "deprecated": false, - "description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.", - "homepage": "http://www.signaling-gateway.org/molecule", - "id": "00000045", - "name": "Signaling Gateway", - "namespaceEmbeddedInLui": false, - "pattern": "A\\d{6}$", - "prefix": "signaling-gateway", - "sampleId": "A001094", - "uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1" - }, - "n2t": { - "description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.", - "example": "A001094", - "homepage": "http://www.signaling-gateway.org/molecule", - "name": "Signaling Gateway Molecule Pages", - "namespaceEmbeddedInLui": false, - "pattern": "A\\d{6}$", - "prefix": "signaling-gateway", - "uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1" - }, - "prefixcommons": { - "description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.", - "example": "A001094", - "homepage": "http://www.signaling-gateway.org/molecule/", - "keywords": [ - "pathway", - "protein", - "small molecule" - ], - "name": "The Signaling Gateway", - "pattern": "^A\\d{6}$", - "prefix": "signaling-gateway", - "pubmed_ids": [ - "17965093", - "12478304", - "21505029" - ], - "uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1" - } - }, - "signor": { - "example": "SIGNOR-C41", - "fairsharing": { - "abbreviation": "SIGNOR", - "description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.", - "id": "2224", - "name": "SIGnaling Network Open Resource", - "prefix": "FAIRsharing.ss78t4", - "subjects": [ - "Biology" - ] - }, - "mappings": { - "fairsharing": "FAIRsharing.ss78t4", - "miriam": "signor", - "uniprot": "SIGNOR" - }, - "miriam": { - "deprecated": false, - "description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.", - "homepage": "https://signor.uniroma2.it/", - "id": "00000808", - "name": "SIGNOR", - "namespaceEmbeddedInLui": false, - "pattern": "^SIGNOR\\-[A-Z]+\\d+$", - "prefix": "signor", - "sampleId": "SIGNOR-C2", - "uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1" - }, - "name": "Signaling Network Open Resource", - "synonyms": [ - "SIGNOR" - ], - "uniprot": { - "category": "Enzyme and pathway databases", - "identifier": "206", - "link_is_explicit": "true", - "name": "SIGNOR Signaling Network Open Resource", - "prefix": "SIGNOR", - "uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1" - } - }, - "signor.relation": { - "comment": "Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern", - "contributor": { - "email": "benjamin_gyori@hms.harvard.edu", - "github": "bgyori", - "name": "Benjamin M. Gyori", - "orcid": "0000-0001-9439-5346" - }, - "description": "Identifiers for relationships between proteins and complexes, along with their type and provenance", - "example": "SIGNOR-252737", - "homepage": "https://signor.uniroma2.it", - "name": "SIGNOR Relation", - "part_of": "signor", - "pattern": "^SIGNOR-\\d+$", - "reviewer": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - } - }, - "sio": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "SIO", - "uri_format": "http://semanticscience.org/resource/SIO_$1" - }, - "biolink": { - "is_identifiers": false, - "is_obo": false, - "prefix": "SIO", - "uri_format": "http://semanticscience.org/resource/SIO_$1" - }, - "bioportal": { - "name": "Semanticscience Integrated Ontology", - "prefix": "SIO" - }, - "example": "000912", - "fairsharing": { - "abbreviation": "SIO", - "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.", - "id": "1286", - "name": "Semanticscience Integrated Ontology", - "prefix": "FAIRsharing.dpkb5f", - "subjects": [ - "Natural Science", - "Subject Agnostic" - ] - }, - "mappings": { - "biocontext": "SIO", - "biolink": "SIO", - "bioportal": "SIO", - "fairsharing": "FAIRsharing.dpkb5f", - "miriam": "sio", - "ols": "sio", - "ontobee": "SIO" - }, - "miriam": { - "deprecated": false, - "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.", - "homepage": "https://www.ebi.ac.uk", - "id": "00000851", - "name": "Semanticscience Integrated Ontology", - "namespaceEmbeddedInLui": false, - "pattern": "^SIO_\\d{6,6}$", - "prefix": "sio", - "sampleId": "SIO_000276", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1" - }, - "ols": { - "contact": "sio-ontology@googlegroups.com", - "description": "The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes.", - "download": "https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl", - "homepage": "https://github.com/micheldumontier/semanticscience", - "name": "Semanticscience Integrated Ontology", - "prefix": "sio", - "version": "1.53", - "version.iri": "http://semanticscience.org/ontology/sio/v1.53/sio-release.owl" - }, - "ontobee": { - "library": "Not Specified/No", - "name": "Semanticscience Integrated Ontology", - "prefix": "SIO" - }, - "pattern": "^\\d{6}$", - "repository": "https://github.com/micheldumontier/semanticscience" - }, - "sisu": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "SISU", - "uri_format": "http://identifiers.org/sisu/$1" - }, - "fairsharing": { - "abbreviation": "SISu", - "description": "The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in the Finnish population. It provides valuable summary data for researchers and clinicians as well as other researchers with an interest in genetics in Finland. With SISu, you can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map. The SISu project is an international collaboration between multiple research groups aiming to build tools for genomic medicine.", - "id": "2383", - "name": "Sequencing Initiative Suomi", - "prefix": "FAIRsharing.t1a232", - "subjects": [ - "Medicine", - "Genomics", - "Biomedical Science", - "Epidemiology", - "Preclinical Studies" - ] - }, - "mappings": { - "biocontext": "SISU", - "fairsharing": "FAIRsharing.t1a232", - "miriam": "sisu", - "n2t": "sisu" - }, - "miriam": { - "deprecated": false, - "description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.", - "homepage": "http://www.sisuproject.fi/", - "id": "00000624", - "name": "SISu", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+:[0-9]+$", - "prefix": "sisu", - "sampleId": "17:41223048", - "uri_format": "http://search.sisuproject.fi/#/variant/$1" - }, - "n2t": { - "description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.", - "example": "17:41223048", - "homepage": "http://www.sisuproject.fi/", - "name": "SISu", - "namespaceEmbeddedInLui": false, - "pattern": "^[0-9]+:[0-9]+$", - "prefix": "sisu", - "uri_format": "http://search.sisuproject.fi/#/variant/$1" - }, - "name": "Sequencing Initiative Suomi" - }, - "sitex": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "SITEX", - "uri_format": "http://identifiers.org/sitex/$1" - }, - "fairsharing": { - "abbreviation": "SitEx", - "description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.", - "id": "1672", - "name": "SitEx database of eukaryotic protein functional sites", - "prefix": "FAIRsharing.5mr9c5", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "SITEX", - "fairsharing": "FAIRsharing.5mr9c5", - "miriam": "sitex", - "n2t": "sitex", - "prefixcommons": "sitex" - }, - "miriam": { - "deprecated": false, - "description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.", - "homepage": "http://www-bionet.sscc.ru/sitex/", - "id": "00000252", - "name": "SitEx", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "sitex", - "sampleId": "1000", - "uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1" - }, - "n2t": { - "description": "SitEx is a database containing information on eukaryotic protein functional sites. 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While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", - "example": "Tb927.8.620", - "homepage": "http://tritrypdb.org/tritrypdb/", - "name": "TriTrypDB at EuPathDB", - "namespaceEmbeddedInLui": false, - "pattern": "^\\w+(\\.)?\\w+(\\.)?\\w+", - "prefix": "tritrypdb", - "uri_format": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" - } - }, - "ttd.drug": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "TTD.DRUG", - "uri_format": "http://identifiers.org/ttd.drug/$1" - }, - "mappings": { - "biocontext": "TTD.DRUG", - "miriam": "ttd.drug", - "n2t": "ttd.drug" - }, - "miriam": { - "deprecated": false, - "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", - "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", - "id": "00000092", - "name": "TTD Drug", - "namespaceEmbeddedInLui": false, - "pattern": "^DAP\\d+$", - "prefix": "ttd.drug", - "sampleId": "DAP000773", - "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1" - }, - "n2t": { - "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", - "example": "DAP000773", - "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", - "name": "Therapeutic Target Database Drug", - "namespaceEmbeddedInLui": false, - "pattern": "^DAP\\d+$", - "prefix": "ttd.drug", - "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1" - } - }, - "ttd.target": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "TTD.TARGET", - "uri_format": "http://identifiers.org/ttd.target/$1" - }, - "mappings": { - "biocontext": "TTD.TARGET", - "miriam": "ttd.target", - "n2t": "ttd.target" - }, - "miriam": { - "deprecated": false, - "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", - "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", - "id": "00000093", - "name": "TTD Target", - "namespaceEmbeddedInLui": false, - "pattern": "^TTDS\\d+$", - "prefix": "ttd.target", - "sampleId": "TTDS00056", - "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1" - }, - "n2t": { - "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", - "example": "TTDS00056", - "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", - "name": "Therapeutic Target Database Target", - "namespaceEmbeddedInLui": false, - "pattern": "^TTDS\\d+$", - "prefix": "ttd.target", - "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1" - } - }, - "tto": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "TTO", - "uri_format": "http://purl.obolibrary.org/obo/TTO_$1" - }, - "bioportal": { - "name": "Teleost Taxonomy Ontology", - "prefix": "TTO" - }, - "example": "1058367", - "fairsharing": { - "abbreviation": "TTO", - "description": "This is an ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish.", - "id": "82", - "name": "Teleost Taxonomy Ontology", - "prefix": "FAIRsharing.1rj558", - "subjects": [ - "Life Science" - ] - }, - "mappings": { - "biocontext": "TTO", - "bioportal": "TTO", - "fairsharing": "FAIRsharing.1rj558", - "obofoundry": "tto", - "ols": "tto", - "ontobee": "TTO", - "prefixcommons": "tto" - }, - "obofoundry": { - "contact": "balhoff@renci.org", - "contact.github": "balhoff", - "contact.label": "Jim Balhoff", - "contact.orcid": "0000-0002-8688-6599", - "deprecated": false, - "description": "An ontology covering the taxonomy of teleosts (bony fish)", - "download.obo": "http://purl.obolibrary.org/obo/tto.obo", - "download.owl": "http://purl.obolibrary.org/obo/tto.owl", - "homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology", - "license": "CC0 1.0", - "license.url": "http://creativecommons.org/publicdomain/zero/1.0/", - "name": "Teleost taxonomy ontology", - "preferredPrefix": "TTO", - "prefix": "tto", - "publications": [ - { - "id": "https://doi.org/10.1038/npre.2010.4629.1", - "title": "The Teleost Taxonomy Ontology" - } - ], - "repository": "https://github.com/phenoscape/teleost-taxonomy-ontology" - }, - "ols": { - "description": "An ontology covering the taxonomy of teleosts (bony fish)", - "download": "http://purl.obolibrary.org/obo/tto.owl", - "homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology", - "name": "Teleost taxonomy ontology", - "prefix": "tto", - "version": "2018-03-26", - "version.iri": "http://purl.obolibrary.org/obo/tto/2012-05-18/tto.owl" - }, - "ontobee": { - "library": "Library", - "name": "Teleost taxonomy ontology", - "prefix": "TTO" - }, - "pattern": "^\\d+$", - "prefixcommons": { - "bioportal": "1081", - "description": "The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made.", - "example": "TTO_2", - "homepage": "https://www.nescent.org/phenoscape/Main_Page", - "keywords": [ - "obo", - "phenotype", - "fish" - ], - "name": "Teleost taxonomy Ontology", - "pattern": "^TTO_\\d$", - "prefix": "tto", - "uri_format": "http://purl.obolibrary.org/obo/$1" - }, - "wikidata": { - "database": "Q81661821" - } - }, - "txpo": { - "bioportal": { - "name": "Toxic Process Ontology", - "prefix": "TXPO" - }, - "example": "0002066", - "mappings": { - "bioportal": "TXPO", - "obofoundry": "txpo", - "ols": "txpo", - "ontobee": "TXPO" - }, - "obofoundry": { - "contact": "yuki.yamagata@riken.jp", - "contact.github": "yuki-yamagata", - "contact.label": "Yuki Yamagata", - "contact.orcid": "0000-0002-9673-1283", - "deprecated": false, - "description": "TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.", - "download.owl": "http://purl.obolibrary.org/obo/txpo.owl", - "homepage": "https://toxpilot.nibiohn.go.jp/", - "license": "CC BY 3.0", - "license.url": "https://creativecommons.org/licenses/by/3.0/", - "name": "Toxic Process Ontology", - "preferredPrefix": "TXPO", - "prefix": "txpo", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/32883995", - "title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management" - } - ], - "repository": "https://github.com/txpo-ontology/TXPO" - }, - "ols": { - "description": "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp", - "download": "http://purl.obolibrary.org/obo/txpo.owl", - "homepage": "https://toxpilot.nibiohn.go.jp/", - "name": "TOXic Process Ontology (TXPO)", - "prefix": "txpo", - "version": "2020-07-09", - "version.iri": "http://purl.obolibrary.org/obo/txpo/releases/2020-03-03/txpo.owl" - }, - "ontobee": { - "library": "Library", - "name": "Toxic Process Ontology", - "prefix": "TXPO" - }, - "pattern": "^\\d{7}$" - }, - "uberon": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "UBERON", - "uri_format": "http://purl.obolibrary.org/obo/UBERON_$1" - }, - "bioportal": { - "name": "Uber Anatomy Ontology", - "prefix": "UBERON" - }, - "cellosaurus": { - "category": "Anatomy/cell type resources", - "homepage": "https://uberon.github.io/", - "name": "Uber-anatomy ontology", - "prefix": "UBERON", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1" - }, - "download_obo": "http://purl.obolibrary.org/obo/uberon/basic.obo", - "example": "2005080", - "fairsharing": { - "abbreviation": "UBERON", - "description": "Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. It represents a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", - "id": "1197", - "name": "UBER anatomy ONtology", - "prefix": "FAIRsharing.4c0b6b", - "subjects": [ - "Anatomy", - "Taxonomy", - "Developmental Biology", - "Life Science" - ] - }, - "go": { - "description": "A multi-species anatomy ontology", - "homepage": "http://uberon.org", - "name": "Uber-anatomy ontology", - "prefix": "UBERON" - }, - "mappings": { - "biocontext": "UBERON", - "bioportal": "UBERON", - "cellosaurus": "UBERON", - "fairsharing": "FAIRsharing.4c0b6b", - "go": "UBERON", - "miriam": "uberon", - "n2t": "uberon", - "obofoundry": "uberon", - "ols": "uberon", - "ontobee": "UBERON" - }, - "miriam": { - "deprecated": false, - "description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", - "homepage": "http://bioportal.bioontology.org/ontologies/UBERON", - "id": "00000446", - "name": "UBERON", - "namespaceEmbeddedInLui": true, - "pattern": "^UBERON:\\d+$", - "prefix": "uberon", - "sampleId": "0008203", - "uri_format": "http://purl.bioontology.org/ontology/UBERON/UBERON:$1" - }, - "n2t": { - "description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", - "example": "0008203", - "homepage": "http://bioportal.bioontology.org/ontologies/UBERON", - "name": "UBERON through bioPortal", - "namespaceEmbeddedInLui": true, - "pattern": "^UBERON\\:\\d+$", - "prefix": "uberon", - "uri_format": "http://purl.bioontology.org/ontology/UBERON/UBERON:$1" - }, - "name": "Uber Anatomy Ontology", - "obofoundry": { - "appears_in": [ - "go", - "aism", - "amphx", - "chiro", - "cl", - "clo", - "clyh", - "colao", - "cteno", - "ecao", - "ecocore", - "ecto", - "envo", - "foodon", - "fovt", - "genepio", - "hso", - "lepao", - "maxo", - "mco", - "mfmo", - "ons", - "pcl", - "plana", - "poro", - "zp" - ], - "contact": "cjmungall@lbl.gov", - "contact.github": "cmungall", - "contact.label": "Chris Mungall", - "contact.orcid": "0000-0002-6601-2165", - "depends_on": [ - "chebi", - "cl", - "go", - "pr" - ], - "deprecated": false, - "description": "An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies", - "download.owl": "http://purl.obolibrary.org/obo/uberon.owl", - "homepage": "http://uberon.org", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Uberon multi-species anatomy ontology", - "preferredPrefix": "UBERON", - "prefix": "uberon", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/22293552", - "title": "Uberon, an integrative multi-species anatomy ontology" - }, - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/25009735", - "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon" - } - ], - "repository": "https://github.com/obophenotype/uberon", - "twitter": "uberanat" - }, - "ols": { - "description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", - "download": "http://purl.obolibrary.org/obo/uberon.owl", - "homepage": "http://uberon.org", - "name": "Uber-anatomy ontology", - "prefix": "uberon", - "version": "2022-04-18", - "version.iri": "http://purl.obolibrary.org/obo/uberon/releases/2022-04-18/uberon.owl" - }, - "ontobee": { - "library": "Library", - "name": "Uberon multi-species anatomy ontology", - "prefix": "UBERON" - }, - "pattern": "^\\d+$", - "synonyms": [ - "UBERON", - "Uber-anatomy ontology", - "Uberon" - ], - "wikidata": { - "prefix": "P1554" - } - }, - "ubio.namebank": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "UBIO.NAMEBANK", - "uri_format": "http://identifiers.org/ubio.namebank/$1" - }, - "mappings": { - "biocontext": "UBIO.NAMEBANK", - "miriam": "ubio.namebank", - "n2t": "ubio.namebank" - }, - "miriam": { - "deprecated": false, - "description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.", - "homepage": "http://www.ubio.org", - "id": "00000338", - "name": "uBio NameBank", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "ubio.namebank", - "sampleId": "2555646", - "uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1" - }, - "n2t": { - "description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.", - "example": "2555646", - "homepage": "http://www.ubio.org", - "name": "uBio NameBank at The Marine Biological Laboratory", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "ubio.namebank", - "uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1" - } - }, - "ubprop": { - "comment": "All of these are typedefs in uberon now", - "contributor": { - "email": "cthoyt@gmail.com", - "github": "cthoyt", - "name": "Charles Tapley Hoyt", - "orcid": "0000-0003-4423-4370" - }, - "deprecated": true, - "name": "Uberon Property" - }, - "ucsc": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "UCSC", - "uri_format": "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1" - }, - "description": "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.", - "example": "uc001rvw.5", - "homepage": "https://genome.ucsc.edu/", - "mappings": { - "biocontext": "UCSC", - "uniprot": "UCSC" - }, - "name": "UCSC Genome Browser", - "uniprot": { - "category": "Genome annotation databases", - "identifier": "139", - "link_is_explicit": "true", - "name": "UCSC genome browser", - "prefix": "UCSC", - "uri_format": "https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=$1" - }, - "wikidata": { - "prefix": "P2576" - } - }, - "umbbd.compound": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "UMBBD.COMPOUND", - "uri_format": "http://identifiers.org/umbbd.compound/$1" - }, - "mappings": { - "biocontext": "UMBBD.COMPOUND", - "miriam": "umbbd.compound", - "n2t": "umbbd.compound" - }, - "miriam": { - "deprecated": false, - "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.", - "homepage": "http://umbbd.ethz.ch/", - "id": "00000276", - "name": "UM-BBD Compound", - "namespaceEmbeddedInLui": false, - "pattern": "^c\\d+$", - "prefix": "umbbd.compound", - "sampleId": "c0001", - "uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1" - }, - "n2t": { - "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.", - "example": "c0001", - "homepage": "http://umbbd.ethz.ch/", - "name": "Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich", - "namespaceEmbeddedInLui": false, - "pattern": "^c\\d+$", - "prefix": "umbbd.compound", - "uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1" - }, - "part_of": "umbbd", - "synonyms": [ - "UM-BBD_compID" - ], - "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1", - "wikidata": { - "prefix": "P8121" - } - }, - "umbbd.enzyme": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "UMBBD.ENZYME", - "uri_format": "http://identifiers.org/umbbd.enzyme/$1" - }, - "go": { - "homepage": "http://eawag-bbd.ethz.ch/", - "name": "EAWAG Biocatalysis/Biodegradation Database", - "prefix": "UM-BBD_enzymeID", - "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1" - }, - "mappings": { - "biocontext": "UMBBD.ENZYME", - "go": "UM-BBD_enzymeID", - "miriam": "umbbd.enzyme", - "n2t": "umbbd.enzyme" - }, - "miriam": { - "deprecated": false, - "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.", - "homepage": "http://umbbd.ethz.ch/", - "id": "00000326", - "name": "UM-BBD Enzyme", - "namespaceEmbeddedInLui": false, - "pattern": "^e\\d+$", - "prefix": "umbbd.enzyme", - "sampleId": "e0333", - "uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1" - }, - "n2t": { - "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.", - "example": "e0333", - "homepage": "http://umbbd.ethz.ch/", - "name": "Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich", - "namespaceEmbeddedInLui": false, - "pattern": "^e\\d+$", - "prefix": "umbbd.enzyme", - "uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1" - }, - "part_of": "umbbd", - "synonyms": [ - "UM-BBD_enzymeID" - ], - "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1" - }, - "umbbd.pathway": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "UMBBD.PATHWAY", - "uri_format": "http://identifiers.org/umbbd.pathway/$1" - }, - "go": { - "homepage": "http://eawag-bbd.ethz.ch/", - "name": "EAWAG Biocatalysis/Biodegradation Database", - "prefix": "UM-BBD_pathwayID", - "uri_format": "http://eawag-bbd.ethz.ch/$1/$1_map.html" - }, - "mappings": { - "biocontext": "UMBBD.PATHWAY", - "go": "UM-BBD_pathwayID", - "miriam": "umbbd.pathway", - "n2t": "umbbd.pathway" - }, - "miriam": { - "deprecated": false, - "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. 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In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.", - "example": "35742", - "homepage": "http://vbrc.org/", - "name": "VBRC at University of Alabama", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "vbrc", - "uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1" - }, - "name": "Viral Bioinformatics Resource Center", - "prefixcommons": { - "description": "The VBRC is one of eight NIH/NIAID-funded Bioinformatics Resource Centers nationwide providing a comprehensive web-based battery of informational and analytical tools and resources.", - "example": "VP0033331", - "homepage": "http://vbrc.org", - "name": "Viral Bioinformatics Resource Center", - "pattern": "^VP\\d+$", - "prefix": "vbrc" - } - }, - "vcell": { - "mappings": { - "miriam": "vcell" - }, - "miriam": { - "deprecated": false, - "description": "Models developed with the Virtual Cell (VCell) software prorgam.", - "homepage": "https://health.uconn.edu/", - "id": "00000893", - "name": "VCell Published Models", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d{5,}$", - "prefix": "vcell", - "sampleId": "201022999", - "uri_format": "https://vcell.org/biomodel-$1" - } - }, - "vectorbase": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "VECTORBASE", - "uri_format": "http://identifiers.org/vectorbase/$1" - }, - "fairsharing": { - "abbreviation": "VectorBase", - "description": "VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. 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Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes.", - "id": "2118", - "name": "VectorBase", - "prefix": "FAIRsharing.3etvdn", - "subjects": [ - "Functional Genomics", - "Population Dynamics", - "Genomics", - "Comparative Genomics", - "Population Genetics" - ] - }, - "mappings": { - "biocontext": "VECTORBASE", - "fairsharing": "FAIRsharing.3etvdn", - "miriam": "vectorbase", - "n2t": "vectorbase", - "ncbi": "VectorBase", - "prefixcommons": "vectorbase" - }, - "miriam": { - "deprecated": false, - "description": "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. 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Craig Venter Institute", - "namespaceEmbeddedInLui": false, - "pattern": "^[A-Za-z 0-9]+$", - "prefix": "vipr", - "uri_format": "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena" - }, - "ncbi": { - "example": "HRV-A34_p1058_sR263_2008", - "homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr", - "name": "Virus Pathogen Resource", - "prefix": "ViPR" - } - }, - "viralzone": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "VIRALZONE", - "uri_format": "http://identifiers.org/viralzone/$1" - }, - "fairsharing": { - "abbreviation": "ViralZone", - "description": "ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.", - "id": "2399", - "name": "ViralZone", - "prefix": "FAIRsharing.tppk10", - "subjects": [ - "Molecular biology", - "Virology", - "Life Science", - "Epidemiology" - ] - }, - "mappings": { - "biocontext": "VIRALZONE", - "fairsharing": "FAIRsharing.tppk10", - "miriam": "viralzone", - "n2t": "viralzone" - }, - "miriam": { - "deprecated": false, - "description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. 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The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.", - "homepage": "http://www.yeastrc.org/pdr/", - "id": "00000459", - "name": "YRC PDR", - "namespaceEmbeddedInLui": false, - "pattern": "^\\d+$", - "prefix": "yrcpdr", - "sampleId": "2673500", - "uri_format": "http://yeastrc.org/pdr/viewProtein.do?id=$1" - }, - "n2t": { - "description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). 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If you work on the project responsible for \"Zebrafish anatomy and development\" then please consider helping us by claiming this record and updating it appropriately.", - "id": "564", - "name": "Zebrafish anatomy and development", - "prefix": "FAIRsharing.s3r6sk", - "subjects": [ - "Anatomy", - "Developmental Biology", - "Life Science" - ] - }, - "mappings": { - "biocontext": "ZFA", - "bioportal": "ZFA", - "fairsharing": "FAIRsharing.s3r6sk", - "obofoundry": "zfa", - "ols": "zfa", - "ontobee": "ZFA", - "prefixcommons": "zfa" - }, - "obofoundry": { - "appears_in": [ - "zp" - ], - "contact": "van_slyke@zfin.org", - "contact.github": "cerivs", - "contact.label": "Ceri Van Slyke", - "contact.orcid": "0000-0002-2244-7917", - "deprecated": false, - "description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish", - "download.obo": "http://purl.obolibrary.org/obo/zfa.obo", - "download.owl": "http://purl.obolibrary.org/obo/zfa.owl", - "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Zebrafish anatomy and development ontology", - "preferredPrefix": "ZFA", - "prefix": "zfa", - "publications": [ - { - "id": "https://www.ncbi.nlm.nih.gov/pubmed/24568621", - "title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio." - } - ], - "repository": "https://github.com/cerivs/zebrafish-anatomical-ontology" - }, - "ols": { - "description": "ZFA description.", - "download": "http://purl.obolibrary.org/obo/zfa.owl", - "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources", - "name": "Zebrafish Anatomy Ontology (ZFA)", - "prefix": "zfa", - "version": "2022-03-15", - "version.iri": "http://purl.obolibrary.org/obo/zfa/releases/2022-03-15/zfa.owl" - }, - "ontobee": { - "library": "Foundry", - "name": "Zebrafish anatomy and development ontology", - "prefix": "ZFA" - }, - "pattern": "^\\d{7}$", - "prefixcommons": { - "bioportal": "1051", - "description": "A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio).", - "example": "ZFS_0000011", - "homepage": "http://zfin.org/zf_info/anatomy/dict/sum.html", - "keywords": [ - "obo", - "anatomy", - "zebrafish" - ], - "name": "Zebrafish anatomy and development Ontology", - "pattern": "^ZFS_\\d{7}$", - "prefix": "zfa", - "uri_format": "http://purl.obolibrary.org/obo/$1" - }, - "synonyms": [ - "ZFA_RETIRED" - ] - }, - "zfin": { - "biocontext": { - "is_identifiers": false, - "is_obo": false, - "prefix": "ZFIN", - "uri_format": "http://zfin.org/$1" - }, - "fairsharing": { - "abbreviation": "ZFIN", - "description": "The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.", - "id": "2106", - "name": "The Zebrafish Information Network", - "prefix": "FAIRsharing.ybxnhg", - "subjects": [ - "Genomics", - "Animal Physiology", - "Genetics", - "Developmental Biology" - ] - }, - "go": { - "homepage": "http://zfin.org/", - "name": "Zebrafish Information Network", - "prefix": "ZFIN" - }, - "mappings": { - "biocontext": "ZFIN", - "fairsharing": "FAIRsharing.ybxnhg", - "go": "ZFIN", - "miriam": "zfin", - "n2t": "zfin", - "ncbi": "ZFIN", - "prefixcommons": "zfin", - "uniprot": "ZFIN", - "wikidata": "P3870" - }, - "miriam": { - "deprecated": false, - "description": "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.", - "homepage": "http://zfin.org", - "id": "00000079", - "name": "ZFIN Bioentity", - "namespaceEmbeddedInLui": false, - "pattern": "^ZDB\\-\\w+\\-\\d+\\-\\d+$", - "prefix": "zfin", - "providers": [ - { - "code": "bioentitylink", - "description": "ZFIN through BioEntity Link", - "homepage": "https://bioentity.link/", - "name": "ZFIN through BioEntity Link", - "uri_format": "https://bioentity.link/#/lexicon/public/$1" - }, - { - "code": "agr", - "description": "ZFIN through the Alliance of Genome Resources", - "homepage": "https://www.alliancegenome.org", - "name": "ZFIN through the Alliance of Genome Resources", - "uri_format": "https://test.alliancegenome.org/gene/ZFIN:$1" - } - ], - "sampleId": "ZDB-GENE-041118-11", - "uri_format": "http://zfin.org/$1" - }, - "n2t": { - "description": "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.", - "example": "ZDB-GENE-041118-11", - "homepage": "http://zfin.org", - "name": "ZFIN at University of Oregon", - "namespaceEmbeddedInLui": false, - "pattern": "^ZDB\\-\\w+\\-\\d+\\-\\d+$", - "prefix": "zfin", - "uri_format": "http://zfin.org/$1" - }, - "name": "Zebrafish Information Network Gene", - "ncbi": { - "example": "ZDB-GENE-011205-17", - "homepage": "http://zfin.org", - "name": "Zebrafish Information Network", - "prefix": "ZFIN" - }, - "prefixcommons": { - "description": "ZFIN serves as the zebrafish model organism database.", - "example": "ZDB-GENE-041118-11", - "homepage": "http://zfin.org/", - "keywords": [ - "zebrafish", - "gene", - "genome" - ], - "name": "Zebrafish Information Network genome database", - "pattern": "^ZDB\\-GENE\\-\\d+\\-\\d+$", - "prefix": "zfin", - "pubmed_ids": [ - "17991680" - ], - "uri_format": "http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=$1" - }, - "synonyms": [ - "ZFIN" - ], - "uniprot": { - "category": "Organism-specific databases", - "identifier": "113", - "link_is_explicit": "true", - "name": "Zebrafish Information Network genome database", - "prefix": "ZFIN", - "uri_format": "https://zfin.org/$1" - }, - "wikidata": { - "database": "Q29128476", - "database.homepage": "https://zfin.org/", - "database.label": "Zebrafish Model Organism Database", - "homepage": "http://zfin.org", - "name": "ZFIN Gene ID", - "prefix": "P3870", - "uri_format": "https://zfin.org/$1" - } - }, - "zfs": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "ZFS", - "uri_format": "http://purl.obolibrary.org/obo/ZFS_$1" - }, - "bioportal": { - "name": "Zebrafish Developmental Stages", - "prefix": "ZFS" - }, - "example": "0000050", - "fairsharing": { - "abbreviation": "ZFS", - "description": "An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology.", - "id": "631", - "name": "Zebrafish Developmental Stages", - "prefix": "FAIRsharing.bc8ayj", - "subjects": [] - }, - "mappings": { - "biocontext": "ZFS", - "bioportal": "ZFS", - "fairsharing": "FAIRsharing.bc8ayj", - "obofoundry": "zfs", - "ols": "zfs", - "ontobee": "ZFS" - }, - "obofoundry": { - "contact": "van_slyke@zfin.org", - "contact.github": "cerivs", - "contact.label": "Ceri Van Slyke", - "contact.orcid": "0000-0002-2244-7917", - "deprecated": false, - "description": "Developmental stages of the Zebrafish", - "download.obo": "http://purl.obolibrary.org/obo/zfs.obo", - "download.owl": "http://purl.obolibrary.org/obo/zfs.owl", - "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Zebrafish developmental stages ontology", - "preferredPrefix": "ZFS", - "prefix": "zfs", - "repository": "https://github.com/cerivs/zebrafish-anatomical-ontology" - }, - "ols": { - "description": "Developmental stages of the Zebrafish", - "download": "http://purl.obolibrary.org/obo/zfs.owl", - "homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources", - "name": "Zebrafish developmental stages ontology", - "prefix": "zfs", - "version": "2020-03-10", - "version.iri": "http://purl.obolibrary.org/obo/zfs/releases/2020-03-10/zfs.owl" - }, - "ontobee": { - "library": "Library", - "name": "Zebrafish developmental stages ontology", - "prefix": "ZFS" - }, - "pattern": "^\\d{7}$" - }, - "zinc": { - "biocontext": { - "is_identifiers": true, - "is_obo": false, - "prefix": "ZINC", - "uri_format": "http://identifiers.org/zinc/$1" - }, - "mappings": { - "biocontext": "ZINC", - "miriam": "zinc", - "n2t": "zinc" - }, - "miriam": { - "deprecated": false, - "description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.", - "homepage": "http://zinc15.docking.org/", - "id": "00000529", - "name": "ZINC", - "namespaceEmbeddedInLui": false, - "pattern": "^(ZINC)?\\d+$", - "prefix": "zinc", - "sampleId": "ZINC1084", - "uri_format": "http://zinc15.docking.org/substances/$1" - }, - "n2t": { - "description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.", - "example": "ZINC1084", - "homepage": "http://zinc15.docking.org/", - "name": "ZINC at University of California (San Francisco)", - "namespaceEmbeddedInLui": false, - "pattern": "^(ZINC)?\\d+$", - "prefix": "zinc", - "uri_format": "http://zinc15.docking.org/substances/$1" - }, - "name": "ZINC is not Commercial", - "wikidata": { - "prefix": "P2084" - } - }, - "zp": { - "biocontext": { - "is_identifiers": false, - "is_obo": true, - "prefix": "ZP", - "uri_format": "http://purl.obolibrary.org/obo/ZP_$1" - }, - "bioportal": { - "name": "Zebrafish Phenotype Ontology", - "prefix": "ZP" - }, - "example": "0019030", - "mappings": { - "biocontext": "ZP", - "bioportal": "ZP", - "obofoundry": "zp", - "ols": "zp", - "ontobee": "ZP" - }, - "obofoundry": { - "contact": "ybradford@zfin.org", - "contact.github": "ybradford", - "contact.label": "Yvonne Bradford", - "contact.orcid": "0000-0002-9900-7880", - "depends_on": [ - "bfo", - "bspo", - "go", - "pato", - "ro", - "uberon", - "zfa" - ], - "deprecated": false, - "description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.", - "download.obo": "http://purl.obolibrary.org/obo/zp.obo", - "download.owl": "http://purl.obolibrary.org/obo/zp.owl", - "homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology", - "license": "CC BY 3.0", - "license.url": "http://creativecommons.org/licenses/by/3.0/", - "name": "Zebrafish Phenotype Ontology", - "preferredPrefix": "ZP", - "prefix": "zp", - "repository": "https://github.com/obophenotype/zebrafish-phenotype-ontology" - }, - "ols": { - "description": "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.", - "download": "http://purl.obolibrary.org/obo/zp.owl", - "homepage": "https://github.com/obophenotype/zebrafish-phenotype-ontology", - "name": "Zebrafish Phenotype Ontology (ZP)", - "prefix": "zp", - "version": "2021-12-12", - "version.iri": "http://purl.obolibrary.org/obo/zp/releases/2021-12-12/zp.owl" - }, - "ontobee": { - "library": "Library", - "name": "Zebrafish Phenotype Ontology", - "prefix": "ZP" - }, - "pattern": "^\\d+$" - } -} diff --git a/fuji_server/data/linked_vocabs/bioregistry.yaml b/fuji_server/data/linked_vocabs/bioregistry.yaml new file mode 100644 index 00000000..09caf7f8 --- /dev/null +++ b/fuji_server/data/linked_vocabs/bioregistry.yaml @@ -0,0 +1,52384 @@ +3dmet: + biocontext: + is_identifiers: true + is_obo: false + prefix: 3DMET + uri_format: http://identifiers.org/3dmet/$1 + fairsharing: + abbreviation: 3DMET + description: 3DMET is a database of three-dimensional structures of natural metabolites. + id: '1999' + name: Three-Dimensional Structure Database of Natural Metabolites + prefix: FAIRsharing.5ab0n7 + subjects: + - Life Science + - Metabolomics + mappings: + biocontext: 3DMET + fairsharing: FAIRsharing.5ab0n7 + miriam: 3dmet + n2t: 3dmet + prefixcommons: 3dmet + miriam: + deprecated: false + description: 3DMET is a database collecting three-dimensional structures of natural metabolites. + homepage: http://www.3dmet.dna.affrc.go.jp/ + id: '00000066' + name: 3DMET + namespaceEmbeddedInLui: false + pattern: ^B\d{5}$ + prefix: 3dmet + sampleId: B00162 + uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 + n2t: + description: 3DMET is a database collecting three-dimensional structures of natural metabolites. + example: B00162 + homepage: http://www.3dmet.dna.affrc.go.jp/ + name: 3DMET database + namespaceEmbeddedInLui: false + pattern: ^B\d{5}$ + prefix: 3dmet + uri_format: http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 + name: 3D Metabolites + prefixcommons: + description: 3DMET is a database of three-dimensional structures of natural metabolites. + example: B00162 + homepage: http://www.3dmet.dna.affrc.go.jp + keywords: + - chemical + - metabolite + - structure + miriam: 3dmet + name: Three-Dimensional Structure Database of Natural Metabolites + pattern: ^B\d{5}$ + prefix: 3dmet + pubmed_ids: + - '23293959' + - '29892514' + wikidata: + database: Q23948774 + prefix: P2796 +4dn.biosource: + cellosaurus: + category: Biological sample resources + homepage: https://data.4dnucleome.org/ + name: 4D Nucleome Data Portal + prefix: 4DN + uri_format: https://data.4dnucleome.org/biosources/$1 + example: 4DNSR73BT2A2 + fairsharing: + abbreviation: 4DN + description: The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data. + id: '2771' + name: 4DNucleome Data Portal + prefix: FAIRsharing.CugtbQ + subjects: + - Life Science + homepage: https://data.4dnucleome.org/biosources + mappings: + cellosaurus: 4DN + fairsharing: FAIRsharing.CugtbQ + miriam: 4dn + prefixcommons: 4dn + miriam: + deprecated: false + description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. + homepage: https://data.4dnucleome.org/ + id: '00000833' + name: 4D Nucleome + namespaceEmbeddedInLui: false + pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$ + prefix: 4dn + sampleId: 4DNES265ETYQ + uri_format: https://data.4dnucleome.org/$1 + name: 4D Nucleome Data Portal Biosource + prefixcommons: + description: The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. + example: 4DNESBOY2QLJ + homepage: https://data.4dnucleome.org/ + keywords: + - DNA + - protein + miriam: 4dn + name: 4D Nucleome + pattern: ^4DN[A-Z]{2}[A-Z0-9]{7}$ + prefix: 4dn + pubmed_ids: + - '28905911' + uri_format: https://data.4dnucleome.org/$1 + synonyms: + - 4DN + uri_format: https://data.4dnucleome.org/biosources/$1 + wikidata: + database: Q110613621 +4dn.replicate: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + contributor_extras: + - email: laylamichan@ciencias.unam.mx + github: lmichan + name: Layla Michán Aguirre + orcid: 0000-0002-5798-662X + - email: mineromero2901@ciencias.unam.mx + github: MinRo60 + name: Minerva María Romero Pérez + orcid: 0000-0002-6240-9325 + - email: victorinolavida@ciencias.unam.mx + github: Victorinolavida + name: José Victorino Ruiz Lavida + orcid: 0000-0001-5130-7705 + description: Database portal containing replicate experiments of different assays and samples + example: 4DNESWX1J3QU + homepage: https://data.4dnucleome.org/experiment-set-replicates/ + name: 4D Nucleome Data Portal Experiment Replicate + uri_format: https://data.4dnucleome.org/experiment-set-replicates/$1 + wikidata: + database: Q110613797 +aao: + biocontext: + is_identifiers: false + is_obo: true + prefix: AAO + uri_format: http://purl.obolibrary.org/obo/AAO_$1 + description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. + fairsharing: + abbreviation: AAO + description: A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO has been integrated into Uberon. + id: '876' + name: Amphibian gross Anatomy Ontology + prefix: FAIRsharing.mxx5rp + mappings: + biocontext: AAO + fairsharing: FAIRsharing.mxx5rp + obofoundry: aao + prefixcommons: aao + no_own_terms: true + obofoundry: + contact: david.c.blackburn@gmail.com + contact.label: David Blackburn + deprecated: true + homepage: http://github.com/seger/aao + name: Amphibian gross anatomy + prefix: aao + prefixcommons: + bioportal: '1090' + description: The Amphibian Anatomical Ontology (AmphibAnat) is an NSF-sponsored project dedicated to constructing semi-automatically a draft ontology of amphibian anatomy. In this project, small, subset ontologies are constructed manually, and data-mining software (that we develop) is used to mine electronic media for instances of concepts and properties to be added to the ontologies. + example: ASD:0000138 + homepage: http://www.amphibanat.org + keywords: + - obo + - anatomy + name: Amphibian Anatomical Ontology + pattern: ^[A-Z]+:\d+$ + prefix: aao + pubmed_ids: + - '17992749' +abcd: + cellosaurus: + category: Biological sample resources + homepage: https://web.expasy.org/abcd/ + name: AntiBodies Chemically Defined database + prefix: ABCD + uri_format: https://web.expasy.org/abcd/$1 + description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies + example: AD834 + fairsharing: + abbreviation: ABCD + description: The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies. + id: '2969' + name: ABCD database + prefix: FAIRsharing.Z8OKi5 + subjects: + - Molecular biology + - Immunology + homepage: https://web.expasy.org/abcd/ + mappings: + cellosaurus: ABCD + fairsharing: FAIRsharing.Z8OKi5 + uniprot: ABCD + name: AntiBodies Chemically Defined database + uniprot: + category: Protocols and materials databases + identifier: '236' + link_is_explicit: 'true' + name: ABCD curated depository of sequenced antibodies + prefix: ABCD + uri_format: https://web.expasy.org/cgi-bin/abcd/search_abcd.pl?input=$1 + uri_format: https://web.expasy.org/abcd/ABCD_$1 +abm: + cellosaurus: + category: Cell line collections + homepage: https://www.abmgood.com/Cell-Biology.html + name: Applied Biological Materials cell line products + prefix: ABM + uri_format: https://www.abmgood.com/catalogsearch/result/?cat=&q=$1 + example: T0599 + mappings: + cellosaurus: ABM +abs: + biocontext: + is_identifiers: true + is_obo: false + prefix: ABS + uri_format: http://identifiers.org/abs/$1 + fairsharing: + abbreviation: ABS + description: ABS is a database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes. + id: '1899' + name: Annotated regulatory Binding Sites from Orthologous Promoters + prefix: FAIRsharing.7mnebr + subjects: + - Biology + mappings: + biocontext: ABS + fairsharing: FAIRsharing.7mnebr + miriam: abs + n2t: abs + prefixcommons: abs + miriam: + deprecated: false + description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. + homepage: http://genome.crg.es/datasets/abs2005/ + id: '00000277' + name: ABS + namespaceEmbeddedInLui: false + pattern: ^A\d+$ + prefix: abs + sampleId: A0014 + uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html + n2t: + description: The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. + example: A0014 + homepage: http://genome.crg.es/datasets/abs2005/ + name: ABS at IMIM + namespaceEmbeddedInLui: false + pattern: ^A\d+$ + prefix: abs + uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html + name: Annotated Regulatory Binding Sites + prefixcommons: + description: 'ABS: A database of Annotated regulatory Binding Sites from known binding sites identified in promoters of orthologous vertebrate genes.' + example: A0014 + homepage: http://genome.imim.es/datasets/abs2005/ + keywords: + - interaction + - gene + - regulation + miriam: abs + name: 'ABS: a database of Annotated regulatory Binding Sites from Orthologous Promoters' + pattern: ^A\d+$ + prefix: abs + pubmed_ids: + - '16381947' + uri_format: http://genome.crg.es/datasets/abs2005/entries/$1.html + wikidata: + database: Q111134507 +ac: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities. + example: Add + homepage: http://www.w3.org/ns/activitystreams + name: Activity Streams + uri_format: http://www.w3.org/ns/activitystreams#$1 +aceview.worm: + biocontext: + is_identifiers: true + is_obo: false + prefix: ACEVIEW.WORM + uri_format: http://identifiers.org/aceview.worm/$1 + mappings: + biocontext: ACEVIEW.WORM + miriam: aceview.worm + n2t: aceview.worm + prefixcommons: aceview.worm + miriam: + deprecated: false + description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. + homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm + id: '00000282' + name: Aceview Worm + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9-]+$ + prefix: aceview.worm + sampleId: aap-1 + uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 + n2t: + description: AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. + example: aap-1 + homepage: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm + name: AceView Worm at NCBI + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9-]+$ + prefix: aceview.worm + uri_format: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 + prefixcommons: + description: AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. + example: AP2B1 + homepage: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ + keywords: + - RNA + - DNA + - gene + miriam: aceview.worm + name: AceView Worm Genome + pattern: ^[a-z0-9-]+$ + prefix: aceview.worm + pubmed_ids: + - '16925834' + uri_format: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=[?species_database]&c=Gene&l=$1 +addexbio: + cellosaurus: + category: Cell line collections + homepage: https://www.addexbio.com/productshow?id=4 + name: AddexBio cell line products + prefix: AddexBio + uri_format: https://www.addexbio.com/productdetail?pid=$1 + example: C0020004/4992 + mappings: + cellosaurus: AddexBio +addgene: + fairsharing: + abbreviation: Addgene + description: Addgene is a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Addgene are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request. + id: '1738' + name: Addgene + prefix: FAIRsharing.8hcczk + subjects: + - Life Science + mappings: + fairsharing: FAIRsharing.8hcczk + miriam: addgene + n2t: addgene + prefixcommons: addgene + miriam: + deprecated: false + description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. + homepage: http://addgene.org/ + id: '00000675' + name: Addgene Plasmid Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ + prefix: addgene + sampleId: '50943' + uri_format: http://addgene.org/$1 + n2t: + description: Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. + example: '50943' + homepage: http://addgene.org/ + name: Addgene Plasmid Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ + prefix: addgene + uri_format: http://addgene.org/$1 + prefixcommons: + description: Addgene is a global, nonprofit repository that was created to help scientists share plasmids. + example: '41816' + homepage: http://www.addgene.org + keywords: + - plasmid + miriam: addgene + name: Addgene + pattern: ^\d+$ + prefix: addgene + pubmed_ids: + - '25392412' + uri_format: http://www.addgene.org/$1 +adw: + biocontext: + is_identifiers: false + is_obo: true + prefix: ADW + uri_format: http://purl.obolibrary.org/obo/ADW_$1 + bioportal: + name: Animal Natural History and Life History Ontology + prefix: ADW + fairsharing: + abbreviation: ADW + description: An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities. + id: '1038' + name: Animal natural history and life history + prefix: FAIRsharing.t9fvdn + mappings: + biocontext: ADW + bioportal: ADW + fairsharing: FAIRsharing.t9fvdn + miriam: adw + n2t: adw + obofoundry: adw + miriam: + deprecated: false + description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. + homepage: https://animaldiversity.org/ + id: '00000492' + name: Animal Diversity Web + namespaceEmbeddedInLui: false + pattern: ^[A-Z_a-z]+$ + prefix: adw + sampleId: Lycalopex_vetulus + uri_format: https://animaldiversity.org/accounts/$1/ + n2t: + description: Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. + example: Lycalopex_vetulus + homepage: https://animaldiversity.org/ + name: Animal Diversity Web at University of Michigan + namespaceEmbeddedInLui: false + pattern: ^[A-Z_a-z]+$ + prefix: adw + uri_format: https://animaldiversity.org/accounts/$1/ + obofoundry: + contact: adw_geeks@umich.edu + contact.label: Animal Diversity Web technical staff + deprecated: true + homepage: http://www.animaldiversity.org + name: Animal natural history and life history + prefix: adw + uri_format: https://animaldiversity.org/accounts/$1 +aeo: + biocontext: + is_identifiers: false + is_obo: true + prefix: AEO + uri_format: http://purl.obolibrary.org/obo/AEO_$1 + bioportal: + name: Anatomical Entity Ontology + prefix: AEO + download_obo: https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo + example: '0001017' + fairsharing: + abbreviation: AEO + description: The AEO ontology of anatomical structures is a resource to facilitate the increase in knowledge in anatomy ontologies, supporting annotation and enabling compatibility with other anatomy ontologies. The ontology can be used to classify most organisms as its terms are appropriate for most plant and fungal tissues. It is envisaged that in future the ontology will include more non-animal anatomical terms. + id: '1175' + name: Anatomical Entity Ontology + prefix: FAIRsharing.93ee19 + subjects: + - Anatomy + - Life Science + mappings: + biocontext: AEO + bioportal: AEO + fairsharing: FAIRsharing.93ee19 + obofoundry: aeo + ols: aeo + ontobee: AEO + obofoundry: + appears_in: + - ehdaa2 + contact: J.Bard@ed.ac.uk + contact.label: Jonathan Bard + deprecated: true + description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology + download.owl: http://purl.obolibrary.org/obo/aeo.owl + homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Anatomical Entity Ontology + preferredPrefix: AEO + prefix: aeo + repository: https://github.com/obophenotype/human-developmental-anatomy-ontology + ols: + description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology + download: http://purl.obolibrary.org/obo/aeo.owl + homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ + name: Anatomical Entity Ontology + prefix: aeo + version: 2014-12-05 + version.iri: http://purl.obolibrary.org/obo/aeo/releases/2014-12-05/aeo.owl + ontobee: + library: Library + name: Anatomical Entity Ontology + prefix: AEO + pattern: ^\d{7}$ + synonyms: + - AEO_RETIRED +aero: + biocontext: + is_identifiers: false + is_obo: true + prefix: AERO + uri_format: http://purl.obolibrary.org/obo/AERO_$1 + bioportal: + name: Adverse Event Reporting Ontology + prefix: AERO + example: '0000125' + fairsharing: + abbreviation: AERO + description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. + id: '221' + name: Adverse Event Reporting ontology + prefix: FAIRsharing.rycy2x + mappings: + biocontext: AERO + bioportal: AERO + fairsharing: FAIRsharing.rycy2x + obofoundry: aero + obofoundry: + contact: mcourtot@gmail.com + contact.label: Melanie Courtot + contact.orcid: 0000-0002-9551-6370 + deprecated: true + description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events + download.owl: http://purl.obolibrary.org/obo/aero.owl + homepage: http://purl.obolibrary.org/obo/aero + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Adverse Event Reporting Ontology + prefix: aero + pattern: ^\d{7}$ +affy.probeset: + biocontext: + is_identifiers: true + is_obo: false + prefix: AFFY.PROBESET + uri_format: http://identifiers.org/affy.probeset/$1 + mappings: + biocontext: AFFY.PROBESET + miriam: affy.probeset + n2t: affy.probeset + miriam: + deprecated: false + description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. + homepage: http://www.affymetrix.com/ + id: '00000394' + name: Affymetrix Probeset + namespaceEmbeddedInLui: false + pattern: \d{4,}((_[asx])?_at)? + prefix: affy.probeset + providers: + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: http://cu.affymetrix.bio2rdf.org/fct/ + name: Bio2RDF + uri_format: http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1 + sampleId: 243002_at + uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1 + n2t: + description: An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. + example: 243002_at + homepage: http://www.affymetrix.com/ + name: Affymetrix ProbeSet in Santa Clara + namespaceEmbeddedInLui: false + pattern: \d{4,}((_[asx])?_at)? + prefix: affy.probeset + uri_format: https://www.affymetrix.com/LinkServlet?probeset=$1 +afo: + bioportal: + name: Allotrope Merged Ontology Suite + prefix: AFO + fairsharing: + abbreviation: AFO + description: The Agriculture and Forestry Ontology (AFO), also known as the Agriforest Ontology, combines the concepts of the Agriforest Thesaurus with The Finnish General Upper Ontology (YSO). This combination of ontologies can be used for describing resources especially in domain of agriculture, forestry, veterinary medicine, food science, environmental science and biology. + id: '924' + name: Agriculture and Forestry Ontology + prefix: FAIRsharing.595710 + subjects: + - Environmental Science + - Forest Management + - Agricultural Engineering + - Agriculture + - Veterinary Medicine + - Food Chemistry + - Biology + homepage: https://www.allotrope.org/ + mappings: + bioportal: AFO + fairsharing: FAIRsharing.595710 + ols: afo + no_own_terms: true + ols: + description: Allotrope Merged Ontology Suite + download: http://afo-ols.semanticsfirst.com/ontologies/afo + name: Allotrope Merged Ontology Suite + prefix: afo + version: 2019-05-10 + version.iri: http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10 +aftol.taxonomy: + biocontext: + is_identifiers: true + is_obo: false + prefix: AFTOL.TAXONOMY + uri_format: http://identifiers.org/aftol.taxonomy/$1 + contributor_extras: + - email: laylamichan@ciencias.unam.mx + github: lmichan + name: Layla Michán Aguirre + orcid: 0000-0002-5798-662X + homepage: https://aftol.umn.edu + mappings: + biocontext: AFTOL.TAXONOMY + miriam: aftol.taxonomy + n2t: aftol.taxonomy + miriam: + deprecated: false + description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. + homepage: http://aftol.org/data.php + id: '00000411' + name: AFTOL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aftol.taxonomy + sampleId: '959' + uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 + n2t: + description: The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. + example: '959' + homepage: http://aftol.org/data.php + name: AFTOL at University of Minnesota + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aftol.taxonomy + uri_format: http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 + name: Assembling the Fungal Tree of Life - Taxonomy +agilent.probe: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.' + example: A_24_P98555 + homepage: https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt + name: Agilent Probe + pattern: ^A_\d+_.+$ + references: + - http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt +agricola: + biocontext: + is_identifiers: true + is_obo: false + prefix: AGRICOLA + uri_format: http://identifiers.org/agricola/$1 + contributor_extras: + - email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + - email: cjmungall@lbl.gov + github: cmungall + name: Chris Mungall + orcid: 0000-0002-6601-2165 + go: + homepage: http://agricola.nal.usda.gov/ + name: AGRICultural OnLine Access + prefix: AGRICOLA_ID + mappings: + biocontext: AGRICOLA + go: AGRICOLA_ID + miriam: agricola + n2t: agricola + miriam: + deprecated: false + description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. + homepage: http://agricola.nal.usda.gov/ + id: '00000589' + name: AGRICOLA + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: agricola + sampleId: '50018' + uri_format: http://ddr.nal.usda.gov/dspace/handle/10113/$1 + n2t: + description: AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. + example: '50018' + homepage: http://agricola.nal.usda.gov/ + name: AGRICOLA at National Agricultural Library + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: agricola + uri_format: http://ddr.nal.usda.gov/dspace/handle/10113/$1 + name: Agricultural Online Access + synonyms: + - AGR + - AGRICOLA_ID + uri_format: https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1 +agro: + biocontext: + is_identifiers: false + is_obo: true + prefix: AGRO + uri_format: http://purl.obolibrary.org/obo/AGRO_$1 + bioportal: + name: AGRonomy Ontology + prefix: AGRO + download_obo: https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo + example: '00020007' + fairsharing: + abbreviation: AgrO + description: AgrO, the Agronomy Ontology, describes agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments. AgrO is being built by CGIAR using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, and PATO. It will complement existing crop, livestock, and fish ontologies to enable harmonized approaches to data collection, facilitating easier data sharing and reuse. A key use case for AgrO is the Agronomy Field Information Management System (AgroFIMS). AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO. + id: '714' + name: Agronomy Ontology + prefix: FAIRsharing.m40bhw + subjects: + - Farming Systems Research + - Plant Breeding + - Agronomy + - Agriculture + mappings: + biocontext: AGRO + bioportal: AGRO + fairsharing: FAIRsharing.m40bhw + obofoundry: agro + ols: agro + ontobee: AGRO + obofoundry: + contact: m.a.laporte@cgiar.org + contact.github: marieALaporte + contact.label: Marie-Angélique Laporte + contact.orcid: 0000-0002-8461-9745 + depends_on: + - bfo + - envo + - foodon + - go + - iao + - ncbitaxon + - obi + - pato + - peco + - po + - ro + - to + - uo + - xco + deprecated: false + description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments + download.owl: http://purl.obolibrary.org/obo/agro.owl + homepage: https://github.com/AgriculturalSemantics/agro + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Agronomy Ontology + preferredPrefix: AGRO + prefix: agro + publications: + - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf + title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.' + repository: https://github.com/AgriculturalSemantics/agro + ols: + description: AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities + download: http://purl.obolibrary.org/obo/agro.owl + homepage: https://github.com/AgriculturalSemantics/agro + name: Agronomy Ontology + prefix: agro + version: 2021-11-05 + version.iri: http://purl.obolibrary.org/obo/agro/releases/2021-11-05/agro.owl + ontobee: + library: Library + name: Agronomy Ontology + prefix: AGRO + pattern: ^\d{8}$ +agrovoc: + description: AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages. + example: '2842' + fairsharing: + abbreviation: AGROVOC + description: AGROVOC is a controlled vocabulary covering all areas of interest of the Food and Agriculture Organization (FAO) of the United Nations, including food, nutrition, agriculture, fisheries, forestry, environment etc. It is published by FAO and edited by a community of experts. AGROVOC consists of over 40,100 concepts available in up to 41 languages. AGROVOC uses semantic web technologies, linking to other multilingual knowledge organization systems and building bridges between datasets. Your library can use AGROVOC to index its documents or datasets, or you can use it from inside your content management system (e.g., Drupal) to organize your documents or web site. You can also use AGROVOC as an hub to access many other vocabularies available on the web. To date, AGROVOC is used by researchers, librarians and information managers for indexing, retrieving and organizing data in agricultural information systems and Web pages. Currently, AGROVOC is an SKOS-XL concept scheme and a Linked Open Data (LOD*) set aligned with over 20 other multilingual knowledge organization systems related to agriculture. You may browse AGROVOC, access its Web Services or SPARQL endpoint. + id: '399' + name: AGROVOC + prefix: FAIRsharing.anpj91 + subjects: + - Botany + - Fisheries Science + - Environmental Science + - Forest Management + - Data Management + - Agriculture + - Nutritional Science + homepage: https://data.apps.fao.org/catalog/organization/agrovoc + mappings: + fairsharing: FAIRsharing.anpj91 + name: Agronomy Vocabulary + pattern: ^[a-z0-9]+$ + references: + - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip + - http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip + - https://en.wikipedia.org/wiki/AGROVOC + uri_format: http://aims.fao.org/aos/agrovoc/c_$1 +aism: + bioportal: + name: Ontology for the Anatomy of the Insect SkeletoMuscular system + prefix: AISM + example: '0000027' + mappings: + bioportal: AISM + obofoundry: aism + ols: aism + ontobee: AISM + name: Ontology for the Anatomy of the Insect SkeletoMuscular system + obofoundry: + appears_in: + - colao + - lepao + contact: entiminae@gmail.com + contact.github: JCGiron + contact.label: Jennifer C. Girón + contact.orcid: 0000-0002-0851-6883 + depends_on: + - bfo + - bspo + - caro + - pato + - ro + - uberon + deprecated: false + description: The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology. + download.json: http://purl.obolibrary.org/obo/aism.json + download.obo: http://purl.obolibrary.org/obo/aism.obo + download.owl: http://purl.obolibrary.org/obo/aism.owl + homepage: https://github.com/insect-morphology/aism + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) + preferredPrefix: AISM + prefix: aism + repository: https://github.com/insect-morphology/aism + ols: + description: The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. + download: http://purl.obolibrary.org/obo/aism.owl + homepage: https://github.com/insect-morphology/aism + name: Ontology for the Anatomy of the Insect SkeletoMuscular system + prefix: aism + version: 2022-03-17 + version.iri: http://purl.obolibrary.org/obo/aism/releases/2022-03-17/aism.owl + ontobee: + library: Library + name: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) + prefix: AISM + pattern: ^\d{7}$ +allergome: + biocontext: + is_identifiers: true + is_obo: false + prefix: ALLERGOME + uri_format: http://identifiers.org/allergome/$1 + fairsharing: + abbreviation: Allergome + description: Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria). The resource is funded through the Allergen Data Laboratories via unrestricted grants from companies and institutions. + id: '1746' + name: Allergome + prefix: FAIRsharing.w6cxgb + subjects: + - Medicine + - Health Science + - Life Science + - Biomedical Science + mappings: + biocontext: ALLERGOME + fairsharing: FAIRsharing.w6cxgb + miriam: allergome + n2t: allergome + prefixcommons: allergome + uniprot: Allergome + miriam: + deprecated: false + description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. + homepage: http://www.allergome.org/ + id: '00000334' + name: Allergome + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: allergome + sampleId: '1948' + uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1 + n2t: + description: Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. + example: '1948' + homepage: http://www.allergome.org/ + name: Allergome at Rome + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: allergome + uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1 + prefixcommons: + description: Allergome aims to supply information on Allergenic Molecules (Allergens) causing an IgE-mediated (allergic, atopic) disease (anaphylaxis, asthma, atopic dermatitis, conjunctivitis, rhinitis, urticaria). + example: '1948' + homepage: http://www.allergome.org + keywords: + - allergen + miriam: allergome + name: 'Allergome: a platform for allergen knowledge' + pattern: ^\d+$ + prefix: allergome + pubmed_ids: + - '17393720' + - '17434469' + uri_format: http://www.allergome.org/script/refArray_view.php?idMol=$1 + uniprot: + category: Protein family/group databases + identifier: '160' + link_is_explicit: 'true' + name: Allergome; a platform for allergen knowledge + prefix: Allergome + uri_format: http://www.allergome.org/script/dettaglio.php?id_molecule=$1 +alzforum.mutation: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease. + example: app-d678n-tottori + homepage: https://www.alzforum.org/mutations + name: Alzforum Mutations + synonyms: + - Alzforum_mut + uri_format: https://www.alzforum.org/mutations/$1 +amoebadb: + biocontext: + is_identifiers: true + is_obo: false + prefix: AMOEBADB + uri_format: http://identifiers.org/amoebadb/$1 + fairsharing: + abbreviation: AmoebaDB + description: AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining. + id: '2095' + name: AmoebaDB + prefix: FAIRsharing.swbypy + subjects: + - Genomics + - Life Science + mappings: + biocontext: AMOEBADB + fairsharing: FAIRsharing.swbypy + miriam: amoebadb + n2t: amoebadb + prefixcommons: amoebadb + miriam: + deprecated: false + description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: http://amoebadb.org/amoeba/ + id: '00000148' + name: AmoebaDB + namespaceEmbeddedInLui: false + pattern: ^EDI_\d+$ + prefix: amoebadb + sampleId: EDI_244000 + uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 + n2t: + description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: EDI_244000 + homepage: http://amoebadb.org/amoeba/ + name: AmoebaDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^EDI_\d+$ + prefix: amoebadb + uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 + prefixcommons: + description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: EDI_244000 + homepage: http://amoebadb.org + keywords: + - model organism + miriam: amoebadb + name: AmoebaDB + pattern: ^EDI_\d+$ + prefix: amoebadb + pubmed_ids: + - '19914931' + uri_format: https://amoebadb.org/amoeba/app/record/gene/$1 +amphx: + bioportal: + name: The Amphioxus Development and Anatomy Ontology + prefix: AMPHX + example: '1000160' + mappings: + bioportal: AMPHX + obofoundry: amphx + ols: amphx + ontobee: AMPHX + obofoundry: + contact: hescriva@obs-banyuls.fr + contact.github: hescriva + contact.label: Hector Escriva + contact.orcid: 0000-0001-7577-5028 + depends_on: + - uberon + deprecated: false + description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). + download.obo: http://purl.obolibrary.org/obo/amphx.obo + download.owl: http://purl.obolibrary.org/obo/amphx.owl + homepage: https://github.com/EBISPOT/amphx_ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: The Amphioxus Development and Anatomy Ontology + preferredPrefix: AMPHX + prefix: amphx + repository: https://github.com/EBISPOT/amphx_ontology + ols: + description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). + download: https://raw.githubusercontent.com/EBISPOT/amphx_ontology/master/amphx.owl + name: Amphioxus Development and Anatomy Ontology (AMPHX) + prefix: amphx + version: 2020-12-18 + version.iri: http://purl.obolibrary.org/obo/amphx/releases/2020-12-18/amphx.owl + ontobee: + library: Library + name: The Amphioxus Development and Anatomy Ontology + prefix: AMPHX + pattern: ^\d+$ +antibodyregistry: + biocontext: + is_identifiers: true + is_obo: false + prefix: ANTIBODYREGISTRY + uri_format: http://identifiers.org/antibodyregistry/$1 + mappings: + biocontext: ANTIBODYREGISTRY + miriam: antibodyregistry + n2t: antibodyregistry + miriam: + deprecated: false + description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. + homepage: http://antibodyregistry.org/ + id: '00000516' + name: Antibody Registry + namespaceEmbeddedInLui: false + pattern: ^\d{6}$ + prefix: antibodyregistry + sampleId: '493771' + uri_format: http://antibodyregistry.org/AB_$1 + n2t: + description: The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. + example: '493771' + homepage: http://antibodyregistry.org/ + name: Antibody Registry at University of California + namespaceEmbeddedInLui: false + pattern: ^\d{6}$ + prefix: antibodyregistry + uri_format: http://antibodyregistry.org/AB_$1 +antweb: + biocontext: + is_identifiers: true + is_obo: false + prefix: ANTWEB + uri_format: http://identifiers.org/antweb/$1 + fairsharing: + abbreviation: AntWeb + description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. + id: '1749' + name: AntWeb + prefix: FAIRsharing.yk38tw + subjects: + - Anatomy + - Life Science + mappings: + biocontext: ANTWEB + fairsharing: FAIRsharing.yk38tw + miriam: antweb + n2t: antweb + ncbi: AntWeb + prefixcommons: antweb + miriam: + deprecated: false + description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. + homepage: http://www.antweb.org/ + id: '00000146' + name: AntWeb + namespaceEmbeddedInLui: false + pattern: ^casent\d+(\-D\d+)?$ + prefix: antweb + sampleId: casent0106247 + uri_format: http://www.antweb.org/specimen.do?name=$1 + n2t: + description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. + example: casent0106247 + homepage: http://www.antweb.org/ + name: AntWeb at California Academy of Sciences + namespaceEmbeddedInLui: false + pattern: ^casent\d+(\-D\d+)?$ + prefix: antweb + uri_format: http://www.antweb.org/specimen.do?name=$1 + ncbi: + example: CASENT0058943-D01 + homepage: http://www.antweb.org + name: Ant Database + prefix: AntWeb + prefixcommons: + description: AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. + example: casent0106247 + homepage: https://www.antweb.org + keywords: + - classification + - anatomy + miriam: antweb + name: 'AntWeb: Ant of the World' + pattern: ^casent\d+(\-\w+\d+)?$ + prefix: antweb + pubmed_ids: + - '12867945' + uri_format: http://www.antweb.org/specimen.do?name=$1 +aop: + biocontext: + is_identifiers: true + is_obo: false + prefix: AOP + uri_format: http://identifiers.org/aop/$1 + mappings: + biocontext: AOP + miriam: aop + n2t: aop + miriam: + deprecated: false + description: International repository of Adverse Outcome Pathways. + homepage: https://aopwiki.org/ + id: '00000617' + name: AOPWiki + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop + sampleId: '98' + uri_format: https://aopwiki.org/aops/$1 + n2t: + description: International repository of Adverse Outcome Pathways. + example: '98' + homepage: https://aopwiki.org/ + name: AOPWiki + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop + uri_format: https://aopwiki.org/aops/$1 +aop.events: + biocontext: + is_identifiers: true + is_obo: false + prefix: AOP.EVENTS + uri_format: http://identifiers.org/aop.events/$1 + mappings: + biocontext: AOP.EVENTS + miriam: aop.events + n2t: aop.events + miriam: + deprecated: false + description: International repository of Adverse Outcome Pathways. + homepage: https://aopwiki.org/ + id: '00000652' + name: AOPWiki (Key Event) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop.events + sampleId: '3' + uri_format: https://aopwiki.org/events/$1 + n2t: + description: International repository of Adverse Outcome Pathways. + example: '3' + homepage: https://aopwiki.org/ + name: AOPWiki (Key Event) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop.events + uri_format: https://aopwiki.org/events/$1 +aop.relationships: + biocontext: + is_identifiers: true + is_obo: false + prefix: AOP.RELATIONSHIPS + uri_format: http://identifiers.org/aop.relationships/$1 + mappings: + biocontext: AOP.RELATIONSHIPS + miriam: aop.relationships + n2t: aop.relationships + miriam: + deprecated: false + description: International repository of Adverse Outcome Pathways. + homepage: https://aopwiki.org/ + id: '00000653' + name: AOPWiki (Key Event Relationship) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop.relationships + sampleId: '5' + uri_format: https://aopwiki.org/relationships/$1 + n2t: + description: International repository of Adverse Outcome Pathways. + example: '5' + homepage: https://aopwiki.org/ + name: AOPWiki (Key Event Relationship) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop.relationships + uri_format: https://aopwiki.org/relationships/$1 +aop.stressor: + biocontext: + is_identifiers: true + is_obo: false + prefix: AOP.STRESSOR + uri_format: http://identifiers.org/aop.stressor/$1 + mappings: + biocontext: AOP.STRESSOR + miriam: aop.stressor + n2t: aop.stressor + miriam: + deprecated: false + description: International repository of Adverse Outcome Pathways. + homepage: https://aopwiki.org/ + id: '00000654' + name: AOPWiki (Stressor) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop.stressor + sampleId: '9' + uri_format: https://aopwiki.org/stressors/$1 + n2t: + description: International repository of Adverse Outcome Pathways. + example: '9' + homepage: https://aopwiki.org/ + name: AOPWiki (Stressor) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: aop.stressor + uri_format: https://aopwiki.org/stressors/$1 +apaonto: + bioportal: + name: Psychology Ontology + prefix: APAONTO + description: Ontology from the APA + example: Abdomen + fairsharing: + abbreviation: APAONTO + description: APA thesaurus . Flat ontology file + id: '567' + name: Psychology Ontology + prefix: FAIRsharing.gkw1w8 + subjects: [] + homepage: https://bioportal.bioontology.org/ontologies/APAONTO + mappings: + bioportal: APAONTO + fairsharing: FAIRsharing.gkw1w8 + uri_format: http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1 +apd: + biocontext: + is_identifiers: true + is_obo: false + prefix: APD + uri_format: http://identifiers.org/apd/$1 + fairsharing: + abbreviation: APD + description: The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the mature and active form, and primarily from natural sources, ranging from bacteria, fungi, plants, to animals. + id: '2105' + name: Antimicrobial Peptide Database + prefix: FAIRsharing.ctwd7b + subjects: + - Biology + mappings: + biocontext: APD + fairsharing: FAIRsharing.ctwd7b + miriam: apd + n2t: apd + prefixcommons: apd + miriam: + deprecated: false + description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. + homepage: http://aps.unmc.edu/AP/ + id: '00000278' + name: APD + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: apd + sampleId: '01001' + uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1 + n2t: + description: The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. + example: '01001' + homepage: http://aps.unmc.edu/AP/ + name: APD at Nebraska + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: apd + uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1 + name: Antimicrobial Peptide Database + prefixcommons: + description: The Antimicrobial Peptide Database (APD) contains data from the Protein Data Bank (PDB), Swiss-Prot Protein Knowledgebase and PubMed National Library of Medicine. The antimicrobial peptides in this database contain less than 100 amino acid residues, are in the mature and active form, and primarily from natural sources, ranging from bacteria, fungi, plants, to animals. + example: '1228' + homepage: http://aps.unmc.edu/AP/ + keywords: + - protein + miriam: apd + name: Antimicrobial Peptide Database + pattern: ^\d+$ + prefix: apd + pubmed_ids: + - '26602694' + uri_format: http://aps.unmc.edu/AP/database/query_output.php?ID=$1 +aphidbase.transcript: + biocontext: + is_identifiers: true + is_obo: false + prefix: APHIDBASE.TRANSCRIPT + uri_format: http://identifiers.org/aphidbase.transcript/$1 + mappings: + biocontext: APHIDBASE.TRANSCRIPT + miriam: aphidbase.transcript + n2t: aphidbase.transcript + miriam: + deprecated: false + description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. + homepage: http://www.aphidbase.com/aphidbase + id: '00000393' + name: AphidBase Transcript + namespaceEmbeddedInLui: false + pattern: ^ACYPI\d{6}(-RA)?$ + prefix: aphidbase.transcript + sampleId: ACYPI000159 + uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 + n2t: + description: AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. + example: ACYPI000159 + homepage: http://www.aphidbase.com/aphidbase + name: AphidBase at INRA + namespaceEmbeddedInLui: false + pattern: ^ACYPI\d{6}(-RA)?$ + prefix: aphidbase.transcript + uri_format: http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 +apid.interactions: + biocontext: + is_identifiers: true + is_obo: false + prefix: APID.INTERACTIONS + uri_format: http://identifiers.org/apid.interactions/$1 + mappings: + biocontext: APID.INTERACTIONS + miriam: apid.interactions + n2t: apid.interactions + miriam: + deprecated: false + description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. + homepage: http://cicblade.dep.usal.es:8080/APID/ + id: '00000576' + name: APID Interactomes + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ + prefix: apid.interactions + sampleId: P01116 + uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 + n2t: + description: APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. + example: P01116 + homepage: http://cicblade.dep.usal.es:8080/APID/ + name: APID at Salamanca + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ + prefix: apid.interactions + uri_format: http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 + provides: uniprot +apo: + biocontext: + is_identifiers: false + is_obo: true + prefix: YPO + uri_format: http://purl.obolibrary.org/obo/YPO_$1 + bioportal: + name: Ascomycete Phenotype Ontology + prefix: APO + example: '0000184' + fairsharing: + abbreviation: APO + description: Ascomycete Phenotype Ontology is a structured controlled vocabulary for the phenotypes of Ascomycete fungi. + id: '113' + name: Ascomycete Phenotype Ontology + prefix: FAIRsharing.dyqz3y + subjects: + - Life Science + - Cell Biology + mappings: + biocontext: YPO + bioportal: APO + fairsharing: FAIRsharing.dyqz3y + obofoundry: apo + ols: apo + ontobee: APO + obofoundry: + contact: stacia@stanford.edu + contact.github: srengel + contact.label: Stacia R Engel + contact.orcid: 0000-0001-5472-917X + deprecated: false + description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi + download.obo: http://purl.obolibrary.org/obo/apo.obo + download.owl: http://purl.obolibrary.org/obo/apo.owl + homepage: http://www.yeastgenome.org/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Ascomycete phenotype ontology + preferredPrefix: APO + prefix: apo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 + title: New mutant phenotype data curation system in the Saccharomyces Genome Database + repository: https://github.com/obophenotype/ascomycete-phenotype-ontology + ols: + description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi. + download: http://purl.obolibrary.org/obo/apo.owl + homepage: http://www.yeastgenome.org/ + name: Ascomycete Phenotype Ontology (APO) + prefix: apo + version: 2022-04-19 + version.iri: http://purl.obolibrary.org/obo/apo/releases/2022-04-19/apo.owl + ontobee: + library: Library + name: Ascomycete phenotype ontology + prefix: APO + pattern: ^\d{7}$ + preferred_prefix: APO + uri_format: https://www.yeastgenome.org/observable/APO:$1 +apollosv: + bioportal: + name: Apollo Structured Vocabulary + prefix: APOLLO-SV + example: '00000443' + fairsharing: + abbreviation: Apollo-SV + description: An ontology of infectious disease epidemiology and ecology (a.k.a. population biology). + id: '88' + name: Apollo-SV + prefix: FAIRsharing.ngv2xx + subjects: + - Ecology + - Biomedical Science + - Epidemiology + - Population Genetics + mappings: + bioportal: APOLLO-SV + fairsharing: FAIRsharing.ngv2xx + obofoundry: apollo_sv + ols: apollo_sv + ontobee: APOLLO_SV + obofoundry: + appears_in: + - scdo + contact: hoganwr@ufl.edu + contact.github: hoganwr + contact.label: William Hogan + contact.orcid: 0000-0002-9881-1017 + deprecated: false + description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models + download.owl: http://purl.obolibrary.org/obo/apollo_sv.owl + homepage: https://github.com/ApolloDev/apollo-sv + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Apollo Structured Vocabulary + preferredPrefix: APOLLO_SV + prefix: apollo_sv + publications: + - id: https://doi.org/10.1186/s13326-016-0092-y + title: 'The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation' + repository: https://github.com/ApolloDev/apollo-sv + ols: + description: Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models + download: http://purl.obolibrary.org/obo/apollo_sv.owl + homepage: https://github.com/ApolloDev/apollo-sv + name: Apollo Structured Vocabulary (Apollo-SV) + prefix: apollo_sv + version: 4.1.1 + version.iri: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl + ontobee: + library: Library + name: Apollo Structured Vocabulary + prefix: APOLLO_SV + pattern: ^\d{8}$ +arachnoserver: + biocontext: + is_identifiers: true + is_obo: false + prefix: ARACHNOSERVER + uri_format: http://identifiers.org/arachnoserver/$1 + fairsharing: + abbreviation: ArachnoServer + description: ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. + id: '2037' + name: 'ArachnoServer: Spider toxin database' + prefix: FAIRsharing.c54ywe + subjects: + - Life Science + mappings: + biocontext: ARACHNOSERVER + fairsharing: FAIRsharing.c54ywe + miriam: arachnoserver + n2t: arachnoserver + prefixcommons: arachnoserver + uniprot: ArachnoServer + miriam: + deprecated: false + description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. + homepage: http://www.arachnoserver.org/ + id: '00000193' + name: ArachnoServer + namespaceEmbeddedInLui: false + pattern: ^AS\d{6}$ + prefix: arachnoserver + sampleId: AS000060 + uri_format: http://www.arachnoserver.org/toxincard.html?id=$1 + n2t: + description: ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. + example: AS000060 + homepage: http://www.arachnoserver.org/ + name: ArachnoServer at Brisbane + namespaceEmbeddedInLui: false + pattern: ^AS\d{6}$ + prefix: arachnoserver + uri_format: http://www.arachnoserver.org/toxincard.html?id=$1 + prefixcommons: + description: ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. + example: AS000060 + homepage: http://www.arachnoserver.org + keywords: + - drug + - protein + miriam: arachnoserver + name: 'ArachnoServer: Spider toxin database' + pattern: ^AS\d{6}$ + prefix: arachnoserver + pubmed_ids: + - '21036864' + - '29069336' + uri_format: http://www.arachnoserver.org/toxincard.html?id=$1 + uniprot: + category: Organism-specific databases + identifier: '145' + link_is_explicit: 'true' + name: 'ArachnoServer: Spider toxin database' + prefix: ArachnoServer + uri_format: http://www.arachnoserver.org +araport: + description: Website with general information about Arabidopsis and functionalities such as a genomic viewer + homepage: https://www.araport.org/ + mappings: + ncbi: Araport + uniprot: Araport + name: Arabidopsis Information Portal + ncbi: + example: AT1G01010 + homepage: https://www.araport.org/ + name: Arabidopsis Information Portal + prefix: Araport + uniprot: + category: Organism-specific databases + identifier: '221' + link_is_explicit: 'true' + name: Arabidopsis Information Portal + prefix: Araport + uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1 + uri_format: https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 +ardb: + biocontext: + is_identifiers: true + is_obo: false + prefix: ARDB + uri_format: http://identifiers.org/ardb/$1 + mappings: + biocontext: ARDB + miriam: ardb + n2t: ardb + miriam: + deprecated: false + description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. + homepage: http://ardb.cbcb.umd.edu/ + id: '00000522' + name: Antibiotic Resistance Genes Database + namespaceEmbeddedInLui: false + pattern: ^[A-Z_]{3}[0-9]{4,}$ + prefix: ardb + sampleId: CAE46076 + uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 + n2t: + description: The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. + example: CAE46076 + homepage: http://ardb.cbcb.umd.edu/ + name: ARDB at University of Maryland + namespaceEmbeddedInLui: false + pattern: ^[A-Z_]{3}[0-9]{4,}$ + prefix: ardb + uri_format: http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 +ark: + banana: ark + biocontext: + is_identifiers: true + is_obo: false + prefix: ARK + uri_format: http://identifiers.org/ark/$1 + mappings: + biocontext: ARK + miriam: ark + n2t: ark + miriam: + deprecated: false + description: An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type. + homepage: http://n2t.net/ + id: '00000592' + name: ARK + namespaceEmbeddedInLui: true + pattern: ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ + prefix: ark + sampleId: /12345/fk1234 + uri_format: http://n2t.net/ark:$1 + n2t: + example: /88435/hq37vq534 + homepage: https://wiki.ucop.edu/display/Curation/ARK + name: Archival Resource Key + namespaceEmbeddedInLui: false + prefix: ark + uri_format: n2t.net/ark:$1 + name: Archival Resource Key + pattern: ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ + uri_format: http://n2t.net/ark:$1 +aro: + biocontext: + is_identifiers: false + is_obo: true + prefix: ARO + uri_format: http://purl.obolibrary.org/obo/ARO_$1 + bioportal: + name: Antibiotic Resistance Ontology + prefix: ARO + example: '1000001' + mappings: + biocontext: ARO + bioportal: ARO + obofoundry: aro + ols: aro + ontobee: ARO + obofoundry: + appears_in: + - scdo + contact: mcarthua@mcmaster.ca + contact.github: agmcarthur + contact.label: Andrew G. McArthur + contact.orcid: 0000-0002-1142-3063 + deprecated: false + description: Antibiotic resistance genes and mutations + download.owl: http://purl.obolibrary.org/obo/aro.owl + homepage: https://github.com/arpcard/aro + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Antibiotic Resistance Ontology + preferredPrefix: ARO + prefix: aro + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/31665441 + title: 'CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.' + repository: https://github.com/arpcard/aro + ols: + description: Antibiotic resistance genes and mutations + download: http://purl.obolibrary.org/obo/aro.owl + homepage: https://github.com/arpcard/aro + name: Antibiotic Resistance Ontology + prefix: aro + ontobee: + library: Library + name: Antibiotic Resistance Ontology + prefix: ARO + pattern: ^\d{7}$ +arrayexpress: + biocontext: + is_identifiers: true + is_obo: false + prefix: ARRAYEXPRESS + uri_format: http://identifiers.org/arrayexpress/$1 + cellosaurus: + category: Gene expression databases + homepage: https://www.ebi.ac.uk/arrayexpress/ + name: ArrayExpress Archive of Functional Genomics + prefix: ArrayExpress + uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1 + fairsharing: + abbreviation: ArrayExpress + description: ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database. + id: '1845' + name: ArrayExpress + prefix: FAIRsharing.6k0kwd + subjects: + - Functional Genomics + mappings: + biocontext: ARRAYEXPRESS + cellosaurus: ArrayExpress + fairsharing: FAIRsharing.6k0kwd + miriam: arrayexpress + n2t: arrayexpress + prefixcommons: arrayexpress + miriam: + deprecated: false + description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. + homepage: https://www.ebi.ac.uk/arrayexpress/ + id: '00000036' + name: ArrayExpress + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: arrayexpress + providers: + - code: omicsdi + description: ArrayExpress through OmicsDI + homepage: https://www.omicsdi.org/ + name: ArrayExpress through OmicsDI + uri_format: https://www.omicsdi.org/dataset/arrayexpress-repository/$1 + sampleId: E-MEXP-1712 + uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1 + n2t: + description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. + example: E-MEXP-1712 + homepage: https://www.ebi.ac.uk/arrayexpress/ + name: ArrayExpress + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: arrayexpress + uri_format: https://www.ebi.ac.uk/arrayexpress/experiments/$1 + prefixcommons: + description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. + example: E-MEXP-1712 + homepage: http://www.ebi.ac.uk/arrayexpress + keywords: + - expression + - microarray + - nucleotide + miriam: arrayexpress + name: ArrayExpress + pattern: ^[AEP]-\w{4}-\d+$ + prefix: arrayexpress + pubmed_ids: + - '12519949' + uri_format: http://www.ebi.ac.uk/arrayexpress/experiments/$1 +arrayexpress.platform: + biocontext: + is_identifiers: true + is_obo: false + prefix: ARRAYEXPRESS.PLATFORM + uri_format: http://identifiers.org/arrayexpress.platform/$1 + mappings: + biocontext: ARRAYEXPRESS.PLATFORM + miriam: arrayexpress.platform + n2t: arrayexpress.platform + miriam: + deprecated: false + description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. + homepage: https://www.ebi.ac.uk/arrayexpress/ + id: '00000294' + name: ArrayExpress Platform + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: arrayexpress.platform + sampleId: A-GEOD-50 + uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1 + n2t: + description: ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. + example: A-GEOD-50 + homepage: https://www.ebi.ac.uk/arrayexpress/ + name: ArrayExpress Platform at EBI + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: arrayexpress.platform + uri_format: https://www.ebi.ac.uk/arrayexpress/arrays/$1 +arraymap: + biocontext: + is_identifiers: true + is_obo: false + prefix: ARRAYMAP + uri_format: http://identifiers.org/arraymap/$1 + fairsharing: + abbreviation: arrayMap + description: Part of the Progenetix project, the arrayMap database facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed by the group "Theoretical Cytogenetics and Oncogenomics" at the Department of Molecular Life Sciences of the University of Zurich. + id: '2135' + name: arrayMap - Genomic Array Data for Cancer CNV Profiles + prefix: FAIRsharing.1fbc5y + subjects: + - Genomics + - Bioinformatics + - Life Science + - Biomedical Science + mappings: + biocontext: ARRAYMAP + fairsharing: FAIRsharing.1fbc5y + miriam: arraymap + n2t: arraymap + miriam: + deprecated: false + description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. + homepage: https://www.arraymap.org + id: '00000621' + name: ArrayMap + namespaceEmbeddedInLui: false + pattern: ^[\w\-:,]{3,64}$ + prefix: arraymap + sampleId: icdom:8500_3 + uri_format: https://www.arraymap.org/pgx:$1 + n2t: + description: arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. + example: icdom:8500_3 + homepage: https://www.arraymap.org + name: ArrayMap + namespaceEmbeddedInLui: false + pattern: ^[\w\-:,]{3,64}$ + prefix: arraymap + uri_format: https://www.arraymap.org/pgx:$1 +arxiv: + biocontext: + is_identifiers: true + is_obo: false + prefix: ARXIV + uri_format: http://identifiers.org/arxiv/$1 + mappings: + biocontext: ARXIV + miriam: arxiv + n2t: arxiv + prefixcommons: arxiv + scholia: arxiv + miriam: + deprecated: false + description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. + homepage: https://arxiv.org/ + id: '00000035' + name: arXiv + namespaceEmbeddedInLui: false + pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ + prefix: arxiv + sampleId: 0807.4956v1 + uri_format: https://arxiv.org/abs/$1 + n2t: + description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. + example: 0807.4956v1 + homepage: https://arxiv.org/ + name: Cornell University arXiv + namespaceEmbeddedInLui: false + pattern: ^(\w+(\-\w+)?(\.\w+)?)?\d{4,7}(\.\d+(v\d+)?)?$ + prefix: arxiv + uri_format: https://arxiv.org/abs/$1 + prefixcommons: + description: arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. + example: 0807.4956v1 + homepage: http://arxiv.org + keywords: + - bibliography + name: arXiv + pattern: ^(\w+(\-\w+)?(\.\w+)?/)?\d{4,7}(\.\d{4}(v\d+)?)?$ + prefix: arxiv + uri_format: http://arxiv.org/abs/$1 +asap: + biocontext: + is_identifiers: true + is_obo: false + prefix: ASAP + uri_format: http://identifiers.org/asap/$1 + fairsharing: + abbreviation: ASAP + description: ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. + id: '2115' + name: A Systematic Annotation Package + prefix: FAIRsharing.anpa6 + subjects: + - Developmental Biology + - Life Science + - Comparative Genomics + go: + homepage: https://asap.genetics.wisc.edu/asap/ASAP1.htm + name: A Systematic Annotation Package for Community Analysis of Genomes + prefix: ASAP + uri_format: https://asap.genetics.wisc.edu/asap/feature_info.php?FeatureID=$1 + mappings: + biocontext: ASAP + fairsharing: FAIRsharing.anpa6 + go: ASAP + miriam: asap + n2t: asap + ncbi: ASAP + prefixcommons: asap + miriam: + deprecated: false + description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. + homepage: http://asap.ahabs.wisc.edu/asap/home.php + id: '00000283' + name: ASAP + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+$ + prefix: asap + sampleId: ABE-0009634 + uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1 + n2t: + description: ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. + example: ABE-0009634 + homepage: http://asap.ahabs.wisc.edu/asap/home.php + name: ASAP at University of Wisconsin + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+$ + prefix: asap + uri_format: http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1 + name: A Systematic Annotation Package for Community Analysis of Genomes + ncbi: + example: ABE-0000006 + homepage: https://asap.genetics.wisc.edu/asap/logon.php + name: A Systematic Annotation Package for Community Analysis of Genomes + prefix: ASAP + prefixcommons: + description: ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. + example: ABZ-0129277 + homepage: https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm + keywords: + - genome + - gene expression + name: A Systematic Annotation Package + pattern: ^ABZ-\d+$ + prefix: asap + pubmed_ids: + - '12519969' + - '16381899' + uri_format: https://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=$1 +ascl: + biocontext: + is_identifiers: true + is_obo: false + prefix: ASCL + uri_format: http://identifiers.org/ascl/$1 + fairsharing: + abbreviation: ASCL + description: The Astrophysics Source Code Library (ASCL) is a free online registry for source code of interest to astronomers and astrophysicists. It provides code that has been used in research that has appeared in, or been submitted to, peer-reviewed publications.Peer-reviewed papers that describe methods or experiments involving the development or use of source code are added by the ASCL team. + id: '2546' + name: Astrophysics Source Code Library + prefix: FAIRsharing.wb0txg + subjects: + - Astrophysics and Astronomy + mappings: + biocontext: ASCL + fairsharing: FAIRsharing.wb0txg + miriam: ascl + n2t: ascl + miriam: + deprecated: false + description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). + homepage: http://ascl.net/ + id: '00000641' + name: Astrophysics Source Code Library + namespaceEmbeddedInLui: false + pattern: ^[0-9\.]+$ + prefix: ascl + sampleId: '1801.012' + uri_format: http://ascl.net/$1 + n2t: + description: The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). + example: '1801.012' + homepage: http://ascl.net/ + name: Astrophysics Source Code Library + namespaceEmbeddedInLui: false + pattern: ^[0-9\.]+$ + prefix: ascl + uri_format: http://ascl.net/$1 +asin: + biocontext: + is_identifiers: true + is_obo: false + prefix: ASIN + uri_format: http://identifiers.org/asin/$1 + mappings: + biocontext: ASIN + miriam: asin + n2t: asin + miriam: + deprecated: false + description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue. + homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182 + id: '00000670' + name: Amazon Standard Identification Number (ASIN) + namespaceEmbeddedInLui: false + pattern: ^[0-9]{10}$ + prefix: asin + sampleId: '0471491039' + uri_format: https://amzn.com/$1 + n2t: + description: Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue. + example: '0471491039' + homepage: https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182 + name: Amazon Standard Identification Number (ASIN) + namespaceEmbeddedInLui: false + pattern: ^[0-9]{10}$ + prefix: asin + uri_format: https://amzn.com/$1 + name: Amazon Standard Identification Number +aspgd.locus: + biocontext: + is_identifiers: true + is_obo: false + prefix: ASPGD.LOCUS + uri_format: http://identifiers.org/aspgd.locus/$1 + go: + homepage: http://www.aspergillusgenome.org/ + name: Aspergillus Genome Database + prefix: AspGD_LOCUS + uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=$1 + mappings: + biocontext: ASPGD.LOCUS + go: AspGD_LOCUS + miriam: aspgd.locus + n2t: aspgd.locus + miriam: + deprecated: false + description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. + homepage: http://www.aspgd.org/ + id: '00000412' + name: AspGD Locus + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: aspgd.locus + sampleId: ASPL0000349247 + uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1 + n2t: + description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. + example: ASPL0000349247 + homepage: http://www.aspgd.org/ + name: AspGD at Stanford Medical School + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: aspgd.locus + uri_format: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1 +aspgd.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: ASPGD.PROTEIN + uri_format: http://identifiers.org/aspgd.protein/$1 + mappings: + biocontext: ASPGD.PROTEIN + miriam: aspgd.protein + n2t: aspgd.protein + miriam: + deprecated: false + description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. + homepage: http://www.aspgd.org/ + id: '00000413' + name: AspGD Protein + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: aspgd.protein + sampleId: ASPL0000349247 + uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1 + n2t: + description: The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. + example: ASPL0000349247 + homepage: http://www.aspgd.org/ + name: AspGD Protein at Stanford Medical School + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: aspgd.protein + uri_format: http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1 +asrp: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes. + example: ASRP1423 + homepage: https://asrp.danforthcenter.org/ + mappings: + prefixcommons: asrp + name: Arabidopsis Small RNA Project + prefixcommons: + description: This project focuses on small RNAs. It involves function analysis, regulation, and the evolution of RNA silencing pathways at a genome-wide level. Technologies are being used in the sequence-based profiling of the genome of A. thaliana small RNAs and their classification associated with silencing effector proteins. + example: '365115' + homepage: http://asrp.cgrb.oregonstate.edu + keywords: + - RNA + - genome + - regulation + name: Arabidopsis Small RNA Project + pattern: ^\d+$ + prefix: asrp + pubmed_ids: + - '15608278' + - '17999994' + uri_format: http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1 +atc: + biocontext: + is_identifiers: true + is_obo: false + prefix: ATC + uri_format: http://identifiers.org/atc/$1 + bioportal: + name: Anatomical Therapeutic Chemical Classification + prefix: ATC + fairsharing: + abbreviation: ATC + description: The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. It is controlled by the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC), and was first published in 1976. + id: '1152' + name: Anatomical Therapeutic Chemical Classification + prefix: FAIRsharing.1a27h8 + subjects: + - Chemical Biology + - Pharmacology + - Biomedical Science + mappings: + biocontext: ATC + bioportal: ATC + fairsharing: FAIRsharing.1a27h8 + miriam: atc + n2t: atc + prefixcommons: atc + miriam: + deprecated: false + description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. + homepage: http://www.whocc.no/atc_ddd_index/ + id: '00000088' + name: Anatomical Therapeutic Chemical + namespaceEmbeddedInLui: false + pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ + prefix: atc + sampleId: A10BA02 + uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 + n2t: + description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. + example: A10BA02 + homepage: http://www.whocc.no/atc_ddd_index/ + name: Anatomical Therapeutic Chemical Index at WHO + namespaceEmbeddedInLui: false + pattern: ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$ + prefix: atc + uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 + name: Anatomical Therapeutic Chemical Classification System + prefixcommons: + bioportal: '3021' + description: The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. + example: A10BA02 + homepage: http://www.whocc.no/atc_ddd_index/ + keywords: + - chemical + name: Anatomical Therapeutic Chemical + pattern: ^\w(\d+)?(\w{1,2})?(\d+)?$ + prefix: atc + uri_format: http://www.whocc.no/atc_ddd_index/?code=$1 + synonyms: + - ATC_code + - ATTC + wikidata: + prefix: P267 +atcc: + biocontext: + is_identifiers: true + is_obo: false + prefix: ATCC + uri_format: http://identifiers.org/atcc/$1 + cellosaurus: + category: Cell line collections + homepage: https://www.atcc.org/ + name: American Type Culture Collection + prefix: ATCC + uri_format: https://www.atcc.org/Products/$1 + fairsharing: + abbreviation: ATCC + description: ATCC authenticates microorganisms and cell lines and manages logistics of long-term preservation and distribution of cultures for the scientific community. ATCC supports the cultures it acquires and authenticates with expert technical support, intellectual property management and characterization data. + id: '1752' + name: American Type Culture Collection database + prefix: FAIRsharing.j0ezpm + subjects: + - Virology + - Life Science + - Epidemiology + homepage: https://www.lgcstandards-atcc.org + mappings: + biocontext: ATCC + cellosaurus: ATCC + fairsharing: FAIRsharing.j0ezpm + miriam: atcc + n2t: atcc + ncbi: ATCC + miriam: + deprecated: false + description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. + homepage: http://www.atcc.org/ + id: '00000284' + name: ATCC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: atcc + sampleId: '11303' + uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx + n2t: + description: The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. + example: '11303' + homepage: http://www.atcc.org/ + name: ATCC in Virginia + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: atcc + uri_format: http://www.lgcstandards-atcc.org/Products/All/$1.aspx + name: American Type Culture Collection + ncbi: + example: '123456' + homepage: http://www.atcc.org/ + name: American Type Culture Collection database + prefix: ATCC + pattern: ^([A-Z]+-)?\d+$ + synonyms: + - ATCC + - ATCC number + - ATCC(dna) + - ATCC(in host) + uri_format: https://www.atcc.org/products/$1 +atcvet: + biocontext: + is_identifiers: true + is_obo: false + prefix: ATCVET + uri_format: http://identifiers.org/atcvet/$1 + mappings: + biocontext: ATCVET + miriam: atcvet + n2t: atcvet + miriam: + deprecated: false + description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. + homepage: http://www.whocc.no/atcvet/atcvet_index/ + id: '00000267' + name: Anatomical Therapeutic Chemical Vetinary + namespaceEmbeddedInLui: false + pattern: ^Q[A-Z0-9]+$ + prefix: atcvet + sampleId: QJ51RV02 + uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1 + n2t: + description: The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. + example: QJ51RV02 + homepage: http://www.whocc.no/atcvet/atcvet_index/ + name: Anatomical Therapeutic Chemical Vet Index at WHO + namespaceEmbeddedInLui: false + pattern: ^Q[A-Z0-9]+$ + prefix: atcvet + uri_format: http://www.whocc.no/atcvet/atcvet_index/?code=$1 +atfdb.family: + biocontext: + is_identifiers: true + is_obo: false + prefix: ATFDB.FAMILY + uri_format: http://identifiers.org/atfdb.family/$1 + mappings: + biocontext: ATFDB.FAMILY + miriam: atfdb.family + n2t: atfdb.family + miriam: + deprecated: false + description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. + homepage: http://www.bioguo.org/AnimalTFDB/family_index.php + id: '00000316' + name: Animal TFDB Family + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: atfdb.family + sampleId: CUT + uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 + n2t: + description: The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. + example: CUT + homepage: http://www.bioguo.org/AnimalTFDB/family_index.php + name: Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: atfdb.family + uri_format: http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 +ato: + biocontext: + is_identifiers: false + is_obo: true + prefix: ATO + uri_format: http://purl.obolibrary.org/obo/ATO_$1 + bioportal: + name: Amphibian Taxonomy Ontology + prefix: ATO + example: '0000000' + fairsharing: + abbreviation: ATO + description: Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource + id: '583' + name: Amphibian Taxonomy Ontology + prefix: FAIRsharing.ayjdsm + mappings: + biocontext: ATO + bioportal: ATO + fairsharing: FAIRsharing.ayjdsm + obofoundry: ato + obofoundry: + contact: david.c.blackburn@gmail.com + contact.label: David Blackburn + deprecated: true + homepage: http://www.amphibanat.org + name: Amphibian taxonomy + prefix: ato + pattern: ^\d{7}$ +atol: + bioportal: + name: Animal Trait Ontology for Livestock + prefix: ATOL + download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl + example: '0002233' + fairsharing: + abbreviation: ATOL + description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment. ATOL aims to: provide a reference ontology of phenotypic traits of farm animals for the international scientific and educational - communities, farmers, etc.; deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; represent traits as generic as possible for livestock vertebrates; make the ATOL ontology as operational as possible and closely related to measurement techniques; and structure the ontology in relation to animal production.' + id: '1535' + name: Animal Trait Ontology for Livestock + prefix: FAIRsharing.wsfk5z + subjects: + - Animal Husbandry + - Agriculture + - Life Science + mappings: + bioportal: ATOL + fairsharing: FAIRsharing.wsfk5z + ols: atol + ols: + contact: pylebail@rennes.inra.fr + description: 'ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.' + download: http://www.atol-ontology.com/public/telechargement/atol.owl + homepage: http://www.atol-ontology.com + name: Animal Trait Ontology for Livestock + prefix: atol + version: 2018-09-13 + pattern: ^\d{7}$ +autdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: AUTDB + uri_format: http://identifiers.org/autdb/$1 + mappings: + biocontext: AUTDB + miriam: autdb + n2t: autdb + miriam: + deprecated: false + description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. + homepage: http://autism.mindspec.org/autdb/ + id: '00000415' + name: AutDB + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[A-Z-0-9]{2,}$ + prefix: autdb + sampleId: ADA + uri_format: http://autism.mindspec.org/GeneDetail/$1 + n2t: + description: AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. + example: ADA + homepage: http://autism.mindspec.org/autdb/ + name: AutDB at MindSpec + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[A-Z-0-9]{2,}$ + prefix: autdb + uri_format: http://autism.mindspec.org/GeneDetail/$1 +bacdive: + fairsharing: + abbreviation: BacDive + description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology. + id: '2674' + name: Bacterial Diversity Metadatabase + prefix: FAIRsharing.aSszvY + subjects: + - Biodiversity + - Life Science + - Microbiology + mappings: + fairsharing: FAIRsharing.aSszvY + miriam: bacdive + n2t: bacdive + miriam: + deprecated: false + description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. + homepage: https://bacdive.dsmz.de/ + id: '00000676' + name: Bacterial Diversity Metadatabase + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: bacdive + sampleId: '131392' + uri_format: https://bacdive.dsmz.de/strain/$1 + n2t: + description: BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. + example: '131392' + homepage: https://bacdive.dsmz.de/ + name: Bacterial Diversity Metadatabase + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: bacdive + uri_format: https://bacdive.dsmz.de/strain/$1 +bacmap.biog: + biocontext: + is_identifiers: true + is_obo: false + prefix: BACMAP.BIOG + uri_format: http://identifiers.org/bacmap.biog/$1 + mappings: + biocontext: BACMAP.BIOG + miriam: bacmap.biog + n2t: bacmap.biog + miriam: + deprecated: false + description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. + homepage: http://bacmap.wishartlab.com/ + id: '00000361' + name: BacMap Biography + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bacmap.biog + sampleId: '1050' + uri_format: http://bacmap.wishartlab.com/organisms/$1 + n2t: + description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. + example: '1050' + homepage: http://bacmap.wishartlab.com/ + name: BacMap Biography at University of Alberta + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bacmap.biog + uri_format: http://bacmap.wishartlab.com/organisms/$1 +bacmap.map: + biocontext: + is_identifiers: true + is_obo: false + prefix: BACMAP.MAP + uri_format: http://identifiers.org/bacmap.map/$1 + mappings: + biocontext: BACMAP.MAP + miriam: bacmap.map + n2t: bacmap.map + miriam: + deprecated: false + description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. + homepage: http://bacmap.wishartlab.com/ + id: '00000416' + name: BacMap Map + namespaceEmbeddedInLui: false + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: bacmap.map + sampleId: AP011135 + uri_format: http://bacmap.wishartlab.com/maps/$1/index.html + n2t: + description: BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. + example: AP011135 + homepage: http://bacmap.wishartlab.com/ + name: BacMap Genome Map at University of Alberta + namespaceEmbeddedInLui: false + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: bacmap.map + uri_format: http://bacmap.wishartlab.com/maps/$1/index.html +bactibase: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria. + example: BAC045 + fairsharing: + abbreviation: BACTIBASE + description: BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors. + id: '1928' + name: 'Bactibase: database dedicated to bacteriocins' + prefix: FAIRsharing.5f5mfm + subjects: + - Life Science + homepage: http://bactibase.hammamilab.org + mappings: + fairsharing: FAIRsharing.5f5mfm + prefixcommons: bactibase + name: Bactibase + prefixcommons: + description: BACTIBASE contains calculated or predicted physicochemical properties of 177 bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors. + example: BAC152 + homepage: http://bactibase.pfba-lab-tun.org/main.php + keywords: + - protein + name: 'Bactibase: database dedicated to bacteriocins' + pattern: ^BA\d+$ + prefix: bactibase + uri_format: http://bactibase.pfba-lab-tun.org/$1 + uri_format: http://bactibase.hammamilab.org/$1 +bams: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + description: 'BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.' + homepage: https://bams1.org + name: Brain Architecture Knowledge Management System Neuroanatomical Ontology + references: + - https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full +bao: + biocontext: + is_identifiers: true + is_obo: false + prefix: BAO + uri_format: http://identifiers.org/bao/$1 + bioportal: + name: BioAssay Ontology + prefix: BAO + fairsharing: + abbreviation: BAO + description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. + id: '874' + name: BioAssay Ontology + prefix: FAIRsharing.mye76w + subjects: + - Biochemistry + - Life Science + - Biomedical Science + mappings: + biocontext: BAO + bioportal: BAO + fairsharing: FAIRsharing.mye76w + miriam: bao + n2t: bao + ols: bao + ontobee: BAO + miriam: + deprecated: false + description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. + homepage: http://bioportal.bioontology.org/ontologies/BAO/ + id: '00000597' + name: BioAssay Ontology + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: bao + sampleId: '0002989' + uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1 + n2t: + description: The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. + example: '0002989' + homepage: http://bioportal.bioontology.org/ontologies/BAO/ + name: BioAssay Ontology through BioPortal + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: bao + uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1 + ols: + description: The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation. + download: http://www.bioassayontology.org/bao/ + homepage: http://bioassayontology.org + name: BioAssay Ontology + prefix: bao + version: 2.7.2 + version.iri: http://www.bioassayontology.org/bao/bao_complete.owl + ontobee: + library: Not Specified/No + name: BioAssay Ontology + prefix: BAO + synonyms: + - BAO +bbkg: + mappings: + miriam: bbkg + miriam: + deprecated: false + description: Blue Brain Project's published data as knowledge graphs and Web Studios. + homepage: https://portal.bluebrain.epfl.ch + id: '00000903' + name: Blue Brain Project Knowledge Graph + namespaceEmbeddedInLui: false + pattern: ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$ + prefix: bbkg + sampleId: topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a + uri_format: https://bbp.epfl.ch/nexus/web/studios/public/$1 +bbtp: + mappings: + miriam: bbtp + miriam: + deprecated: false + description: Input data and analysis results for the paper "Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ). + homepage: https://portal.bluebrain.epfl.ch + id: '00000889' + name: Blue Brain Project Topological sampling Knowledge Graph + namespaceEmbeddedInLui: false + pattern: \b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b + prefix: bbtp + sampleId: f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a + uri_format: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1 +bcgo: + biocontext: + is_identifiers: false + is_obo: true + prefix: BCGO + uri_format: http://purl.obolibrary.org/obo/BCGO_$1 + bioportal: + name: Breast Cancer Grading Ontology + prefix: BCGO + cellosaurus: + category: Anatomy/cell type resources + homepage: https://github.com/obi-bcgo/bcgo + name: Beta Cell Genomics Ontology + prefix: BCGO + uri_format: http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1 + download_owl: https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl + mappings: + biocontext: BCGO + bioportal: BCGO + cellosaurus: BCGO + obofoundry: bcgo + ontobee: BCGO + obofoundry: + contact: jiezheng@pennmedicine.upenn.edu + contact.github: zhengj2007 + contact.label: Jie Zheng + contact.orcid: 0000-0002-2999-0103 + deprecated: true + description: An application ontology built for beta cell genomics studies. + download.owl: http://purl.obolibrary.org/obo/bcgo.owl + homepage: https://github.com/obi-bcgo/bcgo + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Beta Cell Genomics Ontology + prefix: bcgo + repository: https://github.com/obi-bcgo/bcgo + ontobee: + library: Library + name: Beta Cell Genomics Ontology + prefix: BCGO +bcio: + bioportal: + name: Brain-Computer Interaction (BCI) Ontology + prefix: BCI-O + download_owl: http://humanbehaviourchange.org/ontology/bcio.owl + example: '040000' + mappings: + bioportal: BCI-O + ols: bcio + ols: + description: The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation. + download: http://humanbehaviourchange.org/ontology/bcio.owl + homepage: https://www.humanbehaviourchange.org/ + name: The Behaviour Change Intervention Ontology + prefix: bcio + version.iri: http://humanbehaviourchange.org/ontology/bcio.owl/2022-04-30 + pattern: ^\d{6}$ +bco: + biocontext: + is_identifiers: false + is_obo: true + prefix: BCO + uri_format: http://purl.obolibrary.org/obo/BCO_$1 + bioportal: + name: Biological Collections Ontology + prefix: BCO + example: '0000081' + fairsharing: + abbreviation: BCO + description: The Biological Collections Ontology (BCO) supports the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. The BCO covers distinctions between individuals, organisms, voucher specimens, lots, samples, the relations between these entities, and the processes governing the creation and use of "samples". Also within scope are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. + id: '1080' + name: Biological Collections Ontology + prefix: FAIRsharing.8ktkqy + subjects: + - Metagenomics + - Taxonomy + - Ecology + - Biodiversity + mappings: + biocontext: BCO + bioportal: BCO + fairsharing: FAIRsharing.8ktkqy + obofoundry: bco + ols: bco + ontobee: BCO + obofoundry: + appears_in: + - fovt + contact: rlwalls2008@gmail.com + contact.github: ramonawalls + contact.label: Ramona Walls + contact.orcid: 0000-0001-8815-0078 + deprecated: false + description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. + download.owl: http://purl.obolibrary.org/obo/bco.owl + homepage: https://github.com/BiodiversityOntologies/bco + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Biological Collections Ontology + preferredPrefix: BCO + prefix: bco + repository: https://github.com/BiodiversityOntologies/bco + ols: + description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. + download: http://purl.obolibrary.org/obo/bco.owl + homepage: https://github.com/BiodiversityOntologies/bco + name: Biological Collections Ontology + prefix: bco + version: 2021-11-14 + version.iri: http://purl.obolibrary.org/obo/bco/releases/2021-11-14/bco.owl + ontobee: + library: Library + name: Biological Collections Ontology + prefix: BCO + pattern: ^\d{7}$ +bcrc: + cellosaurus: + category: Cell line collections + homepage: https://catalog.bcrc.firdi.org.tw/ + name: Taiwan Bioresource Collection and Research Center + prefix: BCRC + uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: '60316' + homepage: https://catalog.bcrc.firdi.org.tw + mappings: + cellosaurus: BCRC + name: BCRC Strain Collection Catalog + pattern: ^\d+$ + uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 +bcrj: + cellosaurus: + category: Cell line collections + homepage: http://bcrj.org.br/celula/bcrj + name: Banco de Celulas do Rio de Janeiro + prefix: BCRJ + uri_format: http://bcrj.org.br/celula/$1 + example: '0278' + mappings: + cellosaurus: BCRJ + pattern: ^\d{4}$ +bdgp.est: + biocontext: + is_identifiers: true + is_obo: false + prefix: BDGP.EST + uri_format: http://identifiers.org/bdgp.est/$1 + has_canonical: dbest + mappings: + biocontext: BDGP.EST + miriam: bdgp.est + n2t: bdgp.est + ncbi: BDGP_EST + miriam: + deprecated: false + description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). + homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html + id: '00000285' + name: BDGP EST + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?(\d+)?$ + prefix: bdgp.est + sampleId: EY223054.1 + uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 + n2t: + description: The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). + example: EY223054.1 + homepage: https://www.ncbi.nlm.nih.gov/dbEST/index.html + name: BDGP EST at NCBI + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?(\d+)?$ + prefix: bdgp.est + uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 + ncbi: + example: '123456' + homepage: http://www.fruitfly.org/EST/index.shtml + name: Berkeley Drosophila Genome Project EST database + prefix: BDGP_EST +bdgp.insertion: + biocontext: + is_identifiers: true + is_obo: false + prefix: BDGP.INSERTION + uri_format: http://identifiers.org/bdgp.insertion/$1 + mappings: + biocontext: BDGP.INSERTION + miriam: bdgp.insertion + n2t: bdgp.insertion + miriam: + deprecated: false + description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. + homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/ + id: '00000156' + name: BDGP insertion DB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: bdgp.insertion + sampleId: KG09531 + uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 + n2t: + description: BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. + example: KG09531 + homepage: http://flypush.imgen.bcm.tmc.edu/pscreen/ + name: BDGP Gene Disruption Project + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: bdgp.insertion + uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 +bdsc: + mappings: + miriam: bdsc + n2t: bdsc + miriam: + deprecated: false + description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. + homepage: https://bdsc.indiana.edu/about/mission.html + id: '00000332' + name: Bloomington Drosophila Stock Center + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bdsc + sampleId: '33607' + uri_format: https://bdsc.indiana.edu/stocks/$1 + n2t: + description: The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. + example: '33607' + homepage: https://bdsc.indiana.edu/about/mission.html + name: BDSC at Indiana University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bdsc + uri_format: https://bdsc.indiana.edu/stocks/$1 +beetlebase: + biocontext: + is_identifiers: true + is_obo: false + prefix: BEETLEBASE + uri_format: http://identifiers.org/beetlebase/$1 + fairsharing: + abbreviation: BeetleBase + description: BeetleBase is a community resource for Tribolium genetics, genomics and developmental biology. The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes. + id: '1940' + name: BeetleBase + prefix: FAIRsharing.h5f091 + subjects: + - Computational Biology + - Life Science + mappings: + biocontext: BEETLEBASE + fairsharing: FAIRsharing.h5f091 + miriam: beetlebase + n2t: beetlebase + ncbi: BEETLEBASE + prefixcommons: beetlebase + miriam: + deprecated: false + description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. + homepage: http://beetlebase.org/ + id: '00000157' + name: BeetleBase + namespaceEmbeddedInLui: false + pattern: ^TC\d+$ + prefix: beetlebase + sampleId: TC010103 + uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 + n2t: + description: BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. + example: TC010103 + homepage: http://beetlebase.org/ + name: BeetleBase at Kansas State University + namespaceEmbeddedInLui: false + pattern: ^TC\d+$ + prefix: beetlebase + uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 + ncbi: + example: TC030551 + homepage: http://www.beetlebase.org/ + name: Tribolium Genome Database -- Insertion + prefix: BEETLEBASE + prefixcommons: + description: BeetleBase is being developed as an important community resource for Tribolium genetics, genomics and developmental biology.The database is built on the Chado generic data model, and is able to store various types of data, ranging from genome sequences to mutant phenotypes. + example: TC010103 + homepage: http://www.beetlebase.org/ + keywords: + - genome + name: BeetleBase + pattern: ^TC\d+$ + prefix: beetlebase + pubmed_ids: + - '19820115' + uri_format: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 +begdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: BEGDB + uri_format: http://identifiers.org/begdb/$1 + fairsharing: + abbreviation: BEGDB + description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. + id: '2365' + name: The Benchmark Energy & Geometry Database + prefix: FAIRsharing.nbe4fq + subjects: + - Life Science + mappings: + biocontext: BEGDB + fairsharing: FAIRsharing.nbe4fq + miriam: begdb + n2t: begdb + miriam: + deprecated: false + description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. + homepage: http://www.begdb.com + id: '00000622' + name: Benchmark Energy & Geometry Database + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: begdb + sampleId: '4214' + uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 + n2t: + description: The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. + example: '4214' + homepage: http://www.begdb.com + name: Benchmark Energy & Geometry Database + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: begdb + uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 +beiresources: + cellosaurus: + category: Cell line collections + homepage: https://www.beiresources.org/Home.aspx + name: BEI Resources + prefix: BEI_Resources + uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: MRA-253 + homepage: https://www.beiresources.org + mappings: + cellosaurus: BEI_Resources + name: BEI Resources + synonyms: + - BEI_Resources + uri_format: https://www.beiresources.org/Catalog/cellBanks/$1.aspx +bel: + comment: INDRA uses bel as a catch-all for scomp/sfam + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. + example: 9-1-1 Complex + fairsharing: + abbreviation: BEL + description: BEL is a language for representing scientific findings in the life sciences in a reusable, shareable, and computable form. BEL is designed to represent scientific findings by capturing causal and correlative relationships in context, where context can include information about the biological and experimental system in which the relationships were observed, the supporting publications cited and the process of curation. BEL is intended as a knowledge capture and interchange medium, supporting the operation of systems that integrate knowledge derived from independent efforts. The language is designed to be use-neutral, facilitating the storage and use of structured knowledge for inference by applications through a knowledge assembly process that can create computable biological networks. While BEL does not prescribe any particular assembly process or any particular knowledge format for the output of an assembly process, a suite of software components called the BEL Framework provides everything necessary to create, compile, assemble, and deliver computable knowledge models to BEL-aware applications. The current version of BEL provides the means to describe biological interactions qualitatively but not to quantify the magnitude or rate of these interactions. This limitation is by design because this quantitative information has significant variability and is not consistently reported in the literature. It is our hope that future versions of BEL can accommodate these additional data. + id: '1243' + name: Biological Expression Language + prefix: FAIRsharing.dp0jvd + subjects: + - Biology + homepage: https://biological-expression-language.github.io/ + mappings: + fairsharing: FAIRsharing.dp0jvd + name: Biological Expression Language +bfo: + biocontext: + is_identifiers: false + is_obo: true + prefix: BFO + uri_format: http://purl.obolibrary.org/obo/BFO_$1 + bioportal: + name: Basic Formal Ontology + prefix: BFO + example: '0000001' + fairsharing: + abbreviation: ISO/IEC 21838-2:2021 BFO + description: ISO/IEC 21838-2:2021 describes Basic Formal Ontology (BFO), which is an ontology that is conformant to the requirements specified for top-level ontologies in ISO/IEC 21838‑1. + id: '1248' + name: 'ISO/IEC 21838-2:2021 Information technology — Top-level ontologies (TLO) — Part 2: Basic Formal Ontology (BFO)' + prefix: FAIRsharing.wcpd6f + subjects: + - Subject Agnostic + go: + description: An upper ontology used by Open Bio Ontologies (OBO) Foundry. BFO contains upper-level classes as well as core relations such as part_of (BFO_0000050) + name: Basic Formal Ontology + prefix: BFO + mappings: + biocontext: BFO + bioportal: BFO + fairsharing: FAIRsharing.wcpd6f + go: BFO + obofoundry: bfo + ols: bfo + ontobee: BFO + obofoundry: + appears_in: + - agro + - aism + - cdno + - colao + - duo + - ecocore + - epio + - foodon + - fovt + - hso + - lepao + - mco + - ons + - pcl + - pco + - pco + - psdo + - rbo + - xpo + - zp + contact: phismith@buffalo.edu + contact.github: phismith + contact.label: Barry Smith + contact.orcid: 0000-0003-1384-116X + deprecated: false + description: The upper level ontology upon which OBO Foundry ontologies are built. + download.obo: http://purl.obolibrary.org/obo/bfo.obo + download.owl: http://purl.obolibrary.org/obo/bfo.owl + homepage: http://ifomis.org/bfo/ + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Basic Formal Ontology + preferredPrefix: BFO + prefix: bfo + repository: https://github.com/BFO-ontology/BFO + ols: + description: The upper level ontology upon which OBO Foundry ontologies are built. + download: http://purl.obolibrary.org/obo/bfo.owl + homepage: https://github.com/BFO-ontology/BFO + name: Basic Formal Ontology + prefix: bfo + version: 2019-08-26 + version.iri: http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl + ontobee: + library: Foundry + name: Basic Formal Ontology + prefix: BFO + pattern: ^\d{7}$ +bgee.family: + biocontext: + is_identifiers: true + is_obo: false + prefix: BGEE.FAMILY + uri_format: http://identifiers.org/bgee.family/$1 + mappings: + biocontext: BGEE.FAMILY + miriam: bgee.family + n2t: bgee.family + miriam: + deprecated: false + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. + homepage: http://bgee.unil.ch/bgee/bgee + id: '00000417' + name: Bgee family + namespaceEmbeddedInLui: false + pattern: ^(ENSFM|ENSGTV:)\d+$ + prefix: bgee.family + sampleId: ENSFM00500000270089 + uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 + n2t: + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. + example: ENSFM00500000270089 + homepage: http://bgee.unil.ch/bgee/bgee + name: Bgee at Lausanne + namespaceEmbeddedInLui: false + pattern: ^(ENSFM|ENSGTV:)\d+$ + prefix: bgee.family + uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 +bgee.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: BGEE.GENE + uri_format: http://identifiers.org/bgee.gene/$1 + mappings: + biocontext: BGEE.GENE + miriam: bgee.gene + n2t: bgee.gene + miriam: + deprecated: false + description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. + homepage: https://bgee.org/ + id: '00000418' + name: Bgee gene + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+\d+$ + prefix: bgee.gene + sampleId: FBgn0000015 + uri_format: https://bgee.org/?page=gene&gene_id=$1 + n2t: + description: Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. + example: FBgn0000015 + homepage: https://bgee.org/ + name: Bgee gene + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+\d+$ + prefix: bgee.gene + uri_format: https://bgee.org/?page=gene&gene_id=$1 +bgee.organ: + biocontext: + is_identifiers: true + is_obo: false + prefix: BGEE.ORGAN + uri_format: http://identifiers.org/bgee.organ/$1 + mappings: + biocontext: BGEE.ORGAN + miriam: bgee.organ + n2t: bgee.organ + miriam: + deprecated: false + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. + homepage: http://bgee.unil.ch/bgee/bgee + id: '00000420' + name: Bgee organ + namespaceEmbeddedInLui: false + pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ + prefix: bgee.organ + sampleId: EHDAA:2185 + uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on + n2t: + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. + example: EHDAA:2185 + homepage: http://bgee.unil.ch/bgee/bgee + name: Bgee at Lausanne + namespaceEmbeddedInLui: false + pattern: ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ + prefix: bgee.organ + uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on + uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1 +bgee.stage: + biocontext: + is_identifiers: true + is_obo: false + prefix: BGEE.STAGE + uri_format: http://identifiers.org/bgee.stage/$1 + mappings: + biocontext: BGEE.STAGE + miriam: bgee.stage + n2t: bgee.stage + miriam: + deprecated: false + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. + homepage: http://bgee.unil.ch/bgee/bgee + id: '00000419' + name: Bgee stage + namespaceEmbeddedInLui: false + pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ + prefix: bgee.stage + sampleId: HsapDO:0000004 + uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on + n2t: + description: Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. + example: HsapDO:0000004 + homepage: http://bgee.unil.ch/bgee/bgee + name: Bgee at Lausanne + namespaceEmbeddedInLui: false + pattern: ^(FBvd|XtroDO|HsapDO|MmusDO)\:\d+$ + prefix: bgee.stage + uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$1&stage_children=on + uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1 +bigg.compartment: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIGG.COMPARTMENT + uri_format: http://identifiers.org/bigg.compartment/$1 + mappings: + biocontext: BIGG.COMPARTMENT + miriam: bigg.compartment + n2t: bigg.compartment + miriam: + deprecated: false + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. + homepage: http://bigg.ucsd.edu/compartments/ + id: '00000555' + name: BiGG Compartment + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z]+$ + prefix: bigg.compartment + sampleId: c + uri_format: http://bigg.ucsd.edu/compartments/$1 + n2t: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. + example: c + homepage: http://bigg.ucsd.edu/compartments/ + name: BiGG Compartment at University of California + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z]+$ + prefix: bigg.compartment + uri_format: http://bigg.ucsd.edu/compartments/$1 +bigg.metabolite: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIGG.METABOLITE + uri_format: http://identifiers.org/bigg.metabolite/$1 + mappings: + biocontext: BIGG.METABOLITE + miriam: bigg.metabolite + n2t: bigg.metabolite + miriam: + deprecated: false + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes. + homepage: http://bigg.ucsd.edu/universal/metabolites + id: '00000556' + name: BiGG Metabolite + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.metabolite + sampleId: 12dgr161 + uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1 + n2t: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes. + example: 12dgr161 + homepage: http://bigg.ucsd.edu/universal/metabolites + name: BiGG Metabolite at University of Cakifornia + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.metabolite + uri_format: http://bigg.ucsd.edu/models/universal/metabolites/$1 +bigg.model: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIGG.MODEL + uri_format: http://identifiers.org/bigg.model/$1 + mappings: + biocontext: BIGG.MODEL + miriam: bigg.model + n2t: bigg.model + miriam: + deprecated: false + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. + homepage: http://bigg.ucsd.edu/models + id: '00000554' + name: BiGG Model + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.model + sampleId: iECABU_c1320 + uri_format: http://bigg.ucsd.edu/models/$1 + n2t: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. + example: iECABU_c1320 + homepage: http://bigg.ucsd.edu/models + name: BiGG Model at University of California + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.model + uri_format: http://bigg.ucsd.edu/models/$1 +bigg.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIGG.REACTION + uri_format: http://identifiers.org/bigg.reaction/$1 + mappings: + biocontext: BIGG.REACTION + miriam: bigg.reaction + n2t: bigg.reaction + miriam: + deprecated: false + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. + homepage: http://bigg.ucsd.edu/universal/reactions + id: '00000557' + name: BiGG Reaction + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.reaction + sampleId: 13GS + uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1 + n2t: + description: BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. + example: 13GS + homepage: http://bigg.ucsd.edu/universal/reactions + name: BiGG Reaction at University of California + namespaceEmbeddedInLui: false + pattern: ^[a-z_A-Z0-9]+$ + prefix: bigg.reaction + uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1 +bila: + biocontext: + is_identifiers: false + is_obo: true + prefix: BILA + uri_format: http://purl.obolibrary.org/obo/BILA_$1 + deprecated: true + fairsharing: + abbreviation: BILA + description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. + id: '1035' + name: Bilateria anatomy + prefix: FAIRsharing.eqgjeq + mappings: + biocontext: BILA + fairsharing: FAIRsharing.eqgjeq + obofoundry: + name: Bilateria anatomy + prefix: bila +bindingdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: BINDINGDB + uri_format: http://identifiers.org/bindingDB/$1 + fairsharing: + abbreviation: BindingDB + description: BindingDB enables research by making a growing collection of high-quality, quantitative, protein-ligand binding data findable and usable. Funded by NIGMS/NIH. + id: '1772' + name: BindingDB database of measured binding affinities + prefix: FAIRsharing.3b36hk + subjects: + - Drug Discovery + - Chemistry + - Life Science + - Computational Chemistry + - Medicinal Chemistry + mappings: + biocontext: BINDINGDB + fairsharing: FAIRsharing.3b36hk + miriam: bindingdb + n2t: bindingdb + prefixcommons: bindingdb + uniprot: BindingDB + miriam: + deprecated: false + description: BindingDB is the first public database of protein-small molecule affinity data. + homepage: https://www.bindingdb.org + id: '00000264' + name: BindingDB + namespaceEmbeddedInLui: false + pattern: ^\w\d+$ + prefix: bindingdb + sampleId: e999 + uri_format: http://www.bindingdb.org/compact/$1 + n2t: + description: BindingDB is the first public database of protein-small molecule affinity data. + example: e999 + homepage: https://www.bindingdb.org + name: BindingDB + namespaceEmbeddedInLui: false + pattern: ^\w\d+$ + prefix: bindingdb + uri_format: http://www.bindingdb.org/compact/$1 + prefixcommons: + description: BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. + example: '22360' + homepage: http://www.bindingdb.org + keywords: + - protein + - interaction + name: BindingDB database of measured binding affinities + pattern: ^\d+$ + prefix: bindingdb + pubmed_ids: + - '17145705' + uri_format: http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$1 + uniprot: + category: Chemistry databases + identifier: '127' + link_is_explicit: 'true' + name: BindingDB database of measured binding affinities + prefix: BindingDB + uri_format: https://www.bindingdb.org/uniprot/$1 +biocarta.pathway: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOCARTA.PATHWAY + uri_format: http://identifiers.org/biocarta.pathway/$1 + mappings: + biocontext: BIOCARTA.PATHWAY + miriam: biocarta.pathway + n2t: biocarta.pathway + miriam: + deprecated: false + description: BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. + homepage: https://www.biocarta.com/ + id: '00000421' + name: BioCarta Pathway + namespaceEmbeddedInLui: false + pattern: ^([hm]\_)?\w+Pathway$ + prefix: biocarta.pathway + sampleId: h_aktPathway + uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1 + n2t: + description: BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. + example: h_aktPathway + homepage: https://www.biocarta.com/ + name: BioCarta Pathway at NCI + namespaceEmbeddedInLui: false + pattern: ^([hm]\_)?\w+Pathway$ + prefix: biocarta.pathway + uri_format: https://cgap.nci.nih.gov/Pathways/BioCarta/$1 +biocatalogue.service: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOCATALOGUE.SERVICE + uri_format: http://identifiers.org/biocatalogue.service/$1 + mappings: + biocontext: BIOCATALOGUE.SERVICE + miriam: biocatalogue.service + n2t: biocatalogue.service + miriam: + deprecated: false + description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. + homepage: https://www.biocatalogue.org/ + id: '00000140' + name: BioCatalogue + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biocatalogue.service + sampleId: '614' + uri_format: https://www.biocatalogue.org/services/$1 + n2t: + description: The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. + example: '614' + homepage: https://www.biocatalogue.org/ + name: BioCatalogue at EMBL-EBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biocatalogue.service + uri_format: https://www.biocatalogue.org/services/$1 + name: BioCatalogue Service +biocyc: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOCYC + uri_format: http://identifiers.org/biocyc/$1 + go: + homepage: http://biocyc.org/ + name: BioCyc collection of metabolic pathway databases + prefix: BioCyc + uri_format: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=$1 + mappings: + biocontext: BIOCYC + go: BioCyc + miriam: biocyc + n2t: biocyc + prefixcommons: biocyc + uniprot: BioCyc + miriam: + deprecated: false + description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. + homepage: http://biocyc.org + id: '00000194' + name: BioCyc + namespaceEmbeddedInLui: false + pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ + prefix: biocyc + sampleId: ECOLI:CYT-D-UBIOX-CPLX + uri_format: http://biocyc.org/getid?id=$1 + n2t: + description: BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. + example: ECOLI:CYT-D-UBIOX-CPLX + homepage: http://biocyc.org + name: BioCyc at SRI International + namespaceEmbeddedInLui: false + pattern: ^[A-Z-0-9]+(\:)?[A-Za-z0-9+_.%-:]+$ + prefix: biocyc + uri_format: http://biocyc.org/getid?id=$1 + prefixcommons: + description: The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of different organisms. + example: ECOLI:CYT-D-UBIOX-CPLX + homepage: http://www.biocyc.org/ + keywords: + - genome + - pathway + - sequence + name: BioCyc Database Collection + pattern: ^\w+\:[A-Za-z0-9-]+$ + prefix: biocyc + pubmed_ids: + - '16246909' + uri_format: http://biocyc.org/ECOLI/NEW-IMAGE?object=$1 + uniprot: + category: Enzyme and pathway databases + identifier: '5' + link_is_explicit: 'true' + name: BioCyc Collection of Pathway/Genome Databases + prefix: BioCyc + uri_format: https://biocyc.org/getid?id=$1 +biogrid: + biocontext: + is_identifiers: false + is_obo: false + prefix: BIOGRID + uri_format: http://thebiogrid.org/$1 + fairsharing: + abbreviation: BioGRID + description: The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID currently holds over 1,740,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 70,000+ publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. All data are freely provided via our search index and available for download in many standardized formats. + id: '2028' + name: Biological General Repository for Interaction Datasets + prefix: FAIRsharing.9d5f5r + subjects: + - Cheminformatics + - Biochemistry + - Bioinformatics + - Chemical Biology + - Proteomics + - Life Science + - Systems Biology + mappings: + biocontext: BIOGRID + fairsharing: FAIRsharing.9d5f5r + miriam: biogrid + n2t: biogrid + prefixcommons: biogrid + uniprot: BioGRID + miriam: + deprecated: false + description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. + homepage: http://thebiogrid.org/ + id: '00000058' + name: BioGRID + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biogrid + sampleId: '31623' + uri_format: http://thebiogrid.org/$1 + n2t: + description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. + example: '31623' + homepage: http://thebiogrid.org/ + name: BioGRID database of physical and genetic interactions + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biogrid + uri_format: http://thebiogrid.org/$1 + prefixcommons: + description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. + example: '31623' + homepage: http://www.thebiogrid.org + keywords: + - protein + - gene + - interaction + name: Biological General Repository for Interaction Datasets + pattern: ^\d+$ + prefix: biogrid + pubmed_ids: + - '16381927' + uri_format: http://thebiogrid.org/$1 + twitter: biogrid + uniprot: + category: Protein-protein interaction databases + identifier: '184' + link_is_explicit: 'true' + name: The Biological General Repository for Interaction Datasets (BioGRID) + prefix: BioGRID + uri_format: https://thebiogrid.org/$1 +biogrid.interaction: + contact: + email: md.tyers@umontreal.ca + name: Mike Tyers + orcid: 0000-0002-9713-9994 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. + example: '2649230' + homepage: https://thebiogrid.org/ + name: BioGRID Interactions + part_of: biogrid + pattern: ^\d+$ + twitter: biogrid + uri_format: https://thebiogrid.org/interaction/$1 +biolegend: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: BioLegend is a life sciences supply vendor. + example: '3403' + homepage: https://www.biolegend.com + name: BioLegend + pattern: ^\d+$ + uri_format: https://www.biolegend.com/Default.aspx?ID=6664&productid=$1 +biolink: + biolink: + is_identifiers: false + is_obo: false + prefix: biolink + uri_format: https://w3id.org/biolink/vocab/$1 + bioportal: + name: Biolink Model + prefix: BIOLINK + fairsharing: + abbreviation: biolink + description: >- + A high level datamodel of biological entities (genes, diseases, + phenotypes, pathways, individuals, substances, etc) and their + associations. + + Biolink Model is designed as a way of standardizing types and relational structures in knowledge graphs (KGs), where the KG may be either a property graph or RDF triple store. + + + The schema is expressed as a YAML, which may be translated into a number of different representations including OWL, Python dataclasses, GraphQL and more. The schema assumes a property graph, where nodes represent individual entities, and edges represent relationship between entities. Biolink Model provides a schema for representing both nodes and edges. The model itself can be divided into a few parts: Entities (subjects and objects), Predicates (relationships between core concepts), Associations (statements including evidence and provenance), Entity Slots (node properties), and Edge Slots (edge properties). + id: '3649' + name: Biolink Model + prefix: FAIRsharing.ad9d85 + subjects: + - Functional Genomics + - Medical Biotechnology + - Biomedical Science + - Translational Medicine + - Medical Informatics + homepage: https://biolink.github.io/biolink-model/ + mappings: + biolink: biolink + bioportal: BIOLINK + fairsharing: FAIRsharing.ad9d85 + miriam: biolink + miriam: + deprecated: false + description: A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. + homepage: https://biolink.github.io/biolink-model + id: '00000782' + name: BioLink Model + namespaceEmbeddedInLui: false + pattern: ^\S+$ + prefix: biolink + sampleId: Gene + uri_format: https://w3id.org/biolink/vocab/$1 +biominder: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOMINDER + uri_format: http://identifiers.org/biominder/$1 + mappings: + biocontext: BIOMINDER + miriam: biominder + n2t: biominder + miriam: + deprecated: false + description: Database of the dielectric properties of biological tissues. + homepage: https://datalab.rwth-aachen.de/MINDER + id: '00000634' + name: Bio-MINDER Tissue Database + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\-]+$ + prefix: biominder + sampleId: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 + uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1 + n2t: + description: Database of the dielectric properties of biological tissues. + example: aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 + homepage: https://datalab.rwth-aachen.de/MINDER + name: Bio-MINDER Tissue Database + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\-]+$ + prefix: biominder + uri_format: https://datalab.rwth-aachen.de/MINDER/resource/$1 +biomodels.db: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOMODELS.DB + uri_format: http://identifiers.org/biomodels.db/$1 + go: + homepage: https://www.ebi.ac.uk/biomodels/ + name: BioModels Database + prefix: BIOMD + synonyms: + - BIOMDID + uri_format: https://www.ebi.ac.uk/biomodels/$1 + mappings: + biocontext: BIOMODELS.DB + go: BIOMD + miriam: biomodels.db + n2t: biomodels.db + miriam: + deprecated: false + description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. + homepage: https://www.ebi.ac.uk/biomodels/ + id: '00000007' + name: BioModels Database + namespaceEmbeddedInLui: false + pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ + prefix: biomodels.db + providers: + - code: CURATOR_REVIEW + description: Caltech mirror + homepage: http://biomodels.caltech.edu/ + name: Caltech mirror + uri_format: http://biomodels.caltech.edu/$1 + - code: omicsdi + description: BioModels through OmicsDI + homepage: https://www.omicsdi.org/ + name: BioModels through OmicsDI + uri_format: https://www.omicsdi.org/dataset/biomodels/$1 + sampleId: BIOMD0000000048 + uri_format: https://www.ebi.ac.uk/biomodels/$1 + n2t: + description: BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. + example: BIOMD0000000048 + homepage: https://www.ebi.ac.uk/biomodels/ + name: BioModels Database + namespaceEmbeddedInLui: false + pattern: ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ + prefix: biomodels.db + uri_format: https://www.ebi.ac.uk/biomodels/$1 + synonyms: + - BIOMD +biomodels.kisao: + biocontext: + is_identifiers: false + is_obo: true + prefix: KISAO + uri_format: http://purl.obolibrary.org/obo/KISAO_$1 + bioportal: + name: Kinetic Simulation Algorithm Ontology + prefix: KISAO + fairsharing: + abbreviation: KiSAO + description: The Kinetic Simulation Algorithm Ontology aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. It describes and classifies existing algorithms and their inter-relationships through the algorithm characteristics and parameters. + id: '974' + name: Kinetic Simulation Algorithm Ontology + prefix: FAIRsharing.jcg19w + subjects: + - Bioinformatics + - Computer Science + mappings: + biocontext: KISAO + bioportal: KISAO + fairsharing: FAIRsharing.jcg19w + miriam: biomodels.kisao + n2t: biomodels.kisao + obofoundry: kisao + ols: kisao + ontobee: KISAO + prefixcommons: kisao + miriam: + deprecated: false + description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. + homepage: http://bioportal.bioontology.org/ontologies/KISAO + id: '00000108' + name: KiSAO + namespaceEmbeddedInLui: false + pattern: ^KISAO_\d+$ + prefix: biomodels.kisao + sampleId: KISAO_0000057 + uri_format: http://purl.bioontology.org/ontology/KISAO/kisao:$1 + n2t: + description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. + example: KISAO_0000057 + homepage: http://bioportal.bioontology.org/ontologies/KISAO + name: KiSAO via NCBO's Bioportal + namespaceEmbeddedInLui: false + pattern: ^KISAO_\d+$ + prefix: biomodels.kisao + uri_format: http://purl.bioontology.org/ontology/KISAO/kisao:$1 + obofoundry: + contact: jonrkarr@gmail.com + contact.github: jonrkarr + contact.label: Jonathan Karr + contact.orcid: 0000-0002-2605-5080 + deprecated: false + description: A classification of algorithms for simulating biology, their parameters, and their outputs + download.owl: http://purl.obolibrary.org/obo/kisao.owl + homepage: https://github.com/SED-ML/KiSAO + license: Artistic License 2.0 + license.url: http://opensource.org/licenses/Artistic-2.0 + name: Kinetic Simulation Algorithm Ontology + preferredPrefix: KISAO + prefix: kisao + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22027554 + title: Controlled vocabularies and semantics in systems biology + repository: https://github.com/SED-ML/KiSAO + ols: + description: A classification of algorithms for simulating biology, their parameters, and their outputs + download: http://purl.obolibrary.org/obo/kisao.owl + homepage: https://github.com/SED-ML/KiSAO + name: Kinetic Simulation Algorithm Ontology + prefix: kisao + version: '2.30' + ontobee: + library: Library + name: Kinetic Simulation Algorithm Ontology + prefix: KISAO + preferred_prefix: biomodels.kisao + prefixcommons: + bioportal: '1410' + description: The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. + example: KISAO_0000057 + homepage: http://biomodels.net/kisao/ + keywords: + - ontology + name: Kinetic Simulation Algorithm Ontology + pattern: ^KISAO_\d+$ + prefix: kisao + synonyms: + - kisao +biomodels.teddy: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOMODELS.TEDDY + uri_format: http://identifiers.org/biomodels.teddy/$1 + bioportal: + name: Terminology for the Description of Dynamics + prefix: TEDDY + download_owl: http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl + example: '0000066' + fairsharing: + abbreviation: TEDDY + description: The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. + id: '923' + name: TErminology for the Description of DYnamics + prefix: FAIRsharing.w9jvbt + subjects: + - Neurophysiology + - Synthetic Biology + - Systems Biology + mappings: + biocontext: BIOMODELS.TEDDY + bioportal: TEDDY + fairsharing: FAIRsharing.w9jvbt + miriam: biomodels.teddy + n2t: biomodels.teddy + ols: teddy + prefixcommons: teddy + miriam: + deprecated: false + description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. + homepage: http://teddyontology.sourceforge.net/ + id: '00000107' + name: TEDDY + namespaceEmbeddedInLui: false + pattern: ^TEDDY_\d{7}$ + prefix: biomodels.teddy + sampleId: TEDDY_0000066 + uri_format: http://purl.bioontology.org/ontology/TEDDY/$1 + n2t: + description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. + example: TEDDY_0000066 + homepage: http://teddyontology.sourceforge.net/ + name: TEDDY through BioPortal + namespaceEmbeddedInLui: false + pattern: ^TEDDY_\d{7}$ + prefix: biomodels.teddy + uri_format: http://purl.bioontology.org/ontology/TEDDY/$1 + ols: + description: TEDDY is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems and Synthetic Biology. + download: http://www.biomodels.net/teddy/TEDDY + name: Terminology for Description of Dynamics + prefix: teddy + version: 2014-04-24 + version.iri: http://identifiers.org/combine.specifications/teddy.rel-2014-04-24 + pattern: ^\d+$ + prefixcommons: + bioportal: '1407' + description: The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. + example: TEDDY_0000066 + homepage: http://teddyontology.sourceforge.net/ + keywords: + - ontology + name: Terminology for the Description of Dynamics + pattern: ^TEDDY_\d{7}$ + prefix: teddy + synonyms: + - teddy + uri_format: https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1 +biomodels.vocabulary: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOMODELS.VOCABULARY + uri_format: http://identifiers.org/biomodels.vocabulary/$1 + mappings: + biocontext: BIOMODELS.VOCABULARY + miriam: biomodels.vocabulary + n2t: biomodels.vocabulary + miriam: + deprecated: false + description: Vocabulary used in the RDF representation of SBML models. + homepage: http://biomodels.net/rdf/vocabulary.rdf + id: '00000514' + name: SBML RDF Vocabulary + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+$ + prefix: biomodels.vocabulary + sampleId: rateRule + uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1 + n2t: + description: Vocabulary used in the RDF representation of SBML models. + example: rateRule + homepage: http://biomodels.net/rdf/vocabulary.rdf + name: Vocabulary via BioModels.net + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+$ + prefix: biomodels.vocabulary + uri_format: http://biomodels.net/rdf/vocabulary.rdf#$1 +bionumbers: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIONUMBERS + uri_format: http://identifiers.org/bionumbers/$1 + mappings: + biocontext: BIONUMBERS + miriam: bionumbers + n2t: bionumbers + prefixcommons: bionumbers + miriam: + deprecated: false + description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. + homepage: https://bionumbers.hms.harvard.edu + id: '00000101' + name: BioNumbers + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bionumbers + sampleId: '104674' + uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 + n2t: + description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. + example: '104674' + homepage: https://bionumbers.hms.harvard.edu + name: BioNumbers database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bionumbers + uri_format: https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 + prefixcommons: + description: BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. + example: '104674' + homepage: http://www.bionumbers.hms.harvard.edu/search.aspx + name: The Database of Useful Biological Numbers + pattern: ^\d+$ + prefix: bionumbers + uri_format: http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$1&ver=1 +bioportal: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOPORTAL + uri_format: http://identifiers.org/bioportal/$1 + fairsharing: + abbreviation: BioPortal + description: BioPortal is a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and Protégé frames and Rich Release Format. BioPortal groups ontologies by domain to aid discoverability and allows users to browse, search and visualize the content of ontologies. BioPortal also provides ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed. + id: '2290' + name: BioPortal + prefix: FAIRsharing.4m97ah + subjects: + - Life Science + - Ontology and Terminology + mappings: + biocontext: BIOPORTAL + fairsharing: FAIRsharing.4m97ah + miriam: bioportal + n2t: bioportal + prefixcommons: bioportal + miriam: + deprecated: false + description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. + homepage: http://bioportal.bioontology.org/ + id: '00000187' + name: BioPortal + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bioportal + sampleId: '1046' + uri_format: http://bioportal.bioontology.org/ontologies/$1 + n2t: + description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. + example: '1046' + homepage: http://bioportal.bioontology.org/ + name: BioPortal at National Center for Biomedical Ontology + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bioportal + uri_format: http://bioportal.bioontology.org/ontologies/$1 + prefixcommons: + description: BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. + example: '1046' + homepage: http://bioportal.bioontology.org/ + keywords: + - ontology + name: BioPortal + pattern: ^\d+$ + prefix: bioportal + pubmed_ids: + - '19483092' + uri_format: http://bioportal.bioontology.org/ontologies/$1 +bioproject: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOPROJECT + uri_format: http://identifiers.org/bioproject/$1 + fairsharing: + abbreviation: BioProject + description: A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. The BioProject database is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. + id: '2210' + name: NCBI BioProject + prefix: FAIRsharing.aqhv1y + subjects: + - Life Science + mappings: + biocontext: BIOPROJECT + fairsharing: FAIRsharing.aqhv1y + miriam: bioproject + n2t: bioproject + miriam: + deprecated: false + description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. + homepage: http://trace.ddbj.nig.ac.jp/bioproject/ + id: '00000349' + name: BioProject + namespaceEmbeddedInLui: false + pattern: ^PRJ[DEN][A-Z]\d+$ + prefix: bioproject + providers: + - code: ncbi + description: BioProject at NCBI + homepage: https://www.ncbi.nlm.nih.gov/bioproject + name: BioProject at NCBI + uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1 + - code: ebi + description: BioProject at European Nucleotide Archive (ENA) + homepage: https://www.ebi.ac.uk/ena/ + name: BioProject at European Nucleotide Archive (ENA) + uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 + sampleId: PRJDB3 + uri_format: http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$1 + n2t: + description: BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. + example: PRJDB3 + homepage: https://www.ncbi.nlm.nih.gov/bioproject + name: BioProject at NCBI + namespaceEmbeddedInLui: false + pattern: ^PRJ[DEN][A-Z]\d+$ + prefix: bioproject + uri_format: https://www.ncbi.nlm.nih.gov/bioproject?term=$1 + uri_format: https://www.ncbi.nlm.nih.gov/bioproject/?term=$1 +bioregistry: + contact: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database. + example: bioregistry + homepage: https://bioregistry.io + name: Bioregistry + uri_format: https://bioregistry.io/registry/$1 +bioregistry.collection: + contact: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Manually curated collections of resources stored in the bioregistry + example: '0000001' + homepage: https://bioregistry.io/collection + name: Bioregistry Collections + pattern: ^\d{7}$ + uri_format: https://bioregistry.io/collection/$1 +bioregistry.registry: + contact: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Bioregistry's meta-registry + example: miriam + homepage: https://bioregistry.io/metaregistry/ + name: Bioregistry Metaregistry + uri_format: https://bioregistry.io/metaregistry/$1 +bioregistry.schema: + contact: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Schema for the export of the Bioregistry as RDF + example: '0000001' + homepage: https://bioregistry.io/schema + name: Bioregistry Schema + pattern: ^\d{7}$ + uri_format: https://bioregistry.io/schema/#$1 +biorxiv: + description: The bioRxiv is a preprint server for biology + example: 2021.07.23.453588 + example_extras: + - '000091' + - 000091v1 + - 2022.01.24.477526v1 + go: + homepage: https://www.biorxiv.org/ + name: bioRxiv + prefix: bioRxiv + synonyms: + - BIORXIV + uri_format: https://www.biorxiv.org/content/$1 + homepage: https://biorxiv.org + mappings: + go: bioRxiv + scholia: biorxiv + name: bioRxiv + pattern: ^(\d{4}\.\d{2}\.\d{2}\.)?\d{6,8}(v\d{1,3})?$ + uri_format: https://www.biorxiv.org/content/10.1101/$1 +biosample: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOSAMPLE + uri_format: http://identifiers.org/biosample/$1 + cellosaurus: + category: Biological sample resources + homepage: https://www.ebi.ac.uk/biosamples/ + name: BioSamples database + prefix: BioSamples + uri_format: https://www.ebi.ac.uk/biosamples/samples/$1 + fairsharing: + abbreviation: BioSample + description: The NCBI BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials from which data stored in NCBI’s primary data archives are derived. NCBI’s archives host data from diverse types of samples from any species, so the BioSample database is similarly diverse; typical examples of a BioSample include a cell line, a primary tissue biopsy, an individual organism or an environmental isolate. The BioSample database promotes the use of structured and consistent attribute names and values that describe what the samples are as well as information about their provenance, where appropriate. + id: '2211' + name: NCBI BioSample + prefix: FAIRsharing.qr6pqk + subjects: + - Biology + mappings: + biocontext: BIOSAMPLE + cellosaurus: BioSamples + fairsharing: FAIRsharing.qr6pqk + miriam: biosample + n2t: biosample + miriam: + deprecated: false + description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. + homepage: https://www.ebi.ac.uk/biosamples/ + id: '00000350' + name: BioSample + namespaceEmbeddedInLui: false + pattern: ^SAM[NED](\w)?\d+$ + prefix: biosample + providers: + - code: ncbi + description: BioSample at NCBI + homepage: http://www.ncbi.nlm.nih.gov/biosample + name: BioSample at NCBI + uri_format: http://www.ncbi.nlm.nih.gov/biosample?term=$1 + - code: CURATOR_REVIEW + description: BioSample at DNA Data Bank of Japan + homepage: http://trace.ddbj.nig.ac.jp/biosample/ + name: BioSample at DNA Data Bank of Japan + uri_format: http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1 + sampleId: SAMEA2397676 + uri_format: https://www.ebi.ac.uk/biosamples/sample/$1 + n2t: + description: The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. + example: SAMEA2397676 + homepage: https://www.ebi.ac.uk/biosamples/ + name: BioSamples Database at EBI + namespaceEmbeddedInLui: false + pattern: ^SAM[NED](\w)?\d+$ + prefix: biosample + uri_format: https://www.ebi.ac.uk/biosamples/sample/$1 + synonyms: + - biosamples +biosimulations: + mappings: + miriam: biosimulations + miriam: + deprecated: false + description: BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools. + homepage: https://icahn.mssm.edu/ + id: '00000880' + name: biosimulations + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9_-]{3,}$ + prefix: biosimulations + sampleId: Yeast-cell-cycle-Irons-J-Theor-Biol-2009 + uri_format: https://biosimulations.org/projects/$1 +biosimulators: + fairsharing: + abbreviation: BioSimulators + description: BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. + id: '3207' + name: BioSimulators + prefix: FAIRsharing.pwEima + subjects: + - Computational Biology + - Systems Biology + mappings: + fairsharing: FAIRsharing.pwEima + miriam: biosimulators + miriam: + deprecated: false + description: BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML). + homepage: https://biosimulators.org/ + id: '00000767' + name: BioSimulators + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9-_]+' + prefix: biosimulators + sampleId: vcell + uri_format: https://biosimulators.org/simulators/$1 +biostudies: + fairsharing: + abbreviation: BioStudies + description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. + id: '2507' + name: BioStudies + prefix: FAIRsharing.mtjvme + subjects: + - Life Science + - Biomedical Science + mappings: + fairsharing: FAIRsharing.mtjvme + miriam: biostudies + n2t: biostudies + miriam: + deprecated: false + description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. + homepage: https://www.ebi.ac.uk/biostudies/ + id: '00000694' + name: BioStudies database + namespaceEmbeddedInLui: false + pattern: ^S-[A-Z]{4}[A-Z\d\-]+$ + prefix: biostudies + sampleId: S-EPMC6266652 + uri_format: https://www.ebi.ac.uk/biostudies/studies/$1 + n2t: + description: The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication. + example: S-EPMC6266652 + homepage: https://www.ebi.ac.uk/biostudies/ + name: BioStudies database + namespaceEmbeddedInLui: false + pattern: ^S-[A-Z]{4}[A-Z\d\-]+$ + prefix: biostudies + uri_format: https://www.ebi.ac.uk/biostudies/studies/$1 +biosystems: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOSYSTEMS + uri_format: http://identifiers.org/biosystems/$1 + fairsharing: + abbreviation: BioSystems + description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information on genes, proteins and small molecules of biosystems. + id: '1964' + name: NCBI BioSystems Database + prefix: FAIRsharing.w2eeqr + subjects: + - Biology + - Systems Biology + mappings: + biocontext: BIOSYSTEMS + fairsharing: FAIRsharing.w2eeqr + miriam: biosystems + n2t: biosystems + prefixcommons: biosystems + miriam: + deprecated: false + description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. + homepage: https://www.ncbi.nlm.nih.gov/biosystems/ + id: '00000097' + name: BioSystems + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biosystems + sampleId: '001' + uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1 + n2t: + description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. + example: '001' + homepage: https://www.ncbi.nlm.nih.gov/biosystems/ + name: BioSystems database at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biosystems + uri_format: https://www.ncbi.nlm.nih.gov/biosystems/$1 + prefixcommons: + description: The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. + example: '1' + homepage: http://www.ncbi.nlm.nih.gov/biosystems/ + keywords: + - molecules + - pathways + name: BioSystems + pattern: ^\d+$ + prefix: biosystems + pubmed_ids: + - '19854944' + uri_format: http://www.ncbi.nlm.nih.gov/biosystems/$1 +biotools: + biocontext: + is_identifiers: true + is_obo: false + prefix: BIOTOOLS + uri_format: http://identifiers.org/biotools/$1 + description: BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research. + fairsharing: + abbreviation: bio.tools + description: bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources. + id: '3300' + name: bio.tools + prefix: FAIRsharing.63520c + subjects: + - Bioinformatics + - Biomedical Science + - Biology + mappings: + biocontext: BIOTOOLS + fairsharing: FAIRsharing.63520c + miriam: biotools + n2t: biotools + miriam: + deprecated: false + description: Tool and data services registry. + homepage: https://bio.tools/ + id: '00000616' + name: BioTools + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\_]*$ + prefix: biotools + sampleId: uniprotkb + uri_format: https://bio.tools/$1 + n2t: + description: Tool and data services registry. + example: uniprotkb + homepage: https://bio.tools/ + name: BioTools + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\_]*$ + prefix: biotools + uri_format: https://bio.tools/$1 + pattern: ^[-A-Za-z0-9\_]*$ +biozil: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Redistributor of bilogics and biomedical supplies + example: ls-c35719-120 + homepage: https://www.biozol.de/en + name: BIOZIL + uri_format: https://www.biozol.de/en/product/$1 +birnlex: + bioportal: + name: Biomedical Informatics Research Network Project Lexicon + prefix: BIRNLEX + comment: Part of the NeuroLex namespace now + description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. + example: birnlex_2023 + fairsharing: + abbreviation: BIRNLEX + description: The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. + id: '522' + name: Biomedical Informatics Research Network Project Lexicon + prefix: FAIRsharing.jedbbt + subjects: [] + homepage: https://bioportal.bioontology.org/ontologies/BIRNLEX + mappings: + bioportal: BIRNLEX + fairsharing: FAIRsharing.jedbbt + name: Biomedical Informatics Research Network Lexicon +bitbucket: + fairsharing: + abbreviation: Bitbucket + description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. It provides a number of different access levels, from free through to premium paid services. Users can create public or private repositories, the latter of which is restricted to 5 users under the free plan. + id: '3275' + name: Bitbucket + prefix: FAIRsharing.fc3431 + subjects: + - Knowledge and Information Systems + - Subject Agnostic + - Software Engineering + mappings: + fairsharing: FAIRsharing.fc3431 + miriam: bitbucket + miriam: + deprecated: false + description: Bitbucket is a Git-based source code repository hosting service owned by Atlassian. + homepage: https://www.atlassian.com/ + id: '00000899' + name: Bitbucket + namespaceEmbeddedInLui: false + pattern: ^[0-9A-Za-z-_\.]+/[0-9A-Za-z-_\.]+$ + prefix: bitbucket + sampleId: andreadega/systems-biology-compiler + uri_format: https://bitbucket.org/$1 +bitterdb.cpd: + biocontext: + is_identifiers: true + is_obo: false + prefix: BITTERDB.CPD + uri_format: http://identifiers.org/bitterdb.cpd/$1 + mappings: + biocontext: BITTERDB.CPD + miriam: bitterdb.cpd + n2t: bitterdb.cpd + miriam: + deprecated: false + description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. + homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php + id: '00000348' + name: BitterDB Compound + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bitterdb.cpd + sampleId: '46' + uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1 + n2t: + description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. + example: '46' + homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php + name: BitterDB Compound at The Hebrew University of Jerusalem + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bitterdb.cpd + uri_format: http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1 +bitterdb.rec: + biocontext: + is_identifiers: true + is_obo: false + prefix: BITTERDB.REC + uri_format: http://identifiers.org/bitterdb.rec/$1 + mappings: + biocontext: BITTERDB.REC + miriam: bitterdb.rec + n2t: bitterdb.rec + miriam: + deprecated: false + description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. + homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php + id: '00000347' + name: BitterDB Receptor + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bitterdb.rec + sampleId: '1' + uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1 + n2t: + description: BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. + example: '1' + homepage: http://bitterdb.agri.huji.ac.il/dbbitter.php + name: BitterDB Receptor at The Hebrew University of Jerusalem + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bitterdb.rec + uri_format: http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1 +bko: + bioportal: + name: Bricks ontology + prefix: BKO + comment: This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/. + contact: + email: adrienrougny@gmail.com + github: adrienrougny + name: Adrien Rougny + orcid: 0000-0002-2118-035X + contributor: + github: bgyori + name: Benjamin Gyori + orcid: 0000-0001-9439-5346 + description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way. + example: '0000204' + homepage: http://www.sbgnbricks.org/ + mappings: + bioportal: BKO + name: SBGN Bricks data and ontology + pattern: ^\d+$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1 +bmrb: + fairsharing: + abbreviation: BMRB + description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. + id: '2114' + name: Biological Magnetic Resonance Data Bank + prefix: FAIRsharing.p06nme + subjects: + - Structural Biology + mappings: + fairsharing: FAIRsharing.p06nme + miriam: bmrb + uniprot: BMRB + miriam: + deprecated: false + description: BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. + homepage: http://www.bmrb.wisc.edu/ + id: '00000716' + name: Biological Magnetic Resonance Data Bank + namespaceEmbeddedInLui: false + pattern: ^(bmr|bmse|bmst)?[0-9]{1,6}$ + prefix: bmrb + sampleId: '15000' + uri_format: http://rest.bmrb.wisc.edu/bmrb/$1/html + uniprot: + category: 3D structure databases + identifier: '256' + link_is_explicit: 'true' + name: Biological Magnetic Resonance Data Bank + prefix: BMRB + uri_format: https://bmrb.io/data_library/summary/protein.php?uniprot=$1 +bmrb.restraint: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively. + example: '28789' + homepage: https://restraintsgrid.bmrb.io/NRG/MRGridServlet + name: NMR Restraints Grid + pattern: ^\d+$ + uri_format: https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1 +bold.taxonomy: + biocontext: + is_identifiers: true + is_obo: false + prefix: BOLD.TAXONOMY + uri_format: http://identifiers.org/bold.taxonomy/$1 + mappings: + biocontext: BOLD.TAXONOMY + miriam: bold.taxonomy + n2t: bold.taxonomy + ncbi: BOLD + miriam: + deprecated: false + description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. + homepage: http://www.boldsystems.org/ + id: '00000158' + name: BOLD Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bold.taxonomy + sampleId: '27267' + uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 + n2t: + description: The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. + example: '27267' + homepage: http://www.boldsystems.org/ + name: BOLD taxonomy browser + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bold.taxonomy + uri_format: http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 + ncbi: + example: EPAF263 + homepage: http://www.barcodinglife.com + name: Barcode of Life database + prefix: BOLD +bootstrep: + biocontext: + is_identifiers: false + is_obo: true + prefix: BOOTSTREP + uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1 + mappings: + biocontext: BOOTSTREP + obofoundry: bootstrep + obofoundry: + contact: vlee@ebi.ac.uk + contact.label: Vivian Lee + deprecated: true + homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html + name: Gene Regulation Ontology + prefix: bootstrep +bpdb: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'Database of biopesticides maintained by the University of Hertfordshire ' + example: '2404' + homepage: https://sitem.herts.ac.uk/aeru/bpdb/index.htm + name: Bio-Pesticides DataBase + pattern: ^\d+$ + uri_format: https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm +brenda: + biocontext: + is_identifiers: true + is_obo: false + prefix: BRENDA + uri_format: http://identifiers.org/brenda/$1 + fairsharing: + abbreviation: BRENDA + description: BRENDA is the main collection of enzyme functional data available to the scientific community. + id: '1789' + name: BRENDA Enzyme Database + prefix: FAIRsharing.etp533 + subjects: + - Life Science + go: + homepage: http://www.brenda-enzymes.info + name: BRENDA, The Comprehensive Enzyme Information System + prefix: BRENDA + uri_format: https://www.brenda-enzymes.info/enzyme.php?ecno=$1 + mappings: + biocontext: BRENDA + fairsharing: FAIRsharing.etp533 + go: BRENDA + miriam: brenda + n2t: brenda + prefixcommons: brenda + uniprot: BRENDA + miriam: + deprecated: false + description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. + homepage: https://www.brenda-enzymes.org/ + id: '00000071' + name: BRENDA + namespaceEmbeddedInLui: false + pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ + prefix: brenda + sampleId: 1.1.1.1 + uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 + n2t: + description: BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. + example: 1.1.1.1 + homepage: https://www.brenda-enzymes.org/ + name: Brenda enzyme database + namespaceEmbeddedInLui: false + pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ + prefix: brenda + uri_format: https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 + prefixcommons: + description: BRENDA is the main collection of enzyme functional data available to the scientific community. + example: 1.1.1.1 + homepage: http://www.brenda-enzymes.org + keywords: + - enzyme + name: The Comprehensive Enzyme Information System + pattern: ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ + prefix: brenda + pubmed_ids: + - '18984617' + uri_format: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 + uniprot: + category: Enzyme and pathway databases + identifier: '131' + link_is_explicit: 'true' + name: BRENDA Comprehensive Enzyme Information System + prefix: BRENDA + uri_format: https://www.brenda-enzymes.org/enzyme.php?ecno=%s&UniProtAcc=%u&OrganismID=%d +brenda.ligand: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Information for ligands in the BRENDA database. + example: '278' + homepage: https://www.brenda-enzymes.de/ligand.php + name: BRENDA Ligand + pattern: ^\d+$ + uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1 +brenda.ligandgroup: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Information for ligand groups (chemical classes). + example: '18030' + homepage: https://www.brenda-enzymes.de/ligand.php + name: BRENDA Ligand Group + pattern: ^\d+$ + uri_format: https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1 +broad: + biocontext: + is_identifiers: true + is_obo: false + prefix: BROAD + uri_format: http://identifiers.org/broad/$1 + mappings: + biocontext: BROAD + miriam: broad + n2t: broad + miriam: + deprecated: false + description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. + homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ + id: '00000438' + name: Broad Fungal Genome Initiative + namespaceEmbeddedInLui: false + pattern: ^S\d+$ + prefix: broad + sampleId: S7000002168151102 + uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 + n2t: + description: Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. + example: S7000002168151102 + homepage: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ + name: Broad Fungal Genome Initiative at Broad Institute + namespaceEmbeddedInLui: false + pattern: ^S\d+$ + prefix: broad + uri_format: https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 +bs: + comment: An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO). + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library. + download_obo: https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo + example: '00042' + homepage: https://github.com/The-Sequence-Ontology/SO-Ontologies + name: Biosapiens Protein Feature Ontology + pattern: ^\d+$ + repository: https://github.com/The-Sequence-Ontology/SO-Ontologies +bspo: + biocontext: + is_identifiers: false + is_obo: true + prefix: BSPO + uri_format: http://purl.obolibrary.org/obo/BSPO_$1 + bioportal: + name: Spatial Ontology + prefix: BSPO + download_obo: https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo + example: '0000029' + fairsharing: + abbreviation: BSPO + description: This ontology represents spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. + id: '1034' + name: Biological SPatial Ontology + prefix: FAIRsharing.newa3z + subjects: + - Anatomy + - Life Science + mappings: + biocontext: BSPO + bioportal: BSPO + fairsharing: FAIRsharing.newa3z + obofoundry: bspo + ols: bspo + ontobee: BSPO + obofoundry: + appears_in: + - aism + - colao + - fovt + - lepao + - zp + contact: cjmungall@lbl.gov + contact.github: cmungall + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + deprecated: false + description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces + download.obo: http://purl.obolibrary.org/obo/bspo.obo + download.owl: http://purl.obolibrary.org/obo/bspo.owl + homepage: https://github.com/obophenotype/biological-spatial-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Biological Spatial Ontology + preferredPrefix: BSPO + prefix: bspo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/25140222 + title: 'Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.' + repository: https://github.com/obophenotype/biological-spatial-ontology + ols: + description: An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. + download: http://purl.obolibrary.org/obo/bspo.owl + homepage: https://github.com/obophenotype/biological-spatial-ontology + name: Biological Spatial Ontology + prefix: bspo + version: 2021-10-13 + version.iri: http://purl.obolibrary.org/obo/bspo/releases/2021-10-13/bspo.owl + ontobee: + library: Library + name: Biological Spatial Ontology + prefix: BSPO + pattern: ^\d{7}$ +bto: + biocontext: + is_identifiers: false + is_obo: true + prefix: BTO + uri_format: http://purl.obolibrary.org/obo/BTO_$1 + bioportal: + name: BRENDA Tissue and Enzyme Source Ontology + prefix: BTO + cellosaurus: + category: Anatomy/cell type resources + homepage: https://bioportal.bioontology.org/ontologies/BTO + name: BRENDA Tissue Ontology + prefix: BTO + uri_format: https://bioportal.bioontology.org/ontologies/BTO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_$1 + example: '0000590' + fairsharing: + abbreviation: BTO + description: A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. + id: '1' + name: BRENDA tissue / enzyme source + prefix: FAIRsharing.1414v8 + subjects: + - Enzymology + - Life Science + go: + description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. + name: BRENDA tissue / enzyme ontology + prefix: BTO + mappings: + biocontext: BTO + bioportal: BTO + cellosaurus: BTO + fairsharing: FAIRsharing.1414v8 + go: BTO + miriam: bto + n2t: bto + obofoundry: bto + ols: bto + ontobee: BTO + prefixcommons: bto + wikidata: P5501 + miriam: + deprecated: false + description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. + homepage: https://www.ebi.ac.uk/ols/ontologies/bto + id: '00000111' + name: Brenda Tissue Ontology + namespaceEmbeddedInLui: true + pattern: ^BTO:\d{7}$ + prefix: bto + sampleId: '0000146' + uri_format: https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1 + n2t: + description: The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. + example: '0000146' + homepage: http://bioportal.bioontology.org/ontologies/BTO + name: Brenda Tissue Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^BTO:\d{7}$ + prefix: bto + uri_format: http://purl.bioontology.org/ontology/BTO/BTO:$1 + obofoundry: + contact: c.dudek@tu-braunschweig.de + contact.github: chdudek + contact.label: Christian-Alexander Dudek + contact.orcid: 0000-0001-9117-7909 + deprecated: false + description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. + download.json: http://purl.obolibrary.org/obo/bto.json + download.obo: http://purl.obolibrary.org/obo/bto.obo + download.owl: http://purl.obolibrary.org/obo/bto.owl + homepage: http://www.brenda-enzymes.org + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: BRENDA tissue / enzyme source + preferredPrefix: BTO + prefix: bto + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/21030441 + title: 'The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources' + repository: https://github.com/BRENDA-Enzymes/BTO + ols: + description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. + download: http://purl.obolibrary.org/obo/bto.owl + name: The BRENDA Tissue Ontology (BTO) + prefix: bto + version: 2021-10-26 + version.iri: http://purl.obolibrary.org/obo/bto/releases/2021-10-26/bto.owl + ontobee: + library: Library + name: BRENDA tissue / enzyme source + prefix: BTO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1005' + description: The Brenda tissue ontology is a structured controlled vocabulary established to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. + example: BTO:0000146 + homepage: http://www.brenda-enzymes.info + keywords: + - obo + - tissue + name: BRENDA Tissue Ontology + pattern: ^BTO:\d{7}$ + prefix: bto + synonyms: + - BTO + wikidata: + database: Q4836352 + database.homepage: https://www.brenda-enzymes.org/ontology.php?ontology_id=3 + database.label: BRENDA tissue ontology + homepage: https://www.brenda-enzymes.org/ontology.php?ontology_id=3 + name: Brenda Tissue Ontology ID + pattern: BTO:\d+ + prefix: P5501 + uri_format: https://www.brenda-enzymes.org/ontology.php?ontology_id=3&id_go=$1 +bugbase.expt: + biocontext: + is_identifiers: true + is_obo: false + prefix: BUGBASE.EXPT + uri_format: http://identifiers.org/bugbase.expt/$1 + mappings: + biocontext: BUGBASE.EXPT + miriam: bugbase.expt + n2t: bugbase.expt + miriam: + deprecated: false + description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. + homepage: http://bugs.sgul.ac.uk/E-BUGS + id: '00000404' + name: BugBase Expt + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bugbase.expt + sampleId: '288' + uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view + n2t: + description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. + example: '288' + homepage: http://bugs.sgul.ac.uk/E-BUGS + name: BugBase Expt at University of London + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bugbase.expt + uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view +bugbase.protocol: + biocontext: + is_identifiers: true + is_obo: false + prefix: BUGBASE.PROTOCOL + uri_format: http://identifiers.org/bugbase.protocol/$1 + mappings: + biocontext: BUGBASE.PROTOCOL + miriam: bugbase.protocol + n2t: bugbase.protocol + miriam: + deprecated: false + description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. + homepage: http://bugs.sgul.ac.uk/E-BUGS + id: '00000403' + name: BugBase Protocol + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bugbase.protocol + sampleId: '67' + uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view + n2t: + description: BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. + example: '67' + homepage: http://bugs.sgul.ac.uk/E-BUGS + name: BugBase Protocol at University of London + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: bugbase.protocol + uri_format: http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view +bykdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: BYKDB + uri_format: http://identifiers.org/bykdb/$1 + fairsharing: + abbreviation: BYKdb + description: The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation. + id: '1557' + name: Bacterial protein tYrosine Kinase database + prefix: FAIRsharing.jr30xc + subjects: + - Life Science + mappings: + biocontext: BYKDB + fairsharing: FAIRsharing.jr30xc + miriam: bykdb + n2t: bykdb + prefixcommons: bykdb + miriam: + deprecated: false + description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. + homepage: https://bykdb.ibcp.fr/BYKdb/ + id: '00000253' + name: BYKdb + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: bykdb + sampleId: A0A009E7X8 + uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html + n2t: + description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. + example: A0A009E7X8 + homepage: https://bykdb.ibcp.fr/BYKdb/ + name: BYKdb at CNRS + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: bykdb + uri_format: https://bykdb.ibcp.fr/data/html/annotated/$1.html + name: Bacterial Tyrosine Kinase Database + prefixcommons: + description: The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. + example: A0AYT5 + homepage: http://bykdb.ibcp.fr/BYKdb/ + keywords: + - domain + - microbial + - sequence + name: Bacterial Tyrosine Kinase Database + pattern: ^\w+$ + prefix: bykdb + pubmed_ids: + - '22080550' + uri_format: http://bykdb.ibcp.fr/data/html/$1.html + provides: uniprot +cabri: + biocontext: + is_identifiers: true + is_obo: false + prefix: CABRI + uri_format: http://identifiers.org/cabri/$1 + fairsharing: + abbreviation: CABRI + description: CABRI provides an integrated resource including catalogues of strains of different organism types, genetic materials and other biologicals resources of European culture collections so that the user world-wide can access these relevant data during one searching session through a common entry point and get in touch with collections for ordering products to be delivered to their place of work. + id: '1815' + name: Common Access to Biological Resources and Information + prefix: FAIRsharing.qx2rvz + subjects: + - Molecular biology + - Medical Microbiology + - Applied Microbiology + - Virology + - Molecular Microbiology + - Microbiology + mappings: + biocontext: CABRI + fairsharing: FAIRsharing.qx2rvz + miriam: cabri + n2t: cabri + ncbi: CABRI + miriam: + deprecated: false + description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. + homepage: http://www.cabri.org/ + id: '00000261' + name: CABRI + namespaceEmbeddedInLui: false + pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ + prefix: cabri + providers: + - code: CURATOR_REVIEW + description: CABRI Cell Lines catalogue in Brussels (SRS) + homepage: http://www.be.cabri.org/ + name: CABRI Cell Lines catalogue in Brussels (SRS) + uri_format: http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] + sampleId: dsmz_mutz-id:ACC 291 + uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] + n2t: + description: CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. + example: dsmz_mutz-id:ACC 291 + homepage: http://www.cabri.org/ + name: CABRI Cell Lines catalogue in Genova (SRS) + namespaceEmbeddedInLui: false + pattern: ^([A-Za-z]+)?(\_)?([A-Za-z-]+)\:([A-Za-z0-9 ]+)$ + prefix: cabri + uri_format: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1] + ncbi: + example: ACC 424 + name: Common Access to Biological Resources and Information Project + prefix: CABRI +cadsr: + mappings: + miriam: cadsr + n2t: cadsr + miriam: + deprecated: false + description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. + homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki + id: '00000695' + name: Cancer Data Standards Registry and Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]*$ + prefix: cadsr + sampleId: '3771992' + uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1] + n2t: + description: The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR. + example: '3771992' + homepage: https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki + name: Cancer Data Standards Registry and Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]*$ + prefix: cadsr + uri_format: https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1] +caloha: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. + download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo + example: TS-0001 + homepage: https://github.com/calipho-sib/controlled-vocabulary + name: CALIPHO Group Ontology of Human Anatomy + pattern: ^TS-\d+$ + references: + - https://twitter.com/neXtProt_news/status/1350105997633867781 + repository: https://github.com/calipho-sib/controlled-vocabulary + twitter: neXtProt_news +cameo: + biocontext: + is_identifiers: true + is_obo: false + prefix: CAMEO + uri_format: http://identifiers.org/cameo/$1 + fairsharing: + abbreviation: CAMEO + description: Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. Benchmarking results are made available as reference data for methods development. + id: '2382' + name: Continuously Automated Model Evaluation + prefix: FAIRsharing.dq34p2 + subjects: + - Life Science + mappings: + biocontext: CAMEO + fairsharing: FAIRsharing.dq34p2 + miriam: cameo + n2t: cameo + miriam: + deprecated: false + description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. + homepage: https://cameo3d.org + id: '00000623' + name: CAMEO + namespaceEmbeddedInLui: false + pattern: ^[0-9\-_]+$ + prefix: cameo + sampleId: 2019-08-03_00000089_1 + uri_format: https://www.cameo3d.org/sp/targets/target/$1 + n2t: + description: The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. + example: 2018-03-24_00000030_1 + homepage: https://cameo3d.org + name: CAMEO + namespaceEmbeddedInLui: false + pattern: ^[0-9\-_]+$ + prefix: cameo + uri_format: https://www.cameo3d.org/sp/targets/target/$1 + name: Continuous Automated Model Evaluation +caps: + biocontext: + is_identifiers: true + is_obo: false + prefix: CAPS + uri_format: http://identifiers.org/caps/$1 + mappings: + biocontext: CAPS + miriam: caps + n2t: caps + miriam: + deprecated: false + description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. + homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home + id: '00000396' + name: CAPS-DB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: caps + sampleId: '434' + uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 + n2t: + description: CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. + example: '434' + homepage: http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home + name: CAPS-DB at Leeds Institute of Molecular Medicine + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: caps + uri_format: http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 +caro: + biocontext: + is_identifiers: false + is_obo: true + prefix: CARO + uri_format: http://purl.obolibrary.org/obo/CARO_$1 + bioportal: + name: Common Anatomy Reference Ontology + prefix: CARO + example: '0000000' + fairsharing: + abbreviation: CARO + description: The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. + id: '551' + name: Common Anatomy Reference Ontology + prefix: FAIRsharing.3kcgmr + subjects: + - Anatomy + - Life Science + go: + description: An upper ontology for anatomy used by OBO Foundry ontologies. Used to facilitate interoperability between existing anatomy ontologies for different species + name: Common Anatomy Reference Ontology + prefix: CARO + mappings: + biocontext: CARO + bioportal: CARO + fairsharing: FAIRsharing.3kcgmr + go: CARO + obofoundry: caro + ols: caro + ontobee: CARO + obofoundry: + appears_in: + - aism + - colao + - lepao + - pco + - ehdaa2 + contact: haendel@ohsu.edu + contact.github: mellybelly + contact.label: Melissa Haendel + contact.orcid: 0000-0001-9114-8737 + deprecated: false + description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species + download.owl: http://purl.obolibrary.org/obo/caro.owl + homepage: https://github.com/obophenotype/caro/ + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Common Anatomy Reference Ontology + preferredPrefix: CARO + prefix: caro + repository: https://github.com/obophenotype/caro + ols: + description: None + download: http://purl.obolibrary.org/obo/caro.owl + homepage: https://github.com/obophenotype/caro/ + name: Common Anatomy Reference Ontology + prefix: caro + version: 2022-02-18 + version.iri: http://purl.obolibrary.org/obo/caro/releases/2022-02-18/caro.owl + ontobee: + library: Library + name: Common Anatomy Reference Ontology + prefix: CARO + pattern: ^\d{7}$ +cas: + biocontext: + is_identifiers: true + is_obo: false + prefix: CAS + uri_format: http://identifiers.org/cas/$1 + cheminf: + description: Identifier used by the Chemical Abstracts Service database. + name: CAS registry number + obsolete: false + prefix: '000446' + fairsharing: + abbreviation: CAS RN + description: Identifier used by the Chemical Abstracts Service Registry. A CAS Registry Number is a numeric identifier that can contain up to 10 digits, divided by hyphens into three parts. The right-most digit is a check digit used to verify the validity and uniqueness of the entire number. + id: '381' + name: CAS Registry Number + prefix: FAIRsharing.r7Kwy7 + subjects: + - Cheminformatics + go: + description: CAS REGISTRY is the most authoritative collection of disclosed chemical substance information, containing more than 54 million organic and inorganic substances and 62 million sequences. CAS REGISTRY covers substances identified from the scientific literature from 1957 to the present, with additional substances going back to the early 1900s. + homepage: http://www.cas.org/expertise/cascontent/registry/index.html + name: CAS Chemical Registry + prefix: CAS + mappings: + biocontext: CAS + cheminf: '000446' + fairsharing: FAIRsharing.r7Kwy7 + go: CAS + miriam: cas + n2t: cas + prefixcommons: cas + scholia: cas + miriam: + deprecated: false + description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. + homepage: https://commonchemistry.cas.org/ + id: '00000237' + name: CAS + namespaceEmbeddedInLui: false + pattern: ^\d{1,7}\-\d{2}\-\d$ + prefix: cas + providers: + - code: scholia + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + homepage: https://scholia.toolforge.org/ + name: Scholia + uri_format: https://scholia.toolforge.org/cas/$1 + sampleId: 50-00-0 + uri_format: https://commonchemistry.cas.org/detail?ref=$1 + n2t: + description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. + example: 50-00-0 + homepage: http://commonchemistry.org + name: CAS through Common Chemistry + namespaceEmbeddedInLui: false + pattern: ^\d{1,7}\-\d{2}\-\d$ + prefix: cas + uri_format: http://commonchemistry.org/ChemicalDetail.aspx?ref=$1 + prefixcommons: + description: CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. + example: 50-00-0 + homepage: http://www.cas.org/ + keywords: + - chemical + - structure + name: 'CAS: A Divison of the American Chemical Society' + pattern: ^\d{1,7}\-\d{2}\-\d$ + prefix: cas + uri_format: http://commonchemistry.org/ChemicalDetail.aspx?ref=$1 + synonyms: + - CASID + - CAS_RN + - SECONDARY_CAS_RN + - cas_id + wikidata: + prefix: P231 +casspc: + comment: Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape. + contributor: + email: benjamin_gyori@hms.harvard.edu + github: bgyori + name: Benjamin M. Gyori + orcid: 0000-0001-9439-5346 + contributor_extras: + - email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + example: '5359' + go: + homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp + name: Catalog of Fishes species database + prefix: CASSPC + synonyms: + - CAS_SPC + uri_format: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1 + homepage: https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp + mappings: + go: CASSPC + name: Eschmeyer's Catalog of Fishes + pattern: ^\d+$ +cath: + biocontext: + is_identifiers: true + is_obo: false + prefix: CATH + uri_format: http://identifiers.org/cath/$1 + fairsharing: + abbreviation: CATH + description: The CATH database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It provides a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). + id: '2082' + name: CATH + prefix: FAIRsharing.xgcyyn + subjects: + - Evolutionary Biology + - Biology + mappings: + biocontext: CATH + fairsharing: FAIRsharing.xgcyyn + miriam: cath + n2t: cath + prefixcommons: cath + miriam: + deprecated: false + description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. + homepage: http://www.cathdb.info + id: '00000612' + name: CATH Protein Structural Domain Superfamily + namespaceEmbeddedInLui: false + pattern: ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ + prefix: cath + sampleId: 1.10.8.10 + uri_format: http://www.cathdb.info/cathnode/$1 + n2t: + description: CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. + example: 1.10.8.10 + homepage: http://www.cathdb.info + name: CATH Node through UCL + namespaceEmbeddedInLui: false + pattern: ^[1-4]\.[0-9]+\.[0-9]+\.[0-9]+$ + prefix: cath + uri_format: http://www.cathdb.info/cathnode/$1 + prefixcommons: + description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This collection is concerned with superfamily classification. + example: '3.15' + homepage: http://www.cathdb.info/ + keywords: + - classification + - protein + - structure + name: CATH Protein Structure Classification + pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ + prefix: cath + pubmed_ids: + - '9309224' + uri_format: http://www.cathdb.info/cathnode/$1 +cath.domain: + biocontext: + is_identifiers: true + is_obo: false + prefix: CATH.DOMAIN + uri_format: http://identifiers.org/cath.domain/$1 + mappings: + biocontext: CATH.DOMAIN + miriam: cath.domain + n2t: cath.domain + miriam: + deprecated: false + description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. + homepage: http://www.cathdb.info/ + id: '00000210' + name: CATH domain + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: cath.domain + sampleId: 1cukA01 + uri_format: http://www.cathdb.info/domain/$1 + n2t: + description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. + example: 1cukA01 + homepage: http://www.cathdb.info/ + name: CATH domain at UCL + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: cath.domain + uri_format: http://www.cathdb.info/domain/$1 +cath.superfamily: + biocontext: + is_identifiers: true + is_obo: false + prefix: CATH.SUPERFAMILY + uri_format: http://identifiers.org/cath.superfamily/$1 + mappings: + biocontext: CATH.SUPERFAMILY + miriam: cath.superfamily + n2t: cath.superfamily + miriam: + deprecated: false + description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. + homepage: http://www.cathdb.info/ + id: '00000209' + name: CATH superfamily + namespaceEmbeddedInLui: false + pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ + prefix: cath.superfamily + sampleId: 1.10.10.200 + uri_format: http://www.cathdb.info/cathnode/$1 + n2t: + description: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. + example: 1.10.10.200 + homepage: http://www.cathdb.info/ + name: CATH superfamily at UCL + namespaceEmbeddedInLui: false + pattern: ^\d+(\.\d+(\.\d+(\.\d+)?)?)?$ + prefix: cath.superfamily + uri_format: http://www.cathdb.info/cathnode/$1 + part_of: cath +cattleqtldb: + biocontext: + is_identifiers: true + is_obo: false + prefix: CATTLEQTLDB + uri_format: http://identifiers.org/cattleqtldb/$1 + mappings: + biocontext: CATTLEQTLDB + miriam: cattleqtldb + n2t: cattleqtldb + prefixcommons: cattleqtldb + miriam: + deprecated: false + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. + homepage: https://www.animalgenome.org/QTLdb + id: '00000504' + name: Animal Genome Cattle QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cattleqtldb + sampleId: '4685' + uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 + n2t: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. + example: '4685' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/BT/index + name: Animal QTL Cattle at Iowa State University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cattleqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1 + part_of: qtldb + prefixcommons: + description: This Cattle Quantitative Trait Locus (QTL) database (Cattle QTLdb) has gathered all cattle QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on cattle chromosomes the most feasible location for genes responsible for quantitative trait important to cattle production. + example: '66' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/BT/index + keywords: + - DNA + - genome + name: Cattle Quantitative Trait Locus database + pattern: ^\d+$ + prefix: cattleqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$1 +cazy: + biocontext: + is_identifiers: true + is_obo: false + prefix: CAZY + uri_format: http://identifiers.org/cazy/$1 + fairsharing: + abbreviation: CAZy + description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. + id: '1834' + name: The Carbohydrate-Active enZYmes Database + prefix: FAIRsharing.ntyq70 + subjects: + - Life Science + - Glycomics + go: + description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. + homepage: http://www.cazy.org/ + name: Carbohydrate Active EnZYmes + prefix: CAZY + uri_format: http://www.cazy.org/$1.html + mappings: + biocontext: CAZY + fairsharing: FAIRsharing.ntyq70 + go: CAZY + miriam: cazy + n2t: cazy + prefixcommons: cazy + uniprot: CAZy + miriam: + deprecated: false + description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. + homepage: http://www.cazy.org/ + id: '00000195' + name: CAZy + namespaceEmbeddedInLui: false + pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ + prefix: cazy + sampleId: GT10 + uri_format: http://www.cazy.org/$1.html + n2t: + description: The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. + example: GT10 + homepage: http://www.cazy.org/ + name: CAZy at CNRS + namespaceEmbeddedInLui: false + pattern: ^(GT|GH|PL|CE|CBM)\d+(\_\d+)?$ + prefix: cazy + uri_format: http://www.cazy.org/$1.html + prefixcommons: + description: The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. + example: GT10 + homepage: http://www.cazy.org/ + keywords: + - classification + - polysaccharide + name: The Carbohydrate-Active enZYmes Database + pattern: ^GT\d+$ + prefix: cazy + pubmed_ids: + - '18838391' + uri_format: http://www.cazy.org/$1.html + uniprot: + category: Protein family/group databases + identifier: '136' + link_is_explicit: 'true' + name: Carbohydrate-Active enZymes + prefix: CAZy + uri_format: http://www.cazy.org/fam/$1.html +cba: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.' + example: '375364' + homepage: http://www.cba.ac.cn + name: Chinese Biological Abstracts + pattern: ^\d+$ + uri_format: https://europepmc.org/article/CBA/$1 +cbioportal: + fairsharing: + abbreviation: cBioPortal + description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. + id: '2605' + name: cBioPortal for Cancer Genomics + prefix: FAIRsharing.6L6MjA + subjects: + - Genomics + - Proteomics + - Biomedical Science + - Preclinical Studies + mappings: + fairsharing: FAIRsharing.6L6MjA + miriam: cbioportal + n2t: cbioportal + miriam: + deprecated: false + description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. + homepage: http://www.cbioportal.org + id: '00000679' + name: The cBioPortal for Cancer Genomics + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\_]+$ + prefix: cbioportal + sampleId: laml_tcga_pub + uri_format: http://www.cbioportal.org/study?id=$1#summary + n2t: + description: The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets. + example: laml_tcga_pub + homepage: http://www.cbioportal.org + name: The cBioPortal for Cancer Genomics + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\_]+$ + prefix: cbioportal + uri_format: http://www.cbioportal.org/study?id=$1#summary + uri_format: https://www.cbioportal.org/study/summary?id=$1 +ccdc: + mappings: + miriam: ccdc + miriam: + deprecated: false + description: The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC. + homepage: https://www.ccdc.cam.ac.uk/ + id: '00000818' + name: CCDC Number + namespaceEmbeddedInLui: false + pattern: ^\d{6,7}$ + prefix: ccdc + sampleId: '1829126' + uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG +ccds: + biocontext: + is_identifiers: false + is_obo: false + prefix: CCDS + uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 + fairsharing: + abbreviation: CCDS + description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. + id: '1966' + name: The Consensus CDS + prefix: FAIRsharing.46s4nt + subjects: + - Life Science + mappings: + biocontext: CCDS + fairsharing: FAIRsharing.46s4nt + miriam: ccds + n2t: ccds + prefixcommons: ccds + uniprot: CCDS + miriam: + deprecated: false + description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. + homepage: http://www.ncbi.nlm.nih.gov/CCDS/ + id: '00000375' + name: Consensus CDS + namespaceEmbeddedInLui: false + pattern: ^CCDS\d+\.\d+$ + prefix: ccds + sampleId: CCDS13573.1 + uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 + n2t: + description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. + example: CCDS13573.1 + homepage: http://www.ncbi.nlm.nih.gov/CCDS/ + name: Consensus CDS at NCBI + namespaceEmbeddedInLui: false + pattern: ^CCDS\d+\.\d+$ + prefix: ccds + uri_format: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 + prefixcommons: + description: The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. + example: '4824' + homepage: http://www.ncbi.nlm.nih.gov/CCDS/ + keywords: + - protein + - gene + name: The Consensus CDS + pattern: ^\d+$ + prefix: ccds + pubmed_ids: + - '19498102' + uri_format: http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1 + uniprot: + category: Sequence databases + identifier: '187' + link_is_explicit: 'true' + name: The Consensus CDS (CCDS) project + prefix: CCDS + uri_format: https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=$1 +ccle: + cellosaurus: + category: Cell line databases/resources + homepage: https://portals.broadinstitute.org/ccle + name: Cancer Cell Line Encyclopedia + prefix: CCLE + uri_format: https://portals.broadinstitute.org/ccle/page?cell_line=$1 + description: Datasets around different cancer cell lines generated by the Broad Institute and Novartis + example: BT20_BREAST + homepage: https://www.cbioportal.org/study/summary?id=ccle_broad_2019 + mappings: + cellosaurus: CCLE + name: Cancer Cell Line Encyclopedia Cells + synonyms: + - ccle.cell + uri_format: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1 +cco: + banana: CCO + biocontext: + is_identifiers: true + is_obo: false + prefix: CCO + uri_format: http://identifiers.org/cco/$1 + bioportal: + name: Cell Cycle Ontology + prefix: CCO + download_obo: https://www.bio.ntnu.no/ontology/CCO/cco.obo + download_owl: https://www.bio.ntnu.no/ontology/CCO/cco.owl + fairsharing: + abbreviation: CCO + description: CCO contains genes, proteins, interactions (comprising genes or proteins that participate in them), processes from the cell cycle subtree of GO, molecular functions (GO), taxa, and ontological constructs (like an upper level ontology and relationships) to stick everything together. + id: '1237' + name: Cell Cycle Ontology + prefix: FAIRsharing.xhwrnr + subjects: + - Functional Genomics + - Genomics + - Proteomics + - Life Science + mappings: + biocontext: CCO + bioportal: CCO + fairsharing: FAIRsharing.xhwrnr + miriam: cco + n2t: cco + ols: cco + prefixcommons: cco + miriam: + deprecated: false + description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. + homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO + id: '00000234' + name: Cell Cycle Ontology + namespaceEmbeddedInLui: true + pattern: ^CCO\:\w+$ + prefix: cco + sampleId: '0000003' + uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1 + n2t: + description: The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. + example: '0000003' + homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO + name: Cell Cycle Ontology through OLS + namespaceEmbeddedInLui: true + pattern: ^CCO\:\w+$ + prefix: cco + uri_format: https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1 + ols: + contact: vladimir.n.mironov@gmail.com + description: The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects. + download: http://www.bio.ntnu.no/ontology/CCO/cco.owl + homepage: http://www.semantic-systems-biology.org/apo + name: Cell Cycle Ontology + prefix: cco + version: 2016-03-23 + pattern: ^\w+$ + prefixcommons: + bioportal: '1507' + description: An application ontology integrating knowledge about the eukaryotic cell cycle. + example: CCO:P0000023 + homepage: http://www.semantic-systems-biology.org/cco/ + keywords: + - obo + - cell cycle + name: Cell Cycle Ontology + pattern: ^CCO\:\w+$ + prefix: cco + pubmed_ids: + - '19480664' +ccrid: + cellosaurus: + category: Cell line databases/resources + homepage: http://cellresource.cn/ + name: Chinese Cell Resource Information Database + prefix: CCRID + uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: 4201PAT-CCTCC00348 + homepage: http://www.cellresource.cn + mappings: + cellosaurus: CCRID + name: National Experimental Cell Resource Sharing Platform + uri_format: http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 +cdao: + biocontext: + is_identifiers: false + is_obo: true + prefix: CDAO + uri_format: http://purl.obolibrary.org/obo/CDAO_$1 + bioportal: + name: Comparative Data Analysis Ontology + prefix: CDAO + example: '0000072' + fairsharing: + abbreviation: CDAO + description: Comparative Data Analysis Ontology (CDAO) is a formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). + id: '1155' + name: Comparative Data Analysis Ontology + prefix: FAIRsharing.kay31r + subjects: + - Molecular biology + - Bioinformatics + - Taxonomy + - Phylogenetics + - Evolutionary Biology + - Life Science + - Biomedical Science + mappings: + biocontext: CDAO + bioportal: CDAO + fairsharing: FAIRsharing.kay31r + obofoundry: cdao + ols: cdao + ontobee: CDAO + obofoundry: + contact: balhoff@renci.org + contact.github: balhoff + contact.label: Jim Balhoff + contact.orcid: 0000-0002-8688-6599 + deprecated: false + description: a formalization of concepts and relations relevant to evolutionary comparative analysis + download.owl: http://purl.obolibrary.org/obo/cdao.owl + homepage: https://github.com/evoinfo/cdao + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Comparative Data Analysis Ontology + preferredPrefix: CDAO + prefix: cdao + publications: + - id: https://doi.org/10.4137/EBO.S2320 + title: Initial Implementation of a Comparative Data Analysis Ontology + repository: https://github.com/evoinfo/cdao + ols: + description: The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. + download: http://purl.obolibrary.org/obo/cdao.owl + homepage: https://github.com/evoinfo/cdao + name: Comparative Data Analysis Ontology + prefix: cdao + version: 2019-06-26 + version.iri: http://purl.obolibrary.org/obo/cdao/2019-06-26/cdao.owl + ontobee: + library: Library + name: Comparative Data Analysis Ontology + prefix: CDAO + pattern: ^\d{7}$ +cdd: + biocontext: + is_identifiers: true + is_obo: false + prefix: CDD + uri_format: http://identifiers.org/cdd/$1 + fairsharing: + abbreviation: CDD + description: The Canadian Disaster Database (CDD) contains detailed disaster information on more than 1000 natural, technological and conflict events (excluding war) that have happened since 1900 at home or abroad and that have directly affected Canadians. The database describes where and when a disaster occurred, the number of injuries, evacuations, and fatalities, as well as a rough estimate of the costs. As much as possible, the CDD contains primary data that is valid, current and supported by reliable and traceable sources, including federal institutions, provincial/territorial governments, non-governmental organizations and media sources. Data is updated and reviewed on a semi-annual basis. + id: '2804' + name: Canadian Disaster Database + prefix: FAIRsharing.ea287c + subjects: + - Geology + - Earth Science + go: + homepage: https://www.ncbi.nlm.nih.gov/cdd + name: Conserved Domain Database at NCBI + prefix: CDD + uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 + mappings: + biocontext: CDD + fairsharing: FAIRsharing.ea287c + go: CDD + miriam: cdd + n2t: cdd + ncbi: CDD + prefixcommons: cdd + uniprot: CDD + miriam: + deprecated: false + description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd + id: '00000119' + name: Conserved Domain Database + namespaceEmbeddedInLui: false + pattern: ^(cd)?\d{5}$ + prefix: cdd + sampleId: cd00400 + uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 + n2t: + description: The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. + example: cd00400 + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd + name: Conserved Domain Database at NCBI + namespaceEmbeddedInLui: false + pattern: ^(cd)?\d{5}$ + prefix: cdd + uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 + ncbi: + example: '02194' + homepage: https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml + name: Conserved Domain Database + prefix: CDD + prefixcommons: + description: The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM). + example: cd00400 + homepage: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml + keywords: + - protein + - structure + name: Conserved Domain Database + pattern: ^cd\d{5}$ + prefix: cdd + pubmed_ids: + - '18984618' + uri_format: http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 + uniprot: + category: Family and domain databases + identifier: '214' + link_is_explicit: 'true' + name: Conserved Domains Database + prefix: CDD + uri_format: https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 +cdno: + bioportal: + name: Compositional Dietary Nutrition Ontology + prefix: CDNO + example: '0000013' + mappings: + bioportal: CDNO + obofoundry: cdno + ols: cdno + ontobee: CDNO + obofoundry: + contact: l.andres.hernandez.18@student.scu.edu.au + contact.github: LilyAndres + contact.label: Liliana Andres Hernandez + contact.orcid: 0000-0002-7696-731X + depends_on: + - bfo + - chebi + - envo + - pato + - ro + deprecated: false + description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. + download.obo: http://purl.obolibrary.org/obo/cdno.obo + download.owl: http://purl.obolibrary.org/obo/cdno.owl + homepage: https://cdno.info/ + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Compositional Dietary Nutrition Ontology + preferredPrefix: CDNO + prefix: cdno + publications: + - id: https://doi.org/10.1002/csc2.20092 + title: Knowledge representation and data sharing to unlock crop variation for nutritional food security + repository: https://github.com/Southern-Cross-Plant-Science/cdno + ols: + description: None + download: http://purl.obolibrary.org/obo/cdno.owl + homepage: https://cdno.info/ + name: Compositional Dietary Nutrition Ontology + prefix: cdno + version: 2022-04-06 + version.iri: http://purl.obolibrary.org/obo/cdno/releases/2022-04-06/cdno.owl + ontobee: + library: Library + name: Compositional Dietary Nutrition Ontology + prefix: CDNO + pattern: ^\d{7}$ +cdpd: + biocontext: + is_identifiers: true + is_obo: false + prefix: CDPD + uri_format: http://identifiers.org/cdpd/$1 + mappings: + biocontext: CDPD + miriam: cdpd + n2t: cdpd + miriam: + deprecated: false + description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). + homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp + id: '00000272' + name: Canadian Drug Product Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cdpd + sampleId: '63250' + uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 + n2t: + description: The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). + example: '63250' + homepage: http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp + name: Canadian Drug Identification Number at Health Canada + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cdpd + uri_format: http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 +cell_biolabs: + cellosaurus: + category: Cell line collections + homepage: https://www.cellbiolabs.com + name: Cell Biolabs cell line products + prefix: Cell_Biolabs + uri_format: https://www.cellbiolabs.com/search?keywords=$1 + example: AKR-270 + mappings: + cellosaurus: Cell_Biolabs +cell_model_passport: + cellosaurus: + category: Cell line databases/resources + homepage: https://cellmodelpassports.sanger.ac.uk/ + name: Sanger Cell Model Passports + prefix: Cell_Model_Passport + uri_format: https://cellmodelpassports.sanger.ac.uk/passports/$1 + example: SIDM01262 + mappings: + cellosaurus: Cell_Model_Passport +cellbank.australia: + cellosaurus: + category: Cell line collections + homepage: http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/ + name: CellBank Australia + prefix: CBA + uri_format: http://www.cellbankaustralia.com/$1 + description: CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world. + example: ab-1-ha + mappings: + cellosaurus: CBA + uri_format: https://www.cellbankaustralia.com/$1.html +cellimage: + biocontext: + is_identifiers: true + is_obo: false + prefix: CELLIMAGE + uri_format: http://identifiers.org/cellimage/$1 + fairsharing: + abbreviation: + description: This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health. It is a repository for images, movies, and animations of cells from a variety of organisms that demonstrate cellular architecture and functions. This comprehensive library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research. + id: '1723' + name: Cell Image Library + prefix: FAIRsharing.8t18te + subjects: + - Life Science + - Cell Biology + mappings: + biocontext: CELLIMAGE + fairsharing: FAIRsharing.8t18te + miriam: cellimage + n2t: cellimage + prefixcommons: cellimage + miriam: + deprecated: false + description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' + homepage: http://cellimagelibrary.org/ + id: '00000257' + name: Cell Image Library + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cellimage + sampleId: '24801' + uri_format: http://cellimagelibrary.org/images/$1 + n2t: + description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' + example: '24801' + homepage: http://cellimagelibrary.org/ + name: Cell Image Library at American Society for Cell Biology + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cellimage + uri_format: http://cellimagelibrary.org/images/$1 + prefixcommons: + description: 'The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.' + example: '24801' + keywords: + - image + name: 'The Cell: An Image Library' + pattern: ^\d+$ + prefix: cellimage + uri_format: http://cellimagelibrary.org/images/$1 +cellopub: + cellosaurus: + category: Reference resources + homepage: https://web.expasy.org/cellosaurus/ + name: Cellosaurus Publication + prefix: CelloPub + uri_format: https://web.expasy.org/cellosaurus/cellopub/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Cellosaurus identifeirs for publications, like Pubmed + example: CLPUB00496 + homepage: https://web.expasy.org/cellosaurus/ + mappings: + cellosaurus: CelloPub + name: Cellosaurus Publication + uri_format: https://web.expasy.org/cellosaurus/cellopub/$1 +cellosaurus: + biocontext: + is_identifiers: true + is_obo: false + prefix: CELLOSAURUS + uri_format: http://identifiers.org/cellosaurus/$1 + cellosaurus: + category: Cell line databases/resources + homepage: https://web.expasy.org/cellosaurus/ + name: Cellosaurus - a knowledge resource on cell lines + prefix: Cellosaurus + uri_format: https://web.expasy.org/cellosaurus/$1 + download_obo: https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo + example: CVCL_0440 + fairsharing: + abbreviation: Cellosaurus + description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' + id: '2348' + name: Cellosaurus + prefix: FAIRsharing.hkk309 + subjects: + - Life Science + mappings: + biocontext: CELLOSAURUS + cellosaurus: Cellosaurus + fairsharing: FAIRsharing.hkk309 + miriam: cellosaurus + n2t: cellosaurus + wikidata: P3289 + miriam: + deprecated: false + description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' + homepage: https://web.expasy.org/cellosaurus/ + id: '00000598' + name: Cellosaurus + namespaceEmbeddedInLui: false + pattern: ^CVCL_[A-Z0-9]{4}$ + prefix: cellosaurus + sampleId: CVCL_0030 + uri_format: https://web.expasy.org/cellosaurus/$1 + n2t: + description: 'The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.' + example: CVCL_0030 + homepage: https://web.expasy.org/cellosaurus/ + name: Cellosaurus through SIB + namespaceEmbeddedInLui: false + pattern: CVCL_[A-Z0-9]{4} + prefix: cellosaurus + uri_format: https://web.expasy.org/cellosaurus/$1 + name: Cellosaurus + pattern: ^CVCL_[A-Z0-9]{4}$ + synonyms: + - CVCL + wikidata: + database: Q24691710 + database.homepage: https://web.expasy.org/cellosaurus/ + database.label: Cellosaurus + name: Cellosaurus ID + pattern: CVCL_[A-Z\d][A-Z\d][A-Z\d][A-Z\d] + prefix: P3289 + uri_format: https://web.expasy.org/cellosaurus/$1 +cellosaurus.resource: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The set of prefixes used in the Cellosaurus resource + example: 4DN + homepage: https://web.expasy.org/cellosaurus/ + name: Cellosaurus Registry + uri_format: https://bioregistry.io/metaregistry/cellosaurus/$1 +cellrepo: + mappings: + miriam: cellrepo + miriam: + deprecated: false + description: The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines + homepage: https://cellrepo.ico2s.org/ + id: '00000829' + name: Cell Version Control Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: cellrepo + sampleId: '82' + uri_format: https://cellrepo.ico2s.org/repositories/$1 +ceph: + biocontext: + is_identifiers: false + is_obo: true + prefix: CEPH + uri_format: http://purl.obolibrary.org/obo/CEPH_$1 + bioportal: + name: Cephalopod Ontology + prefix: CEPH + download_obo: https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo + example: '0000109' + fairsharing: + abbreviation: CEPH + description: An anatomical and developmental ontology for cephalopods + id: '668' + name: Cephalopod Ontology + prefix: FAIRsharing.p58bm4 + subjects: [] + mappings: + biocontext: CEPH + bioportal: CEPH + fairsharing: FAIRsharing.p58bm4 + obofoundry: ceph + ols: ceph + ontobee: CEPH + obofoundry: + contact: cjmungall@lbl.gov + contact.github: cmungall + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + deprecated: true + description: An anatomical and developmental ontology for cephalopods + download.obo: http://purl.obolibrary.org/obo/ceph.obo + download.owl: http://purl.obolibrary.org/obo/ceph.owl + homepage: https://github.com/obophenotype/cephalopod-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Cephalopod Ontology + prefix: ceph + repository: https://github.com/obophenotype/cephalopod-ontology + ols: + description: An anatomical and developmental ontology for cephalopods + download: http://purl.obolibrary.org/obo/ceph.owl + homepage: https://github.com/obophenotype/cephalopod-ontology + name: Cephalopod Ontology + prefix: ceph + version: 2016-01-12 + version.iri: http://purl.obolibrary.org/obo/ceph/releases/2016-01-12/ceph.owl + ontobee: + library: Library + name: Cephalopod Ontology + prefix: CEPH + pattern: ^\d{7}$ +cgd: + biocontext: + is_identifiers: true + is_obo: false + prefix: CGD + uri_format: http://identifiers.org/cgd/$1 + fairsharing: + abbreviation: CGD + description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. + id: '1816' + name: Candida Genome Database + prefix: FAIRsharing.j7j53 + subjects: + - Life Science + go: + homepage: http://www.candidagenome.org/ + name: Candida Genome Database + prefix: CGD + synonyms: + - CGDID + uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 + mappings: + biocontext: CGD + fairsharing: FAIRsharing.j7j53 + go: CGD + miriam: cgd + n2t: cgd + ncbi: CGD + prefixcommons: cgd + uniprot: CGD + miriam: + deprecated: false + description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. + homepage: http://www.candidagenome.org/ + id: '00000145' + name: Candida Genome Database + namespaceEmbeddedInLui: false + pattern: ^CAL\d{7}$ + prefix: cgd + sampleId: CAL0003079 + uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 + n2t: + description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. + example: CAL0003079 + homepage: http://www.candidagenome.org/ + name: Candida Genome Database at Stanford University + namespaceEmbeddedInLui: false + pattern: ^CAL\d{7}$ + prefix: cgd + uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 + ncbi: + example: CAL0005934 + homepage: http://www.candidagenome.org/ + name: Candida Genome Database + prefix: CGD + prefixcommons: + description: The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. + example: CAL0003079 + homepage: http://www.candidagenome.org/ + keywords: + - eukaryotic + - genome + - nucleotide + name: Candida Genome Database + pattern: ^CAL\d{7}$ + prefix: cgd + pubmed_ids: + - '15608216' + uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 + uniprot: + category: Organism-specific databases + identifier: '126' + link_is_explicit: 'true' + name: Candida Genome Database + prefix: CGD + uri_format: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 +cghdb: + cellosaurus: + category: Cell line databases/resources + homepage: http://www.cghtmd.jp/CGHDatabase/index_e.jsp + name: CGH Data Base + prefix: CGH-DB + uri_format: http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en + example: 300165/p13898_2106T + mappings: + cellosaurus: CGH-DB +cgnc: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans) + example: '10087' + homepage: http://birdgenenames.org/cgnc/ + mappings: + prefixcommons: cgnc + name: Chicken Gene Nomenclature Consortium + pattern: ^\d+$ + prefixcommons: + description: The Chicken Gene Nomenclature Consortium (CGNC) provides standardized gene nomenclature for chicken genes. + example: '2218' + homepage: http://www.agnc.msstate.edu/ + keywords: + - gene + name: Chicken Gene Nomenclature Consortium + pattern: ^\d+$ + prefix: cgnc + pubmed_ids: + - '19607656' + uri_format: http://www.agnc.msstate.edu/GeneReport.aspx?a=$1 + synonyms: + - BirdBase + - CGNC + uri_format: http://birdgenenames.org/cgnc/GeneReport?id=$1 +cgsc: + biocontext: + is_identifiers: true + is_obo: false + prefix: CGSC + uri_format: http://identifiers.org/cgsc/$1 + fairsharing: + abbreviation: CGSC + description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. + id: '1818' + name: Coli Genetic Stock Center + prefix: FAIRsharing.1tbrdz + subjects: + - Life Science + go: + homepage: http://cgsc.biology.yale.edu/ + name: CGSC + prefix: CGSC + mappings: + biocontext: CGSC + fairsharing: FAIRsharing.1tbrdz + go: CGSC + miriam: cgsc + n2t: cgsc + prefixcommons: cgsc + miriam: + deprecated: false + description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. + homepage: http://cgsc.biology.yale.edu/index.php + id: '00000295' + name: CGSC Strain + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cgsc + sampleId: '74' + uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1 + n2t: + description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. + example: '74' + homepage: http://cgsc.biology.yale.edu/index.php + name: CGSC at Yale university + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cgsc + uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1 + name: Coli Genetic Stock Center + prefixcommons: + description: The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. + example: '96846' + homepage: http://cgsc.biology.yale.edu/ + keywords: + - gene + name: The Coli Genetic Stock Center + pattern: ^\d+$ + prefix: cgsc + uri_format: http://cgsc.biology.yale.edu/Site.php?ID=$1 +charprot: + biocontext: + is_identifiers: true + is_obo: false + prefix: CHARPROT + uri_format: http://identifiers.org/charprot/$1 + mappings: + biocontext: CHARPROT + miriam: charprot + n2t: charprot + miriam: + deprecated: false + description: CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. + homepage: http://www.jcvi.org/charprotdb + id: '00000341' + name: CharProt + namespaceEmbeddedInLui: false + pattern: ^CH_\d+$ + prefix: charprot + sampleId: CH_001923 + uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1 + n2t: + description: CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. + example: CH_001923 + homepage: http://www.jcvi.org/charprotdb + name: CharProt at JCVI + namespaceEmbeddedInLui: false + pattern: ^CH_\d+$ + prefix: charprot + uri_format: http://www.jcvi.org/charprotdb/index.cgi/view/$1 +chebi: + biocontext: + is_identifiers: false + is_obo: true + prefix: CHEBI + uri_format: http://purl.obolibrary.org/obo/CHEBI_$1 + bioportal: + name: Chemical Entities of Biological Interest Ontology + prefix: CHEBI + cellosaurus: + category: Chemistry resources + homepage: https://www.ebi.ac.uk/chebi/ + name: Chemical Entities of Biological Interest + prefix: ChEBI + uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1 + cheminf: + description: Database identifier used by ChEBI. + name: ChEBI + obsolete: false + prefix: '000407' + example: '24867' + fairsharing: + abbreviation: ChEBI + description: Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'small’ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, etc.. These molecular entities can interact with or affect the processes of living organisms. + id: '1036' + name: Chemical Entities of Biological Interest + prefix: FAIRsharing.62qk8w + subjects: + - Biochemistry + - Chemistry + go: + homepage: http://www.ebi.ac.uk/chebi/ + name: Chemical Entities of Biological Interest + prefix: CHEBI + synonyms: + - ChEBI + uri_format: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 + mappings: + biocontext: CHEBI + bioportal: CHEBI + cellosaurus: ChEBI + cheminf: '000407' + fairsharing: FAIRsharing.62qk8w + go: CHEBI + miriam: chebi + n2t: chebi + obofoundry: chebi + ols: chebi + ontobee: CHEBI + prefixcommons: chebi + wikidata: P683 + miriam: + deprecated: false + description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. + homepage: https://www.ebi.ac.uk/chebi/ + id: '00000002' + name: ChEBI + namespaceEmbeddedInLui: true + pattern: ^CHEBI:\d+$ + prefix: chebi + sampleId: '36927' + uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 + n2t: + description: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. + example: '36927' + homepage: https://www.ebi.ac.uk/chebi/ + name: ChEBI (Chemical Entities of Biological Interest) + namespaceEmbeddedInLui: true + pattern: ^CHEBI:\d+$ + prefix: chebi + uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 + name: Chemical Entities of Biological Interest + obofoundry: + appears_in: + - cdno + - chiro + - cl + - ecocore + - ecto + - envo + - fobi + - foodon + - genepio + - maxo + - mco + - ons + - pcl + - uberon + - xpo + - scdo + contact: amalik@ebi.ac.uk + contact.github: amalik01 + contact.label: Adnan Malik + contact.orcid: 0000-0001-8123-5351 + deprecated: false + description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. + download.obo: http://purl.obolibrary.org/obo/chebi.obo + download.owl: http://purl.obolibrary.org/obo/chebi.owl + homepage: http://www.ebi.ac.uk/chebi + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Chemical Entities of Biological Interest + preferredPrefix: CHEBI + prefix: chebi + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/26467479 + title: 'ChEBI in 2016: Improved services and an expanding collection of metabolites.' + repository: https://github.com/ebi-chebi/ChEBI + twitter: chebit + ols: + description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds. + download: http://purl.obolibrary.org/obo/chebi.owl + homepage: http://www.ebi.ac.uk/chebi + name: Chemical Entities of Biological Interest + prefix: chebi + version: '210' + version.iri: http://purl.obolibrary.org/obo/chebi/210/chebi.owl + ontobee: + library: Foundry + name: Chemical Entities of Biological Interest + prefix: CHEBI + pattern: ^\d+$ + prefixcommons: + bioportal: '1007' + description: A structured classification of chemical compounds of biological relevance. + example: '17234' + homepage: http://www.ebi.ac.uk/chebi/ + keywords: + - obo + - chemical + name: Chemical Entities of Biological Interest + pattern: ^\d+$ + prefix: chebi + pubmed_ids: + - '23180789' + uri_format: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$1 + providers: + - code: chebi-img + description: Image server from chebi + homepage: https://www.ebi.ac.uk/chebi/ + name: ChEBI + uri_format: https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=$1 + synonyms: + - CHEBI + - CHEBIID + - ChEBI + uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 + wikidata: + database: Q902623 + database.homepage: http://www.ebi.ac.uk/chebi + database.label: ChEBI + format.rdf: http://purl.obolibrary.org/obo/CHEBI_$1 + homepage: https://www.ebi.ac.uk/chebi + name: ChEBI ID + pattern: \d+ + prefix: P683 + uri_format: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 +chembl: + cheminf: + description: Identifier used by the ChEMBL database for compounds, assays, target, etc. + name: ChEMBL + obsolete: false + prefix: '000412' + fairsharing: + abbreviation: ChEMBL + description: ChEMBL is an open, manually-curated, large-scale bioactivity database containing information from medicinal chemistry literature. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions. + id: '1561' + name: ChEMBL + prefix: FAIRsharing.m3jtpg + subjects: + - Drug Discovery + - Biochemistry + - Genomics + - Medicinal Chemistry + homepage: https://www.ebi.ac.uk/chembl + mappings: + cheminf: '000412' + fairsharing: FAIRsharing.m3jtpg + miriam: chembl + prefixcommons: chembl + uniprot: ChEMBL + miriam: + deprecated: false + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + homepage: https://www.ebi.ac.uk/chembl + id: '00000799' + name: ChEMBL + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl + sampleId: CHEMBL4303805 + uri_format: https://www.ebi.ac.uk/chembl/entity/$1 + prefixcommons: + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + example: '210313' + homepage: https://www.ebi.ac.uk/chembldb/ + keywords: + - molecules + name: chEMBL + pattern: ^\d+$ + prefix: chembl + uri_format: https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$1 + synonyms: + - ChEMBL + - ChEMBL_ID + - chembl + uniprot: + category: Chemistry databases + identifier: '174' + link_is_explicit: 'true' + name: ChEMBL database of bioactive drug-like small molecules + prefix: ChEMBL + uri_format: https://www.ebi.ac.uk/chembldb/target/inspect/$1 +chembl.cell: + cellosaurus: + category: Chemistry resources + homepage: https://www.ebi.ac.uk/chembldb + name: ChEMBL database of bioactive drug-like small molecules - Cell lines section + prefix: ChEMBL-Cells + uri_format: https://www.ebi.ac.uk/chembldb/cell/inspect/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: CHEMBL3307800 + mappings: + cellosaurus: ChEMBL-Cells + part_of: chembl + synonyms: + - ChEMBL-Cells + uri_format: https://www.ebi.ac.uk/chembl/cell_line_report_card/$1 +chembl.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: CHEMBL.COMPOUND + uri_format: http://identifiers.org/chembl.compound/$1 + example: CHEMBL465070 + mappings: + biocontext: CHEMBL.COMPOUND + miriam: chembl.compound + n2t: chembl.compound + wikidata: P592 + miriam: + deprecated: false + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + homepage: https://www.ebi.ac.uk/chembldb/ + id: '00000084' + name: ChEMBL compound + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl.compound + providers: + - code: CURATOR_REVIEW + description: ChEMBL compound RDF + homepage: https://github.com/egonw/chembl.rdf + name: ChEMBL compound RDF + uri_format: http://linkedchemistry.info/chembl/chemblid/$1 + - code: CURATOR_REVIEW + description: ChEMBL compound RDF through EBI RDF Platform + homepage: https://www.ebi.ac.uk/rdf/services/chembl/ + name: ChEMBL compound RDF through EBI RDF Platform + uri_format: https://rdf.ebi.ac.uk/resource/chembl/molecule/$1 + sampleId: CHEMBL308052 + uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1 + n2t: + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + example: CHEMBL308052 + homepage: https://www.ebi.ac.uk/chembldb/ + name: ChEMBL compound database at EBI + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl.compound + uri_format: https://www.ebi.ac.uk/chembl/compound/inspect/$1 + name: ChEMBL + part_of: chembl + pattern: ^CHEMBL\d+$ + wikidata: + database: Q6120337 + database.homepage: http://www.ebi.ac.uk/chembl + database.label: ChEMBL + format.rdf: http://rdf.ebi.ac.uk/resource/chembl/molecule/$1 + homepage: https://www.ebi.ac.uk/chembl + name: ChEMBL ID + pattern: CHEMBL\d+ + prefix: P592 + uri_format: https://www.ebi.ac.uk/chembl/compound_report_card/$1/ +chembl.target: + biocontext: + is_identifiers: true + is_obo: false + prefix: CHEMBL.TARGET + uri_format: http://identifiers.org/chembl.target/$1 + cellosaurus: + category: Chemistry resources + homepage: https://www.ebi.ac.uk/chembldb + name: ChEMBL database of bioactive drug-like small molecules - Targets section + prefix: ChEMBL-Targets + uri_format: https://www.ebi.ac.uk/chembldb/target/inspect/$1 + mappings: + biocontext: CHEMBL.TARGET + cellosaurus: ChEMBL-Targets + miriam: chembl.target + n2t: chembl.target + miriam: + deprecated: false + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + homepage: https://www.ebi.ac.uk/chembldb/ + id: '00000085' + name: ChEMBL target + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl.target + providers: + - code: CURATOR_REVIEW + description: ChEMBL target RDF + homepage: https://github.com/egonw/chembl.rdf + name: ChEMBL target RDF + uri_format: http://linkedchemistry.info/chembl/chemblid/$1 + - code: CURATOR_REVIEW + description: ChEMBL target RDF through EBI RDF Platform + homepage: https://rdf.ebi.ac.uk/resource/chembl/ + name: ChEMBL target RDF through EBI RDF Platform + uri_format: https://rdf.ebi.ac.uk/resource/chembl/target/$1 + sampleId: CHEMBL3467 + uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1 + n2t: + description: ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. + example: CHEMBL3467 + homepage: https://www.ebi.ac.uk/chembldb/ + name: ChEMBL targets database at EBI + namespaceEmbeddedInLui: false + pattern: ^CHEMBL\d+$ + prefix: chembl.target + uri_format: https://www.ebi.ac.uk/chembl/target/inspect/$1 + part_of: chembl + synonyms: + - ChEMBL-Targets +chemdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: CHEMDB + uri_format: http://identifiers.org/chemdb/$1 + fairsharing: + abbreviation: ChemDB + description: ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. + id: '2088' + name: The UC Irvine ChemDB + prefix: FAIRsharing.dstf7h + subjects: + - Biochemistry + - Life Science + - Biomedical Science + - Systems Biology + - Preclinical Studies + mappings: + biocontext: CHEMDB + fairsharing: FAIRsharing.dstf7h + miriam: chemdb + n2t: chemdb + prefixcommons: chemdb + miriam: + deprecated: false + description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. + homepage: http://cdb.ics.uci.edu/ + id: '00000279' + name: ChemDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chemdb + sampleId: '3966782' + uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 + n2t: + description: ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. + example: '3966782' + homepage: http://cdb.ics.uci.edu/ + name: ChemDB at UC Irvine + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chemdb + uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 + prefixcommons: + description: ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. + example: '3965223' + homepage: http://cdb.ics.uci.edu + keywords: + - small molecule + name: The UC Irvine ChemDB + pattern: ^\d+$ + prefix: chemdb + pubmed_ids: + - '17599932' + uri_format: http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 +chemidplus: + biocontext: + is_identifiers: true + is_obo: false + prefix: CHEMIDPLUS + uri_format: http://identifiers.org/chemidplus/$1 + fairsharing: + abbreviation: ChemIDplus + description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. + id: '2003' + name: ChemIDplus + prefix: FAIRsharing.5949vn + subjects: + - Chemistry + - Biomedical Science + mappings: + biocontext: CHEMIDPLUS + fairsharing: FAIRsharing.5949vn + miriam: chemidplus + n2t: chemidplus + prefixcommons: chemidplus + miriam: + deprecated: false + description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. + homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp + id: '00000096' + name: ChemIDplus + namespaceEmbeddedInLui: false + pattern: ^\d+\-\d+\-\d+$ + prefix: chemidplus + sampleId: 57-27-2 + uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1 + n2t: + description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. + example: 57-27-2 + homepage: https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp + name: ChemIDplus at National Library of Medicine + namespaceEmbeddedInLui: false + pattern: ^\d+\-\d+\-\d+$ + prefix: chemidplus + uri_format: https://chem.nlm.nih.gov/chemidplus/rn/$1 + prefixcommons: + description: ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. + example: '000057272' + homepage: http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp + keywords: + - structure + - molecules + name: ChemIDplus + pattern: ^\d+$ + prefix: chemidplus + uri_format: http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$1 + synonyms: + - ChemIDplus +cheminf: + biocontext: + is_identifiers: false + is_obo: true + prefix: CHEMINF + uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1 + bioportal: + name: Chemical Information Ontology + prefix: CHEMINF + download_owl: https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl + example: '000410' + fairsharing: + abbreviation: CHEMINF + description: The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed. + id: '1056' + name: CHEMical INFormation Ontology + prefix: FAIRsharing.sjhvyy + subjects: + - Biochemistry + - Chemistry + - Life Science + mappings: + biocontext: CHEMINF + bioportal: CHEMINF + fairsharing: FAIRsharing.sjhvyy + obofoundry: cheminf + ols: cheminf + ontobee: CHEMINF + name: Chemical Information Ontology + obofoundry: + contact: egon.willighagen@gmail.com + contact.github: egonw + contact.label: Egon Willighagen + contact.orcid: 0000-0001-7542-0286 + deprecated: false + description: Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. + download.owl: http://purl.obolibrary.org/obo/cheminf.owl + homepage: https://github.com/semanticchemistry/semanticchemistry + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Chemical Information Ontology + preferredPrefix: CHEMINF + prefix: cheminf + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/21991315 + title: 'The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web' + repository: https://github.com/semanticchemistry/semanticchemistry + ols: + download: http://purl.obolibrary.org/obo/cheminf.owl + name: chemical information ontology (cheminf) - information entities about chemical entities + prefix: cheminf + version: '2.0' + ontobee: + library: Library + name: Chemical Information Ontology + prefix: CHEMINF + pattern: ^\d{6}$ +chemspider: + biocontext: + is_identifiers: true + is_obo: false + prefix: CHEMSPIDER + uri_format: http://identifiers.org/chemspider/$1 + cheminf: + description: Database identifier used by ChemSpider. + name: ChemSpider + obsolete: false + prefix: '000405' + fairsharing: + abbreviation: ChemSpider + description: ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. + id: '2042' + name: ChemSpider + prefix: FAIRsharing.96f3gm + subjects: + - Chemistry + - Life Science + mappings: + biocontext: CHEMSPIDER + cheminf: '000405' + fairsharing: FAIRsharing.96f3gm + miriam: chemspider + n2t: chemspider + prefixcommons: chemspider + wikidata: P661 + miriam: + deprecated: false + description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. + homepage: http://www.chemspider.com/ + id: '00000138' + name: ChemSpider + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chemspider + sampleId: '56586' + uri_format: http://www.chemspider.com/Chemical-Structure.$1.html + n2t: + description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. + example: '56586' + homepage: http://www.chemspider.com/ + name: ChemSpider at RSC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chemspider + uri_format: http://www.chemspider.com/Chemical-Structure.$1.html + name: ChemSpider + prefixcommons: + description: ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. + example: '56586' + homepage: http://www.chemspider.com/ + keywords: + - structure + - molecules + name: ChemSpider - Database of Chemical Structures and Property Predictions + pattern: ^\d+$ + prefix: chemspider + uri_format: http://www.chemspider.com/Chemical-Structure.$1.html + synonyms: + - ChemSpiderID + - Chemspider + wikidata: + database: Q2311683 + database.homepage: https://www.chemspider.com/ + database.label: ChemSpider + format.rdf: http://rdf.chemspider.com/$1 + homepage: https://www.chemspider.com/ + name: ChemSpider ID + pattern: '[1-9]\d*' + prefix: P661 + uri_format: https://www.chemspider.com/Chemical-Structure.$1.html +chickenqtldb: + biocontext: + is_identifiers: true + is_obo: false + prefix: CHICKENQTLDB + uri_format: http://identifiers.org/chickenqtldb/$1 + mappings: + biocontext: CHICKENQTLDB + miriam: chickenqtldb + n2t: chickenqtldb + prefixcommons: chickenqtldb + miriam: + deprecated: false + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. + homepage: https://www.animalgenome.org/QTLdb + id: '00000505' + name: Animal Genome Chicken QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chickenqtldb + sampleId: '14362' + uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 + n2t: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. + example: '14362' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/GG/index + name: Animal QTL Chicken at Iowa State University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: chickenqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1 + part_of: qtldb + prefixcommons: + description: This Chicken Quantitative Trait Locus (QTL) database (Chicken QTLdb) has gathered all chicken QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on chicken chromosomes the most feasible location for genes responsible for quantitative trait important to chicken production. + example: '66' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/GG/index + keywords: + - DNA + - genome + name: Chicken Quantitative Trait Locus database + pattern: ^\d+$ + prefix: chickenqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$1 +chiro: + bioportal: + name: CHEBI Integrated Role Ontology + prefix: CHIRO + mappings: + bioportal: CHIRO + obofoundry: chiro + ols: chiro + ontobee: CHIRO + name: ChEBI Integrated Role Ontology + no_own_terms: true + obofoundry: + contact: vasilevs@ohsu.edu + contact.github: nicolevasilevsky + contact.label: Nicole Vasilevsky + contact.orcid: 0000-0001-5208-3432 + depends_on: + - chebi + - go + - hp + - mp + - ncbitaxon + - pr + - uberon + deprecated: false + description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. + download.obo: http://purl.obolibrary.org/obo/chiro.obo + download.owl: http://purl.obolibrary.org/obo/chiro.owl + homepage: https://github.com/obophenotype/chiro + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: CHEBI Integrated Role Ontology + preferredPrefix: CHIRO + prefix: chiro + publications: + - id: https://doi.org/10.26434/chemrxiv.12591221 + title: Extension of Roles in the ChEBI Ontology + repository: https://github.com/obophenotype/chiro + ols: + description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. + download: http://purl.obolibrary.org/obo/chiro.owl + homepage: https://github.com/obophenotype/chiro + name: CHEBI Integrated Role Ontology + prefix: chiro + version: 2015-11-23 + version.iri: http://purl.obolibrary.org/obo/chiro/releases/2015-11-23/chiro.owl + ontobee: + library: Library + name: CHEBI Integrated Role Ontology + prefix: CHIRO +chmo: + biocontext: + is_identifiers: false + is_obo: true + prefix: CHMO + uri_format: http://purl.obolibrary.org/obo/CHMO_$1 + bioportal: + name: Chemical Methods Ontology + prefix: CHMO + example: '0002902' + fairsharing: + abbreviation: CHMO + description: CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis; and synthesise materials such as epitaxy and continuous vapour deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). + id: '1424' + name: Chemical Methods Ontology + prefix: FAIRsharing.9j4wh2 + subjects: + - Chemistry + mappings: + biocontext: CHMO + bioportal: CHMO + fairsharing: FAIRsharing.9j4wh2 + obofoundry: chmo + ols: chmo + ontobee: CHMO + obofoundry: + appears_in: + - rbo + - scdo + contact: batchelorc@rsc.org + contact.github: batchelorc + contact.label: Colin Batchelor + contact.orcid: 0000-0001-5985-7429 + deprecated: false + description: CHMO, the chemical methods ontology, describes methods used to + download.owl: http://purl.obolibrary.org/obo/chmo.owl + homepage: https://github.com/rsc-ontologies/rsc-cmo + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Chemical Methods Ontology + preferredPrefix: CHMO + prefix: chmo + repository: https://github.com/rsc-ontologies/rsc-cmo + ols: + contact: chemistry-ontologies@googlegroups.com + description: CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). + download: http://purl.obolibrary.org/obo/chmo.owl + homepage: https://github.com/rsc-ontologies/rsc-cmo + name: Chemical Methods Ontology + prefix: chmo + version: 2022-04-19 + version.iri: http://purl.obolibrary.org/obo/chmo/releases/2022-04-19/chmo.owl + ontobee: + library: Library + name: Chemical Methods Ontology + prefix: CHMO + pattern: ^\d{7}$ +cido: + bioportal: + name: Coronavirus Infectious Disease Ontology + prefix: CIDO + example: '0000005' + fairsharing: + abbreviation: CIDO + description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles. + id: '1401' + name: Coronavirus Infectious Disease Ontology + prefix: FAIRsharing.aVmpKl + subjects: + - Drug Discovery + - Bioinformatics + - Drug Repositioning + - Virology + - Epidemiology + mappings: + bioportal: CIDO + fairsharing: FAIRsharing.aVmpKl + obofoundry: cido + ols: cido + ontobee: CIDO + obofoundry: + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqun Oliver He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: The Coronavirus Infectious Disease Ontology (CIDO) aims to ontologically represent and standardize various aspects of coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. + download.owl: http://purl.obolibrary.org/obo/cido.owl + homepage: https://github.com/cido-ontology/cido + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Coronavirus Infectious Disease Ontology + preferredPrefix: CIDO + prefix: cido + repository: https://github.com/cido-ontology/cido + ols: + contact: cido-discuss@googlegroups.com + description: The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. + download: http://purl.obolibrary.org/obo/cido.owl + homepage: https://github.com/cido-ontology/cido + name: 'CIDO: Ontology of Coronavirus Infectious Disease' + prefix: cido + version: 1.0.326 + ontobee: + library: Library + name: Coronavirus Infectious Disease Ontology + prefix: CIDO + pattern: ^\d{7}$ +cio: + biocontext: + is_identifiers: false + is_obo: true + prefix: CIO + uri_format: http://purl.obolibrary.org/obo/CIO_$1 + bioportal: + name: Confidence Information Ontology + prefix: CIO + example: '0000040' + fairsharing: + abbreviation: CIO + description: An ontology to capture confidence information about annotations + id: '644' + name: Confidence Information Ontology + prefix: FAIRsharing.e3t0yw + subjects: [] + mappings: + biocontext: CIO + bioportal: CIO + fairsharing: FAIRsharing.e3t0yw + obofoundry: cio + ols: cio + ontobee: CIO + obofoundry: + contact: frederic.bastian@unil.ch + contact.github: fbastian + contact.label: Frédéric Bastian + contact.orcid: 0000-0002-9415-5104 + deprecated: false + description: An ontology to capture confidence information about annotations. + download.obo: http://purl.obolibrary.org/obo/cio.obo + download.owl: http://purl.obolibrary.org/obo/cio.owl + homepage: https://github.com/BgeeDB/confidence-information-ontology + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Confidence Information Ontology + preferredPrefix: CIO + prefix: cio + repository: https://github.com/BgeeDB/confidence-information-ontology + ols: + description: An ontology to capture confidence information about annotations. + download: http://purl.obolibrary.org/obo/cio.owl + homepage: https://github.com/BgeeDB/confidence-information-ontology + name: Confidence Information Ontology + prefix: cio + version: 2015-03-10 + version.iri: http://purl.obolibrary.org/obo/cio/releases/2015-03-10/cio.owl + ontobee: + library: Library + name: Confidence Information Ontology + prefix: CIO + pattern: ^\d{7}$ +citexplore: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes. + example: C6155 + fairsharing: + abbreviation: CTX + description: The ontology represents CTX phenotypes, genetic variants, and bidirectional relationships between them though a patient model. The CTX ontology was build reusing the Human Phenotype Ontology (HPO) and the Snomed ct ontologies. A set of temporal clinical manifestations are semantically annotated with a domain phenotype ontology and registered with a time-stamped value. + id: '936' + name: Cerebrotendinous Xanthomatosis Ontology + prefix: FAIRsharing.619eqr + subjects: + - Genetics + - Biomedical Science + - Preclinical Studies + homepage: https://www.ebi.ac.uk/citexplore/ + mappings: + fairsharing: FAIRsharing.619eqr + prefixcommons: citexplore + name: CiteXplore + prefixcommons: + description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. + example: '16333295' + homepage: http://www.ebi.ac.uk/citexplore/ + name: CiteXplore + pattern: ^\d+$ + prefix: citexplore + uri_format: http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$1 + references: + - https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/ + synonyms: + - CTX + uri_format: https://europepmc.org/article/CTX/$1 +civic.aid: + mappings: + miriam: civic.aid + miriam: + deprecated: false + description: 'A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.' + homepage: https://civicdb.org/ + id: '00000835' + name: CIViC Assertion + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: civic.aid + sampleId: '3' + uri_format: https://civicdb.org/links/assertions/$1 +civic.eid: + mappings: + miriam: civic.eid + miriam: + deprecated: false + description: Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract). + homepage: https://civicdb.org/ + id: '00000839' + name: CIViC Evidence + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: civic.eid + sampleId: '1199' + uri_format: https://civicdb.org/links/evidence/$1 +cl: + biocontext: + is_identifiers: false + is_obo: true + prefix: CL + uri_format: http://purl.obolibrary.org/obo/CL_$1 + bioportal: + name: Cell Ontology + prefix: CL + cellosaurus: + category: Anatomy/cell type resources + homepage: https://obophenotype.github.io/cell-ontology/ + name: Cell Ontology + prefix: CL + uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1 + download_obo: https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo + example: '0000062' + fairsharing: + abbreviation: CL + description: The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies. + id: '1004' + name: Cell Ontology + prefix: FAIRsharing.j9y503 + subjects: + - Anatomy + - Life Science + - Cell Biology + go: + homepage: http://cellontology.org + name: Cell Type Ontology + prefix: CL + mappings: + biocontext: CL + bioportal: CL + cellosaurus: CL + fairsharing: FAIRsharing.j9y503 + go: CL + miriam: cl + n2t: cl + obofoundry: cl + ols: cl + ontobee: CL + prefixcommons: cl + miriam: + deprecated: false + description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. + homepage: https://www.ebi.ac.uk/ols/ontologies/cl + id: '00000110' + name: Cell Type Ontology + namespaceEmbeddedInLui: true + pattern: ^CL:\d{7}$ + prefix: cl + sampleId: '0000232' + uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1 + n2t: + description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. + example: '0000232' + homepage: http://bioportal.bioontology.org/ontologies/CL + name: Cell Type Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^CL:\d{7}$ + prefix: cl + uri_format: http://purl.bioontology.org/ontology/CL/CL:$1 + obofoundry: + appears_in: + - go + - clo + - ecao + - mco + - pcl + - uberon + - xpo + - ehdaa2 + contact: addiehl@buffalo.edu + contact.github: addiehl + contact.label: Alexander Diehl + contact.orcid: 0000-0001-9990-8331 + depends_on: + - chebi + - go + - ncbitaxon + - pato + - pr + - ro + - uberon + deprecated: false + description: The Cell Ontology is a structured controlled vocabulary for cell types in animals. + download.obo: http://purl.obolibrary.org/obo/cl.obo + download.owl: http://purl.obolibrary.org/obo/cl.owl + homepage: https://obophenotype.github.io/cell-ontology/ + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Cell Ontology + preferredPrefix: CL + prefix: cl + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/27377652 + title: 'The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.' + repository: https://github.com/obophenotype/cell-ontology + ols: + description: An ontology of cell types. + download: http://purl.obolibrary.org/obo/cl.owl + name: Cell Ontology + prefix: cl + version: 2022-02-16 + version.iri: http://purl.obolibrary.org/obo/cl/releases/2022-02-16/cl.owl + ontobee: + library: Library + name: Cell Ontology + prefix: CL + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1006' + description: The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. + example: CL:0000232 + homepage: http://lists.sourceforge.net/lists/listinfo/obo-cell-type + keywords: + - obo + - cell + name: Cell Ontology + pattern: ^CL:\d+$ + prefix: cl + wikidata: + database: Q55118285 + database.label: Cell Ontology + homepage: http://www.ontobee.org/ontology/CL + name: Cell Ontology ID + pattern: CL_[0-9]{7} + prefix: P7963 + uri_format: http://purl.obolibrary.org/obo/$1 +clao: + bioportal: + name: Collembola Anatomy Ontology + prefix: CLAO + example: '0000088' + mappings: + bioportal: CLAO + obofoundry: clao + ols: clao + ontobee: CLAO + obofoundry: + contact: lagonzalezmo@unal.edu.co + contact.github: luis-gonzalez-m + contact.label: Luis González-Montaña + contact.orcid: 0000-0002-9136-9932 + depends_on: + - ro + deprecated: false + description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' + download.obo: http://purl.obolibrary.org/obo/clao.obo + download.owl: http://purl.obolibrary.org/obo/clao.owl + homepage: https://github.com/luis-gonzalez-m/Collembola + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Collembola Anatomy Ontology + preferredPrefix: CLAO + prefix: clao + repository: https://github.com/luis-gonzalez-m/Collembola + ols: + description: 'CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).' + download: http://purl.obolibrary.org/obo/clao.owl + homepage: https://github.com/luis-gonzalez-m/Collembola + name: Collembola Anatomy Ontology + prefix: clao + version: 2021-09-27 + version.iri: http://purl.obolibrary.org/obo/clao/releases/2021-09-27/clao.owl + ontobee: + library: Library + name: Collembola Anatomy Ontology + prefix: CLAO + pattern: ^\d{7}$ +classyfire: + comment: There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them. + download_obo: http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip + example: '0004828' + mappings: + miriam: classyfire + miriam: + deprecated: false + description: ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API. + homepage: http://classyfire.wishartlab.com/ + id: '00000770' + name: ClassyFire + namespaceEmbeddedInLui: false + pattern: ^C[0-9]{7}$ + prefix: classyfire + sampleId: C0004828 + uri_format: http://classyfire.wishartlab.com/tax_nodes/$1 + pattern: ^\d{7}$ + synonyms: + - CHEMONTID + uri_format: http://classyfire.wishartlab.com/tax_nodes/C$1 +cldb: + biocontext: + is_identifiers: true + is_obo: false + prefix: CLDB + uri_format: http://identifiers.org/cldb/$1 + cellosaurus: + category: Cell line databases/resources + homepage: http://bioinformatics.hsanmartino.it/cldb/ + name: Cell Line Data Base + prefix: CLDB + uri_format: http://bioinformatics.hsanmartino.it/cldb/$1.html + mappings: + biocontext: CLDB + cellosaurus: CLDB + miriam: cldb + n2t: cldb + miriam: + deprecated: false + description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. + homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html + id: '00000390' + name: CLDB + namespaceEmbeddedInLui: false + pattern: ^(cl|tum)\d+$ + prefix: cldb + sampleId: cl3603 + uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html + n2t: + description: The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. + example: cl3603 + homepage: http://bioinformatics.hsanmartino.it/hypercldb/indexes.html + name: CLDB at Genova + namespaceEmbeddedInLui: false + pattern: ^(cl|tum)\d+$ + prefix: cldb + uri_format: http://bioinformatics.hsanmartino.it/hypercldb/$1.html + name: Cell Line Database +clingene: + biolink: + is_identifiers: false + is_obo: false + prefix: CAID + uri_format: http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 + description: The allele registry provides and maintains identifiers for genetic variants + example: CA981206459 + homepage: https://reg.clinicalgenome.org + mappings: + biolink: CAID + name: ClinGen Allele Registry + uri_format: https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 +clinicaltrials: + biocontext: + is_identifiers: true + is_obo: false + prefix: CLINICALTRIALS + uri_format: http://identifiers.org/clinicaltrials/$1 + mappings: + biocontext: CLINICALTRIALS + miriam: clinicaltrials + n2t: clinicaltrials + prefixcommons: clinicaltrials + miriam: + deprecated: false + description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries + homepage: https://clinicaltrials.gov/ + id: '00000137' + name: ClinicalTrials.gov + namespaceEmbeddedInLui: false + pattern: ^NCT\d{8}$ + prefix: clinicaltrials + sampleId: NCT00222573 + uri_format: https://clinicaltrials.gov/ct2/show/$1 + n2t: + description: ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries + example: NCT00222573 + homepage: https://clinicaltrials.gov/ + name: ClinicalTrials.gov at NIH + namespaceEmbeddedInLui: false + pattern: ^NCT\d{8}$ + prefix: clinicaltrials + uri_format: https://clinicaltrials.gov/ct2/show/$1 + prefixcommons: + description: ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. + example: NCT00050895 + homepage: http://clinicaltrials.gov/ + keywords: + - disease + - drug + - human + name: ClinicalTrials.gov + pattern: ^NCT\d{8}$ + prefix: clinicaltrials + uri_format: http://clinicaltrials.gov/ct2/show/$1 +clinvar: + biocontext: + is_identifiers: false + is_obo: false + prefix: ClinVar + uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1 + biolink: + is_identifiers: true + is_obo: false + prefix: CLINVAR + uri_format: http://identifiers.org/clinvar$1 + cellosaurus: + category: Polymorphism and mutation databases + homepage: https://www.ncbi.nlm.nih.gov/clinvar/ + name: ClinVar + prefix: ClinVar + uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 + fairsharing: + abbreviation: ClinVar + description: ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible. + id: '2265' + name: ClinVar + prefix: FAIRsharing.wx5r6f + subjects: + - Genomics + - Clinical Studies + - Biomedical Science + - Preclinical Studies + mappings: + biocontext: ClinVar + biolink: CLINVAR + cellosaurus: ClinVar + fairsharing: FAIRsharing.wx5r6f + miriam: clinvar + n2t: clinvar + wikidata: P1929 + miriam: + deprecated: false + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. + homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + id: '00000596' + name: ClinVar Variant + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: clinvar + sampleId: '12345' + uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 + n2t: + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. + example: '12345' + homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + name: ClinVar Variant at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: clinvar + uri_format: https://www.ncbi.nlm.nih.gov/clinvar/variation/$1 + name: ClinVar Variation + wikidata: + database: Q20023123 + database.homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + database.label: ClinVar + homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + name: ClinVar Variation ID + prefix: P1929 + uri_format: http://www.ncbi.nlm.nih.gov/clinvar/variation/$1/ +clinvar.record: + biocontext: + is_identifiers: true + is_obo: false + prefix: CLINVAR.RECORD + uri_format: http://identifiers.org/clinvar.record/$1 + mappings: + biocontext: CLINVAR.RECORD + miriam: clinvar.record + n2t: clinvar.record + miriam: + deprecated: false + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. + homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + id: '00000534' + name: ClinVar Record + namespaceEmbeddedInLui: false + pattern: ^RCV\d+(\.\d+)?$ + prefix: clinvar.record + sampleId: RCV000033555.3 + uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1/ + n2t: + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. + example: RCV000033555.3 + homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + name: ClinVar Record at NCBI + namespaceEmbeddedInLui: false + pattern: ^RCV\d+(\.\d+)?$ + prefix: clinvar.record + uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1/ + uri_format: http://www.ncbi.nlm.nih.gov/clinvar/$1 +clinvar.submission: + biocontext: + is_identifiers: true + is_obo: false + prefix: CLINVAR.SUBMISSION + uri_format: http://identifiers.org/clinvar.submission/$1 + mappings: + biocontext: CLINVAR.SUBMISSION + miriam: clinvar.submission + n2t: clinvar.submission + miriam: + deprecated: false + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. + homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + id: '00000595' + name: ClinVar Submission + namespaceEmbeddedInLui: false + pattern: ^SCV\d+(\.\d+)?$ + prefix: clinvar.submission + sampleId: SCV000151292 + uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1 + n2t: + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. + example: SCV000151292 + homepage: http://www.ncbi.nlm.nih.gov/clinvar/ + name: ClinVar Submission at NCBI + namespaceEmbeddedInLui: false + pattern: ^SCV\d+(\.\d+)?$ + prefix: clinvar.submission + uri_format: http://www.ncbi.nlm.nih.gov/clinvar?term=$1 +clinvar.submitter: + mappings: + miriam: clinvar.submitter + miriam: + deprecated: false + description: ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs). + homepage: https://www.ncbi.nlm.nih.gov/clinvar/ + id: '00000769' + name: ClinVar Submitter + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: clinvar.submitter + sampleId: '26957' + uri_format: https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1 +clo: + biocontext: + is_identifiers: false + is_obo: true + prefix: CLO + uri_format: http://purl.obolibrary.org/obo/CLO_$1 + bioportal: + name: Cell Line Ontology + prefix: CLO + cellosaurus: + category: Cell line databases/resources + homepage: http://www.clo-ontology.org + name: Cell Line Ontology + prefix: CLO + uri_format: https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http://purl.obolibrary.org/obo/$1 + example: '0000091' + fairsharing: + abbreviation: CLO + description: The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Thousands of cell lines have been artificially developed and used for different applications. Integration of data from multiple sources is a challenge, confounded by lack of consistent naming conventions, contamination of cell lines, and provision of the same cell lines by multiple commercial sources but with different biological attributes. CLO is a community-based effort to represent all cell lines in a standard ontology approach. + id: '1012' + name: Cell Line Ontology + prefix: FAIRsharing.4dvtcz + subjects: + - Life Science + - Cell Biology + mappings: + biocontext: CLO + bioportal: CLO + cellosaurus: CLO + fairsharing: FAIRsharing.4dvtcz + obofoundry: clo + ols: clo + ontobee: CLO + prefixcommons: clo + obofoundry: + appears_in: + - mco + contact: siiraa@umich.edu + contact.github: siiraa + contact.label: Sirarat Sarntivijai + contact.orcid: 0000-0002-2548-641X + depends_on: + - cl + - doid + - ncbitaxon + - uberon + deprecated: false + description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning. + download.owl: http://purl.obolibrary.org/obo/clo.owl + homepage: http://www.clo-ontology.org + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Cell Line Ontology + preferredPrefix: CLO + prefix: clo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/25852852 + title: 'CLO: The Cell Line Ontology' + repository: https://github.com/CLO-Ontology/CLO + ols: + description: The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. + download: http://purl.obolibrary.org/obo/clo.owl + homepage: http://www.clo-ontology.org + name: 'CLO: Cell Line Ontology' + prefix: clo + version: 2.1.178 + ontobee: + library: Library + name: Cell Line Ontology + prefix: CLO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1314' + description: The Cell Line Ontology (CLO) is a community-based ontology in domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. + example: CL:0000232 + homepage: http://sourceforge.net/projects/clo-ontology/ + keywords: + - ontology + name: Cell Line Ontology + pattern: ^CL:\d{7}$ + prefix: clo + pubmed_ids: + - '15693950' + synonyms: + - CLO + wikidata: + prefix: P2158 +cls: + cellosaurus: + category: Cell line collections + homepage: https://cls.shop/ + name: Cell Lines Service + prefix: CLS + uri_format: https://www.clsgmbh.de/$1.html + example: 300108/p3934_A-172 + mappings: + cellosaurus: CLS +clyh: + bioportal: + name: Clytia hemisphaerica Development and Anatomy Ontology + prefix: CLYH + example: '1000100' + mappings: + bioportal: CLYH + obofoundry: clyh + ols: clyh + ontobee: CLYH + obofoundry: + contact: lucas.leclere@obs-vlfr.fr + contact.github: L-Leclere + contact.label: Lucas Leclere + contact.orcid: 0000-0002-7440-0467 + depends_on: + - iao + - ro + - uberon + deprecated: false + description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. + download.obo: http://purl.obolibrary.org/obo/clyh.obo + download.owl: http://purl.obolibrary.org/obo/clyh.owl + homepage: https://github.com/EBISPOT/clyh_ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Clytia hemisphaerica Development and Anatomy Ontology + preferredPrefix: CLYH + prefix: clyh + repository: https://github.com/EBISPOT/clyh_ontology + ols: + description: Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. + download: https://raw.githubusercontent.com/EBISPOT/clyh_ontology/master/clyh.owl + name: Clytia hemisphaerica Development and Anatomy Ontology (CLYH) + prefix: clyh + version: 2020-05-29 + version.iri: http://purl.obolibrary.org/obo/clyh/releases/2020-05-29/clyh.owl + ontobee: + library: Library + name: Clytia hemisphaerica Development and Anatomy Ontology + prefix: CLYH + pattern: ^\d+$ +cmecs: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard. + example: '595' + homepage: https://cmecscatalog.org/cmecs + name: Costal and Marine Ecological Classification Standard + pattern: ^\d+$ + references: + - http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf + uri_format: https://cmecscatalog.org/cmecs/classification/unit/$1.html +cmf: + biocontext: + is_identifiers: false + is_obo: true + prefix: CMF + uri_format: http://purl.obolibrary.org/obo/CMF_$1 + deprecated: true + description: This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain + mappings: + biocontext: CMF + obofoundry: cmf + ontobee: CMF + obofoundry: + contact: engelsta@ohsu.edu + contact.label: Mark Engelstad + contact.orcid: 0000-0001-5889-4463 + deprecated: true + homepage: https://code.google.com/p/craniomaxillofacial-ontology/ + name: CranioMaxilloFacial ontology + prefix: cmf + ontobee: + library: Library + name: CranioMaxilloFacial ontology + prefix: CMF +cmo: + biocontext: + is_identifiers: false + is_obo: true + prefix: CMO + uri_format: http://purl.obolibrary.org/obo/CMO_$1 + bioportal: + name: Clinical Measurement Ontology + prefix: CMO + example: '0001350' + fairsharing: + abbreviation: CMO + description: The Clinical Measurement Ontology is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. + id: '885' + name: Clinical Measurement Ontology + prefix: FAIRsharing.dq78pn + subjects: + - Life Science + - Biomedical Science + - Preclinical Studies + mappings: + biocontext: CMO + bioportal: CMO + fairsharing: FAIRsharing.dq78pn + obofoundry: cmo + ols: cmo + ontobee: CMO + obofoundry: + appears_in: + - scdo + contact: jrsmith@mcw.edu + contact.github: jrsjrs + contact.label: Jennifer Smith + contact.orcid: 0000-0002-6443-9376 + deprecated: false + description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. + download.obo: http://purl.obolibrary.org/obo/cmo.obo + download.owl: http://purl.obolibrary.org/obo/cmo.owl + homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Clinical measurement ontology + preferredPrefix: CMO + prefix: cmo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 + title: Three ontologies to define phenotype measurement data. + - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 + title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' + repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology + ols: + description: Morphological and physiological measurement records generated from clinical and model organism research and health programs. + download: http://purl.obolibrary.org/obo/cmo.owl + homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html + name: Clinical measurement ontology + prefix: cmo + version: 2019-02-19 + version.iri: http://purl.obolibrary.org/obo/cmo/releases/2019-02-19/cmo.owl + ontobee: + library: Library + name: Clinical measurement ontology + prefix: CMO + pattern: ^\d{7}$ +cmpo: + bioportal: + name: Cellular microscopy phenotype ontology + prefix: CMPO + example: '0000435' + fairsharing: + abbreviation: CMPO + description: Cellular Microscopy Phenotype Ontology (CMPO) is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations + id: '157' + name: Cellular Microscopy Phenotype Ontology + prefix: FAIRsharing.knp11s + subjects: + - Cell Biology + mappings: + bioportal: CMPO + fairsharing: FAIRsharing.knp11s + ols: cmpo + ols: + contact: jupp@ebi.ac.uk + description: CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. + download: http://www.ebi.ac.uk/cmpo/cmpo.owl + homepage: http://www.ebi.ac.uk/cmpo + name: Cellular Microscopy Phenotype Ontology + prefix: cmpo + version: 2017-12-19 + version.iri: http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl + pattern: ^\d{7}$ +co_320: + example: '0000618' + fairsharing: + abbreviation: CO_320 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The IBP Rice Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Based on SES, Rice Descriptor and IRIS DB. + id: '832' + name: Rice Ontology + prefix: FAIRsharing.2jkxp5 + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.2jkxp5 + ols: co_320 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables + download: https://cropontology.org/ontology/CO_320/Rice/owl + homepage: https://cropontology.org/ontology/CO_320/Rice + name: Rice ontology + prefix: co_320 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_320:$1 +co_321: + example: '0000449' + fairsharing: + abbreviation: CO_321 + description: This ontology defines traits of the International Wheat Information System (IWIS) database and wheat descriptor. The Wheat Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '728' + name: Wheat Ontology + prefix: FAIRsharing.czzmpg + subjects: + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.czzmpg + ols: co_321 + ols: + contact: helpdesk@cropontology-curationtool.org + description: July 2018 + download: https://cropontology.org/ontology/CO_321/Wheat/owl + homepage: https://cropontology.org/ontology/CO_321/Wheat + name: Wheat ontology + prefix: co_321 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_321:$1 +co_322: + example: '0000773' + fairsharing: + abbreviation: CO_322 + description: The Maize Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '925' + name: Maize Ontology + prefix: FAIRsharing.eeyne8 + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.eeyne8 + ols: co_322 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Maize Trait Dictionary in template 5 - CIMMYT- September 2016 + download: https://cropontology.org/ontology/CO_322/Maize/owl + homepage: https://cropontology.org/ontology/CO_322/Maize + name: Maize ontology + prefix: co_322 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_322:$1 +co_323: + example: '0000252' + fairsharing: + abbreviation: CO_323 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Barley Ontology is one of these reference plant ontologies integrated within the Crop Ontology. Its focus is on traits and variable used in field trials for breeding. + id: '872' + name: Barley Ontology + prefix: FAIRsharing.f69084 + subjects: + - Botany + - Agriculture + mappings: + fairsharing: FAIRsharing.f69084 + ols: co_323 + ols: + contact: helpdesk@cropontology-curationtool.org + description: ICARDA - TDv5 - Sept 2018 + download: https://cropontology.org/ontology/CO_323/Barley/owl + homepage: https://cropontology.org/ontology/CO_323/Barley + name: Barley ontology + prefix: co_323 + version: 2019-11-20 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_323:$1 +co_324: + example: '0000111' + fairsharing: + abbreviation: CO_324 + description: The Sorghum Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '1077' + name: Sorghum Ontology + prefix: FAIRsharing.dxx0c + subjects: + - Botany + - Agriculture + mappings: + fairsharing: FAIRsharing.dxx0c + ols: co_324 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Sorghum TDv5 - Oct 2019 + download: https://cropontology.org/ontology/CO_324/Sorghum/owl + homepage: https://cropontology.org/ontology/CO_324/Sorghum + name: Sorghum ontology + prefix: co_324 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_324:$1 +co_325: + example: '0000519' + fairsharing: + abbreviation: CO_325 + description: The Banana Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '642' + name: Banana Ontology + prefix: FAIRsharing.gdszhh + subjects: + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.gdszhh + ols: co_325 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019 + download: https://cropontology.org/ontology/CO_325/Banana/owl + homepage: https://cropontology.org/ontology/CO_325/Banana + name: Banana ontology + prefix: co_325 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_325:$1 +co_326: + example: '0000254' + mappings: + ols: co_326 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Draft version + download: https://cropontology.org/ontology/CO_326/Coconut/owl + homepage: https://cropontology.org/ontology/CO_326/Coconut + name: Coconut ontology + prefix: co_326 + pattern: ^\d{7}$ +co_327: + example: '0000095' + fairsharing: + abbreviation: CO_327 + description: The goal of the CGIAR Pearl Millet Ontology is to help improve food security for subsistence smallholder farmers in East and West Africa with productive and nutritious pearl millet food and fodder production technologies. + id: '495' + name: Pearl Millet Ontology + prefix: FAIRsharing.4e3qh9 + subjects: + - Botany + - Agriculture + mappings: + fairsharing: FAIRsharing.4e3qh9 + ols: co_327 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016 + download: http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl + homepage: http://www.cropontology.org/ontology/CO_327/Pearl%20millet + name: Pearl millet ontology + prefix: co_327 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_327:$1 +co_330: + example: '0000106' + fairsharing: + abbreviation: CO_330 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1307' + name: Potato Ontology + prefix: FAIRsharing.4fa657 + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.4fa657 + ols: co_330 + ols: + contact: helpdesk@cropontology-curationtool.org + description: CIP - potato ontology - december 2018 + download: https://cropontology.org/ontology/CO_330/Potato/owl + homepage: https://cropontology.org/ontology/CO_330/Potato + name: Potato ontology + prefix: co_330 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_330:$1 +co_331: + example: '0000088' + fairsharing: + abbreviation: CO_331 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sweet Potato Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '496' + name: Sweet Potato Ontology + prefix: FAIRsharing.4g5qcw + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.4g5qcw + ols: co_331 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Sweet Potato Trait Dictionary in template v5 - CIP - November 2019 + download: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl + homepage: http://www.cropontology.org/ontology/CO_331/Sweet%20Potato + name: Sweet Potato ontology + prefix: co_331 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_331:$1 +co_333: + example: '3000045' + fairsharing: + abbreviation: CO_333 + description: This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution and breeding company within the project. Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Beet Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1079' + name: Beet Ontology + prefix: FAIRsharing.af5655 + subjects: + - Botany + - Plant Breeding + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.af5655 + ols: co_333 + ols: + contact: helpdesk@cropontology-curationtool.org + description: 'This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.' + download: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl + homepage: http://www.cropontology.org/ontology/CO_333/Beet%20Ontology + name: Beet Ontology ontology + prefix: co_333 + pattern: ^\d+$ + uri_format: https://www.cropontology.org/rdf/CO_333:$1 +co_334: + example: '0000070' + fairsharing: + abbreviation: CO_334 + description: Crop-specific trait ontologies enhance the interoperability and effectiveness of data exchange between the data sources which adopt it, by providing standard concepts that are use to describe phenotypes stored in those sources. As one of them, the Cassava Ontology is actively used and shared in different databases such as the BMS (Breeding Management system) of the IBP or the CassavaBase. Cassava, a major staple crop, is the main source of calories for 500 million people across the globe. A perennial woody shrub native to Latin America, cassava is primarily grown as an annual crop in the humid tropics. A cash crop as well as a subsistence crop, cassava's large edible starchy roots are a source of low-cost carbohydrates for millions. Cassava end products range from fresh roots cooked, boiled, baked or fried at the household level, to highly processed starch as a food additive. + id: '1099' + name: IBP Cassava Trait Ontology + prefix: FAIRsharing.v06c4q + subjects: + - Botany + - Agriculture + - Nutritional Science + mappings: + fairsharing: FAIRsharing.v06c4q + ols: co_334 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016 + download: https://cropontology.org/ontology/CO_334/Cassava/owl + homepage: https://cropontology.org/ontology/CO_334/Cassava + name: Cassava ontology + prefix: co_334 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_334:$1 +co_335: + example: '0000189' + fairsharing: + abbreviation: CO_335 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Common Bean Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1096' + name: Common Bean Ontology + prefix: FAIRsharing.a14123 + subjects: + - Botany + - Agriculture + mappings: + fairsharing: FAIRsharing.a14123 + ols: co_335 + ols: + contact: helpdesk@cropontology-curationtool.org + description: CIAT Common bean trait dictionary - version August 2014 + download: http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl + homepage: http://www.cropontology.org/ontology/CO_335/Common%20Bean + name: Common Bean ontology + prefix: co_335 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_335:$1 +co_336: + example: '0000339' + fairsharing: + abbreviation: CO_336 + description: The Soybean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '669' + name: Soybean Ontology + prefix: FAIRsharing.j75srj + subjects: + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.j75srj + ols: co_336 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Soybean Trait Dictionary in template v5 - IITA - July 2015 + download: https://cropontology.org/ontology/CO_336/Soybean/owl + homepage: https://cropontology.org/ontology/CO_336/Soybean + name: Soybean ontology + prefix: co_336 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_336:$1 +co_337: + example: '0000054' + fairsharing: + abbreviation: CO_337 + description: The Groundnut Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '40' + name: Groundnut Ontology + prefix: FAIRsharing.ge8y23 + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.ge8y23 + ols: co_337 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015 + download: https://cropontology.org/ontology/CO_337/Groundnut/owl + homepage: https://cropontology.org/ontology/CO_337/Groundnut + name: Groundnut ontology + prefix: co_337 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_337:$1 +co_338: + example: '0000138' + fairsharing: + abbreviation: CO_338 + description: Development of crop-specific trait ontologies including the Chickpea Ontology began in 2008 as part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '1321' + name: Chickpea Ontology + prefix: FAIRsharing.js20q3 + subjects: + - Botany + - Agriculture + mappings: + fairsharing: FAIRsharing.js20q3 + ols: co_338 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015 + download: https://cropontology.org/ontology/CO_338/Chickpea/owl + homepage: https://cropontology.org/ontology/CO_338/Chickpea + name: Chickpea ontology + prefix: co_338 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_338:$1 +co_339: + example: '0000032' + fairsharing: + abbreviation: CO_339 + description: The Lentil Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '1352' + name: Lentil Ontology + prefix: FAIRsharing.ry1ezg + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.ry1ezg + ols: co_339 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Lentil Trait Dictionary in template v5 - ICARDA - July 2015 + download: https://cropontology.org/ontology/CO_339/Lentil/owl + homepage: https://cropontology.org/ontology/CO_339/Lentil + name: Lentil ontology + prefix: co_339 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_339:$1 +co_340: + example: '0000639' + fairsharing: + abbreviation: CO_340 + description: The Cowpea Trait Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe the data. The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases is important in comparative phenotypic and genotypic studies across species and gene-discovery experiments as it provides harmonized description of the data and therefore facilitates the retrieval of information. + id: '1302' + name: IBP Cowpea Trait Ontology + prefix: FAIRsharing.31apg2 + subjects: + - Botany + - Agriculture + mappings: + fairsharing: FAIRsharing.31apg2 + ols: co_340 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Cowpea Trait Dictionary in template v5 - IITA - August 2015 + download: https://cropontology.org/ontology/CO_340/Cowpea/owl + homepage: https://cropontology.org/ontology/CO_340/Cowpea + name: Cowpea ontology + prefix: co_340 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_340:$1 +co_341: + example: '0000140' + fairsharing: + abbreviation: CO_341 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Pigeon Pea Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1078' + name: Pigeon Pea Ontology + prefix: FAIRsharing.ehe3yp + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.ehe3yp + ols: co_341 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015 + download: https://cropontology.org/ontology/CO_341/Pigeonpea/owl + homepage: https://cropontology.org/ontology/CO_341/Pigeonpea + name: Pigeonpea ontology + prefix: co_341 + version: 2019-11-18 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_341:$1 +co_343: + example: '0100010' + fairsharing: + abbreviation: CO_343 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Yam Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '838' + name: Yam Ontology + prefix: FAIRsharing.7e9cff + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.7e9cff + ols: co_343 + ols: + contact: helpdesk@cropontology-curationtool.org + description: version 2019 - pvs + download: https://cropontology.org/ontology/CO_343/Yam/owl + homepage: https://cropontology.org/ontology/CO_343/Yam + name: Yam ontology + prefix: co_343 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_343:$1 +co_345: + example: '0000127' + fairsharing: + abbreviation: CO_345 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Brachiaria Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '494' + name: Brachiaria Ontology + prefix: FAIRsharing.9e9683 + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.9e9683 + ols: co_345 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Brachiaria (forages) ontology TD v5 - Version Oct 2016 + download: https://cropontology.org/ontology/CO_345/Brachiaria/owl + homepage: https://cropontology.org/ontology/CO_345/Brachiaria + name: Brachiaria ontology + prefix: co_345 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_345:$1 +co_346: + example: '0000199' + fairsharing: + abbreviation: CO_346 + description: The Mungbean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data. + id: '1100' + name: Mungbean Ontology + prefix: FAIRsharing.fgd5gq + subjects: + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.fgd5gq + ols: co_346 + ols: + contact: helpdesk@cropontology-curationtool.org + description: oct 2016 + download: https://cropontology.org/ontology/CO_346/Mungbean/owl + homepage: https://cropontology.org/ontology/CO_346/Mungbean + name: Mungbean ontology + prefix: co_346 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_346:$1 +co_347: + example: '0000108' + fairsharing: + abbreviation: CO_347 + description: The Castor Bean Ontology is part of the Crop Ontology (CO) project. The Crop Ontology has been created to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms. The concepts of the CO are being used to curate agronomic databases and describe data. + id: '1070' + name: Castor Bean Ontology + prefix: FAIRsharing.qrrvyk + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.qrrvyk + ols: co_347 + ols: + contact: helpdesk@cropontology-curationtool.org + description: 'March 2017 version ' + download: http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl + homepage: http://www.cropontology.org/ontology/CO_347/Castor%20bean + name: Castor bean ontology + prefix: co_347 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_347:$1 +co_348: + example: '1100107' + fairsharing: + abbreviation: CO_348 + description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Brassica Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1019' + name: Brassica Ontology + prefix: FAIRsharing.af7a2d + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.af7a2d + ols: co_348 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France). + download: https://cropontology.org/ontology/CO_348/Brassica/owl + homepage: https://cropontology.org/ontology/CO_348/Brassica + name: Brassica ontology + prefix: co_348 + version: 2019-11-29 + pattern: ^\d+$ + uri_format: https://www.cropontology.org/rdf/CO_348:$1 +co_350: + example: '0000215' + fairsharing: + abbreviation: CO_350 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Oat Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. The Oat Trait Dictionary was commissioned by Oat Global (http://oatglobal.org/) to hold the traits used in the T3/Oat database (http://triticeaetoolbox.org/oat/). + id: '652' + name: Oat Trait Ontology + prefix: FAIRsharing.35e1c3 + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.35e1c3 + ols: co_350 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo + download: https://cropontology.org/ontology/CO_350/Oat/owl + homepage: https://cropontology.org/ontology/CO_350/Oat + name: Oat ontology + prefix: co_350 + version: 2019-10-09 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_350:$1 +co_356: + example: '4000027' + fairsharing: + abbreviation: CO_356 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Vitis Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1092' + name: Vitis Ontology + prefix: FAIRsharing.c7f4d7 + subjects: + - Botany + - Agriculture + - Life Science + mappings: + fairsharing: FAIRsharing.c7f4d7 + ols: co_356 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Grape Ontology including OIV and bioversity descriptors. INRA July 2017 + download: https://cropontology.org/ontology/CO_356/Vitis/owl + homepage: https://cropontology.org/ontology/CO_356/Vitis + name: Vitis ontology + prefix: co_356 + version: 2019-11-29 + pattern: ^\d+$ + uri_format: https://www.cropontology.org/rdf/CO_356:$1 +co_357: + example: '1000290' + fairsharing: + abbreviation: CO_357 + description: The Woody Plant Ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Woody Plant Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1103' + name: Woody Plant Ontology + prefix: FAIRsharing.2b04ae + subjects: + - Botany + - Life Science + mappings: + fairsharing: FAIRsharing.2b04ae + ols: co_357 + ols: + contact: helpdesk@cropontology-curationtool.org + description: 'This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.' + download: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl + homepage: http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology + name: Woody Plant Ontology ontology + prefix: co_357 + pattern: ^\d+$ + uri_format: https://www.cropontology.org/rdf/CO_357:$1 +co_358: + example: '0000139' + mappings: + ols: co_358 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Cotton ontology from CottonGen database - June 2019 + download: https://cropontology.org/ontology/CO_358/Cotton/owl + homepage: https://cropontology.org/ontology/CO_358/Cotton + name: Cotton ontology + prefix: co_358 + version: 2020-01-03 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_358:$1 +co_359: + example: '0000947' + mappings: + ols: co_359 + ols: + contact: helpdesk@cropontology-curationtool.org + description: December 2019 + download: https://cropontology.org/ontology/CO_359/Sunflower/owl + homepage: https://cropontology.org/ontology/CO_359/Sunflower + name: Sunflower ontology + prefix: co_359 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_359:$1 +co_360: + example: '0000071' + fairsharing: + abbreviation: CO_360 + description: Reference Plant Ontologies are being developed in the context of the Planteome project and are being integrated with the Crop Ontology, which provides harmonized breeders’ trait names, measurement methods, scales and standard variables for many crops. The Sugar Kelp Trait Ontology is one of these reference plant ontologies integrated within the Crop Ontology. + id: '1093' + name: Sugar Kelp Trait Ontology + prefix: FAIRsharing.1c1738 + subjects: + - Botany + - Life Science + mappings: + fairsharing: FAIRsharing.1c1738 + ols: co_360 + ols: + contact: helpdesk@cropontology-curationtool.org + description: Sugar Kelp trait ontology + download: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl + homepage: http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait + name: Sugar Kelp trait ontology + prefix: co_360 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_360:$1 +co_365: + example: '0000205' + mappings: + ols: co_365 + ols: + contact: helpdesk@cropontology-curationtool.org + description: developed by ICARDA - Dec 2018 + download: https://cropontology.org/ontology/CO_365/Fababean/owl + homepage: https://cropontology.org/ontology/CO_365/Fababean + name: Fababean ontology + prefix: co_365 + version: 2019-10-15 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_365:$1 +co_366: + example: '0000072' + mappings: + ols: co_366 + ols: + contact: helpdesk@cropontology-curationtool.org + description: version Dec 2019 + download: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl + homepage: http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut + name: Bambara groundnut ontology + prefix: co_366 + pattern: ^\d{7}$ + uri_format: https://www.cropontology.org/rdf/CO_366:$1 +cob: + bioportal: + name: Core Ontology for Biology and Biomedicine + prefix: COB + example: '0000080' + mappings: + bioportal: COB + obofoundry: cob + ols: cob + ontobee: COB + obofoundry: + contact: bpeters@lji.org + contact.github: bpeters42 + contact.label: Bjoern Peters + contact.orcid: 0000-0002-8457-6693 + deprecated: false + description: COB brings together key terms from a wide range of OBO projects to improve interoperability. + download.owl: http://purl.obolibrary.org/obo/cob.owl + homepage: https://github.com/OBOFoundry/COB + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Core Ontology for Biology and Biomedicine + preferredPrefix: COB + prefix: cob + repository: https://github.com/OBOFoundry/COB + ols: + description: COB brings together key terms from a wide range of OBO projects to improve interoperability. + download: http://purl.obolibrary.org/obo/cob.owl + homepage: https://github.com/OBOFoundry/COB + name: Core Ontology for Biology and Biomedicine + prefix: cob + version: 2022-05-02 + version.iri: http://purl.obolibrary.org/obo/cob/releases/2022-05-02/cob.owl + ontobee: + library: Library + name: Core Ontology for Biology and Biomedicine + prefix: COB + pattern: ^\d{7}$ +coconut: + comment: '@mSorok is the dev of the resource, hope I got it right!' + contributor: + github: adafede + name: Adriano Rutz + orcid: 0000-0003-0443-9902 + description: COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a "flat" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties. + example: CNP0171505 + homepage: https://coconut.naturalproducts.net + name: COlleCtion of Open Natural ProdUcTs + pattern: ^CNP\d{7}$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: https://coconut.naturalproducts.net/compound/coconut_id/$1 +codelink: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).' + example: GE86325 + homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt + name: GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray + pattern: ^GE\d+$ + references: + - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt + - https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt +cog: + biolink: + is_identifiers: false + is_obo: false + prefix: COG + uri_format: https://www.ncbi.nlm.nih.gov/research/cog-project/$1 + contact: + email: cogs@ncbi.nlm.nih.gov + name: Michael Y Galperin + orcid: 0000-0002-2265-5572 + description: 'COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.' + example: COG0001 + fairsharing: + abbreviation: COG + description: Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. + id: '1968' + name: 'Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes' + prefix: FAIRsharing.djsbw2 + subjects: + - Life Science + go: + homepage: http://www.ncbi.nlm.nih.gov/COG/ + name: NCBI COG cluster + prefix: COG_Cluster + uri_format: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=$1 + homepage: https://www.ncbi.nlm.nih.gov/research/cog/ + mappings: + biolink: COG + fairsharing: FAIRsharing.djsbw2 + go: COG_Cluster + prefixcommons: cog + name: Cluster of orthologous genes + pattern: ^COG\d+$ + prefixcommons: + description: Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. + example: '145262' + homepage: http://www.ncbi.nlm.nih.gov/COG + keywords: + - protein + - genome + name: 'Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes' + pattern: ^\d+$ + prefix: cog + uri_format: http://www.ncbi.nlm.nih.gov/COG/grace/cogenome.cgi?g=$1 + synonyms: + - COG_Cluster + uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cog/$1 +cog.category: + contact: + email: cogs@ncbi.nlm.nih.gov + name: Michael Y Galperin + orcid: 0000-0002-2265-5572 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Higher-level classifications of COG Pathways + example: K + homepage: https://www.ncbi.nlm.nih.gov/research/cog/ + name: COG Categories + part_of: cog + uri_format: https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1 +cog.pathway: + contact: + email: cogs@ncbi.nlm.nih.gov + name: Michael Y Galperin + orcid: 0000-0002-2265-5572 + description: Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. + example: NAD%20biosynthesis + go: + homepage: http://www.ncbi.nlm.nih.gov/COG/ + name: NCBI COG pathway + prefix: COG_Pathway + uri_format: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=$1 + homepage: https://www.ncbi.nlm.nih.gov/research/cog/pathways + mappings: + go: COG_Pathway + name: COG Pathways + part_of: cog + uri_format: https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1 +cohd: + comment: not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for. + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 + homepage: https://github.com/MIT-LCP/mimic-omop + name: MIMIC III Database + no_own_terms: true + repository: https://github.com/MIT-LCP/mimic-omop +colao: + bioportal: + name: Coleoptera Anatomy Ontology + prefix: COLAO + example: '0000000' + mappings: + bioportal: COLAO + obofoundry: colao + ols: colao + ontobee: COLAO + name: Coleoptera Anatomy Ontology + obofoundry: + contact: entiminae@gmail.com + contact.github: JCGiron + contact.label: Jennifer C. Giron + contact.orcid: 0000-0002-0851-6883 + depends_on: + - aism + - bfo + - bspo + - caro + - pato + - ro + - uberon + deprecated: false + description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone. + download.obo: http://purl.obolibrary.org/obo/colao.obo + download.owl: http://purl.obolibrary.org/obo/colao.owl + homepage: https://github.com/insect-morphology/colao + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Coleoptera Anatomy Ontology (COLAO) + preferredPrefix: COLAO + prefix: colao + repository: https://github.com/insect-morphology/colao + ols: + description: The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. + download: http://purl.obolibrary.org/obo/colao.owl + homepage: https://github.com/insect-morphology/colao + name: Coleoptera Anatomy Ontology + prefix: colao + version: 2021-12-14 + version.iri: http://purl.obolibrary.org/obo/colao/releases/2021-12-14/colao.owl + ontobee: + library: Library + name: Coleoptera Anatomy Ontology + prefix: COLAO + pattern: ^\d{7}$ +colonatlas: + cellosaurus: + category: Cell line databases/resources + homepage: http://www.coloncanceratlas.org + name: Colorectal Cancer Atlas + prefix: ColonAtlas + uri_format: http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 + example: ALA + mappings: + cellosaurus: ColonAtlas +combine.specifications: + biocontext: + is_identifiers: true + is_obo: false + prefix: COMBINE.SPECIFICATIONS + uri_format: http://identifiers.org/combine.specifications/$1 + mappings: + biocontext: COMBINE.SPECIFICATIONS + miriam: combine.specifications + n2t: combine.specifications + miriam: + deprecated: false + description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. + homepage: https://co.mbine.org/standards/ + id: '00000258' + name: COMBINE specifications + namespaceEmbeddedInLui: false + pattern: ^\w+(\-|\.|\w)*$ + prefix: combine.specifications + sampleId: sbgn.er.level-1.version-1.2 + uri_format: https://co.mbine.org/specifications/$1 + n2t: + description: The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. + example: sbgn.er.level-1.version-1.2 + homepage: https://co.mbine.org/standards/ + name: COMBINE at EBI + namespaceEmbeddedInLui: false + pattern: ^\w+(\-|\.|\w)*$ + prefix: combine.specifications + uri_format: https://co.mbine.org/specifications/$1 +come: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif. + example: MOL000160 + homepage: https://www.flymine.org/come + mappings: + prefixcommons: come + name: The Bioinorganic Motif Database + prefixcommons: + description: COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif. + example: BIM000347 + homepage: http://www.flymine.org/come/ + keywords: + - protein + name: COMe + pattern: ^BIM\d+$ + prefix: come + uri_format: http://www.flymine.org/come/entry?gn=$1 + uri_format: https://www.flymine.org/come/entry?gn=$1 +complexportal: + biocontext: + is_identifiers: true + is_obo: false + prefix: COMPLEXPORTAL + uri_format: http://identifiers.org/complexportal/$1 + example: CPX-263 + go: + homepage: https://www.ebi.ac.uk/complexportal + name: Complex Portal database of macromolecular complexes + prefix: ComplexPortal + uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 + mappings: + biocontext: COMPLEXPORTAL + go: ComplexPortal + miriam: complexportal + n2t: complexportal + uniprot: ComplexPortal + wikidata: P7718 + miriam: + deprecated: false + description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. + homepage: https://www.ebi.ac.uk/complexportal + id: '00000657' + name: Complex Portal + namespaceEmbeddedInLui: false + pattern: ^CPX-[0-9]+$ + prefix: complexportal + sampleId: CPX-2158 + uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 + n2t: + description: A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases. + example: CPX-2158 + homepage: https://www.ebi.ac.uk/complexportal + name: Complex Portal + namespaceEmbeddedInLui: false + pattern: ^CPX-[0-9]+$ + prefix: complexportal + uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 + name: Complex Portal + synonyms: + - ComplexPortal + uniprot: + category: Protein-protein interaction databases + identifier: '228' + link_is_explicit: 'true' + name: 'ComplexPortal: manually curated resource of macromolecular complexes' + prefix: ComplexPortal + uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 + wikidata: + database: Q47196990 + database.homepage: https://www.ebi.ac.uk/complexportal/home + database.label: Complex Portal + homepage: https://www.ebi.ac.uk/complexportal/home + name: Complex Portal accession ID + pattern: ^CPX-[0-9]+$ + prefix: P7718 + uri_format: https://www.ebi.ac.uk/complexportal/complex/$1 +comptox: + biocontext: + is_identifiers: true + is_obo: false + prefix: COMPTOX + uri_format: http://identifiers.org/comptox/$1 + mappings: + biocontext: COMPTOX + miriam: comptox + n2t: comptox + miriam: + deprecated: false + description: The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. + homepage: https://comptox.epa.gov/dashboard + id: '00000658' + name: CompTox Chemistry Dashboard + namespaceEmbeddedInLui: false + pattern: ^DTXSID\d+$ + prefix: comptox + sampleId: DTXSID2021028 + uri_format: https://comptox.epa.gov/dashboard/$1 + n2t: + description: The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. + example: DTXSID2021028 + homepage: https://comptox.epa.gov/dashboard + name: CompTox Chemistry Dashboard + namespaceEmbeddedInLui: false + pattern: ^DTXSID\d+$ + prefix: comptox + uri_format: https://comptox.epa.gov/dashboard/$1 + wikidata: + prefix: P3117 +compulyeast: + biocontext: + is_identifiers: true + is_obo: false + prefix: COMPULYEAST + uri_format: http://identifiers.org/compulyeast/$1 + fairsharing: + abbreviation: Compulyeast + description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. + id: '2079' + name: Compulyeast + prefix: FAIRsharing.rbjs3e + subjects: [] + mappings: + biocontext: COMPULYEAST + fairsharing: FAIRsharing.rbjs3e + miriam: compulyeast + n2t: compulyeast + miriam: + deprecated: false + description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. + homepage: http://compluyeast2dpage.dacya.ucm.es/ + id: '00000198' + name: Compulyeast + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: compulyeast + sampleId: O08709 + uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 + n2t: + description: Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. + example: O08709 + homepage: http://compluyeast2dpage.dacya.ucm.es/ + name: Compluyeast database at Universidad Complutense Madrid + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: compulyeast + uri_format: http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1 + name: Compluyeast-2D-DB + provides: uniprot +conoserver: + biocontext: + is_identifiers: true + is_obo: false + prefix: CONOSERVER + uri_format: http://identifiers.org/conoserver/$1 + fairsharing: + abbreviation: ConoServer + description: ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. ConoServer's data are first collected from the peer reviewed literature and from publicly available databases, including UniProtKB/Swiss-Prot, NCBI nucleotide (nt), and the World Wide Protein Data Bank. The data are then curated manually, which include the addition of references, the analysis of sequence regions, the identification of cysteine frameworks and gene superfamilies, and the identification of mature peptides in the precusor sequences. + id: '1563' + name: ConoServer + prefix: FAIRsharing.y00hz4 + subjects: + - Neurophysiology + - Statistics + - Life Science + - Synthetic Biology + mappings: + biocontext: CONOSERVER + fairsharing: FAIRsharing.y00hz4 + miriam: conoserver + n2t: conoserver + uniprot: ConoServer + miriam: + deprecated: false + description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. + homepage: http://www.conoserver.org/ + id: '00000254' + name: Conoserver + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: conoserver + sampleId: '2639' + uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 + n2t: + description: ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. + example: '2639' + homepage: http://www.conoserver.org/ + name: ConoServer at University of Queensland + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: conoserver + uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 + name: ConoServer + uniprot: + category: Organism-specific databases + identifier: '156' + link_is_explicit: 'true' + name: 'ConoServer: Cone snail toxin database' + prefix: ConoServer + uri_format: http://www.conoserver.org/?page=card&table=protein&id=$1 +conso: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases. + example: CONSO00010 + homepage: https://pharmacome.github.io/conso/ + name: Curation of Neurodegeneration Supporting Ontology + pattern: ^CONSO\d{5}$ + uri_format: https://pharmacome.github.io/conso/$1 +coriell: + biocontext: + is_identifiers: false + is_obo: false + prefix: Coriell + uri_format: https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1 + cellosaurus: + category: Cell line collections + homepage: https://catalog.coriell.org + name: Coriell Institute Biorepositories + prefix: Coriell + uri_format: https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=$1&Product=CC + go: + description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. + homepage: http://ccr.coriell.org/ + name: Coriell Institute for Medical Research + prefix: CORIELL + uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 + mappings: + biocontext: Coriell + cellosaurus: Coriell + go: CORIELL + miriam: coriell + n2t: coriell + miriam: + deprecated: false + description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. + homepage: http://ccr.coriell.org/ + id: '00000439' + name: Coriell Cell Repositories + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}\d+$ + prefix: coriell + sampleId: GM17027 + uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 + n2t: + description: The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. + example: GM17027 + homepage: http://ccr.coriell.org/ + name: Coriell Cell Repositories at Coriell Institute + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}\d+$ + prefix: coriell + uri_format: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1 +corrdb: + fairsharing: + abbreviation: CorrDB + description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies + id: '2591' + name: Animal Trait Correlation Database + prefix: FAIRsharing.IziuCK + subjects: + - Animal Genetics + - Genetics + - Life Science + - Systems Biology + mappings: + fairsharing: FAIRsharing.IziuCK + miriam: corrdb + miriam: + deprecated: false + description: A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies. + homepage: https://www.animalgenome.org + id: '00000831' + name: CorrDB + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: corrdb + sampleId: '37232' + uri_format: https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1 +corum: + biocontext: + is_identifiers: true + is_obo: false + prefix: CORUM + uri_format: http://identifiers.org/corum/$1 + fairsharing: + abbreviation: CORUM + description: CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. + id: '2839' + name: ' Comprehensive Resource of Mammalian protein complexes' + prefix: FAIRsharing.ohbpNw + subjects: + - Bioinformatics + - Biology + go: + homepage: https://mips.helmholtz-muenchen.de/corum/ + name: CORUM - the Comprehensive Resource of Mammalian protein complexes + prefix: CORUM + uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 + mappings: + biocontext: CORUM + fairsharing: FAIRsharing.ohbpNw + go: CORUM + miriam: corum + n2t: corum + prefixcommons: corum + uniprot: CORUM + miriam: + deprecated: false + description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. + homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ + id: '00000440' + name: CORUM + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: corum + sampleId: '100' + uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 + n2t: + description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. + example: '100' + homepage: https://mips.helmholtz-muenchen.de/genre/proj/corum/ + name: CORUM at Institute for Bioinformatics and Systems Biology (Germany) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: corum + uri_format: https://mips.helmholtz-muenchen.de/corum/?id=$1 + name: Comprehensive Resource of Mammalian protein complexes + prefixcommons: + description: The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. + example: '56' + homepage: http://mips.gsf.de/genre/proj/corum + keywords: + - protein + name: the Comprehensive Resource of Mammalian protein complexes + pattern: ^\d+$ + prefix: corum + uri_format: http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$1 + uniprot: + category: Protein-protein interaction databases + identifier: '224' + link_is_explicit: 'true' + name: CORUM comprehensive resource of mammalian protein complexes + prefix: CORUM + uri_format: http://mips.helmholtz-muenchen.de/corum/#?uniprotID=$1 +cosmic: + biocontext: + is_identifiers: false + is_obo: false + prefix: COSMIC + uri_format: http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=$1 + cellosaurus: + category: Polymorphism and mutation databases + homepage: https://cancer.sanger.ac.uk/cosmic + name: Catalogue of somatic mutations in cancer + prefix: Cosmic + uri_format: https://cancer.sanger.ac.uk/cosmic/sample/overview?id=$1 + fairsharing: + abbreviation: COSMIC + description: The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data. + id: '2204' + name: Catalogue of Somatic Mutations in Cancer + prefix: FAIRsharing.s5zmbp + subjects: + - Genetics + - Biomedical Science + mappings: + biocontext: COSMIC + cellosaurus: Cosmic + fairsharing: FAIRsharing.s5zmbp + miriam: cosmic + n2t: cosmic + miriam: + deprecated: false + description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. + homepage: http://cancer.sanger.ac.uk/cosmic/ + id: '00000601' + name: COSMIC Gene + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: cosmic + sampleId: BRAF + uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1 + n2t: + description: COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. + example: BRAF + homepage: http://cancer.sanger.ac.uk/cosmic/ + name: COSMIC Gene at Sanger + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: cosmic + uri_format: http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1 +cosmic.cell: + cellosaurus: + category: Cell line databases/resources + homepage: https://cancer.sanger.ac.uk/cell_lines + name: COSMIC Cell lines Project + prefix: Cosmic-CLP + uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer + example: '906801' + homepage: https://cancer.sanger.ac.uk/cell_lines/ + mappings: + cellosaurus: Cosmic-CLP + name: COSMIC Cell Lines + pattern: ^\d+$ + uri_format: https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1 +covid19: + bioportal: + name: COVID-19 Ontology + prefix: COVID-19 + mappings: + bioportal: COVID-19 + miriam: covid19 + miriam: + deprecated: false + description: Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease. + homepage: https://covid19.sfb.uit.no + id: '00000789' + name: SARS-CoV-2 + namespaceEmbeddedInLui: false + pattern: ^\w+_COVID19_[-\w]+$ + prefix: covid19 + sampleId: SFB_COVID19_MW286762 + uri_format: https://covid19.sfb.uit.no/api/records/$1 +covoc: + contact: + email: zmp@ebi.ac.uk + github: zoependlington + name: Zoë May Pendlington + orcid: 0000-0002-4071-8397 + example: '0010034' + homepage: https://github.com/EBISPOT/covoc + mappings: + ols: covoc + ols: + description: The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. + download: https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl + homepage: https://github.com/EBISPOT/covoc + name: CoVoc Coronavirus Vocabulary + prefix: covoc + version: 2020-08-28 + version.iri: http://purl.obolibrary.org/obo/covoc/releases/2020-08-28/covoc.owl + pattern: ^\d{7}$ + repository: https://github.com/EBISPOT/covoc +cp: + appears_in: + - cl + comment: Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + name: Cellular Phenotypes +cpc: + biocontext: + is_identifiers: true + is_obo: false + prefix: CPC + uri_format: http://identifiers.org/cpc/$1 + fairsharing: + abbreviation: CPC + description: The Climate Prediction Center (CPC) produces operational predictions of climate variability, real-time monitoring of climate and the required data bases, and assessments of the origins of major climate anomalies. These cover time scales from a week to seasons, extending into the future as far as technically feasible, and cover the land, the ocean, and the atmosphere, extending into the stratosphere. + id: '2998' + name: Climate Prediction Center + prefix: FAIRsharing.e08886 + subjects: + - Hydrogeology + - Geography + - Meteorology + - Geodesy + - Earth Science + - Atmospheric Science + mappings: + biocontext: CPC + fairsharing: FAIRsharing.e08886 + miriam: cpc + n2t: cpc + miriam: + deprecated: false + description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. + homepage: https://worldwide.espacenet.com/classification + id: '00000539' + name: Cooperative Patent Classification + namespaceEmbeddedInLui: false + pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ + prefix: cpc + sampleId: A01M1/026 + uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 + n2t: + description: The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. + example: A01M1/026 + homepage: https://worldwide.espacenet.com/classification + name: Cooperative Patent Classification at Espace + namespaceEmbeddedInLui: false + pattern: ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ + prefix: cpc + uri_format: https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 +cpga: + bioportal: + name: Cereal Plant Gross Anatomy Ontology + prefix: GRO-CPGA + deprecated: true + mappings: + biocontext: gro.cpga + bioportal: GRO-CPGA + obofoundry: gro + obofoundry: + contact: po-discuss@plantontology.org + contact.label: Plant Ontology Administrators + deprecated: true + homepage: http://www.gramene.org/plant_ontology/ + inactive: true + name: Cereal Plant Gross Anatomy + prefix: gro +cpt: + biolink: + is_identifiers: false + is_obo: false + prefix: CPT + uri_format: https://www.ama-assn.org/practice-management/cpt/$1 + bioportal: + name: CPT - Current Procedural Terminology + prefix: CPT + contributor: + github: sierra-moxon + name: Sierra Moxon + orcid: 0000-0002-8719-7760 + contributor_extras: + - github: colleenXu + name: Colleen Xu + orcid: 0000-0003-2975-882X + description: Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)] + example: '00103' + fairsharing: + abbreviation: CPT + description: Current Procedural Terminology is a medical nomenclature used to report medical procedures and services under public and private health insurance programs. + id: '198' + name: Current Procedural Terminology + prefix: FAIRsharing.wpxab1 + subjects: + - Medicine + - Health Science + - Biomedical Science + homepage: https://www.aapc.com + mappings: + biolink: CPT + bioportal: CPT + fairsharing: FAIRsharing.wpxab1 + name: Current Procedural Terminology + pattern: ^\d+$ + references: + - https://github.com/biopragmatics/bioregistry/issues/357 + - https://github.com/biopragmatics/bioregistry/pull/358 + - https://github.com/biolink/biolink-model/pull/993 + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: https://www.aapc.com/codes/cpt-codes/$1 +credit: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. + example: Software + homepage: https://casrai.org/credit/ + name: CASRAI Contributor Roles Taxonomy +crisprdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: CRISPRDB + uri_format: http://identifiers.org/crisprdb/$1 + fairsharing: + abbreviation: CRISPRdb + description: CRISPRdb acts as a gateway to a publicly accessible database and software. It enables the easy detection of CRISPR sequences in locally-produced data and the consultation of CRISPR sequence data present in the database. It also gives information on the presence of CRISPR-associated (cas) genes when they have been annotated as such. + id: '2384' + name: CRISPRdb + prefix: FAIRsharing.7sfedh + subjects: + - Life Science + mappings: + biocontext: CRISPRDB + fairsharing: FAIRsharing.7sfedh + miriam: crisprdb + n2t: crisprdb + miriam: + deprecated: false + description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. + homepage: http://crispr.i2bc.paris-saclay.fr/ + id: '00000626' + name: CRISPRdb + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: crisprdb + sampleId: '551115' + uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 + n2t: + description: Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. + example: '551115' + homepage: http://crispr.i2bc.paris-saclay.fr/ + name: CRISPRdb + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: crisprdb + uri_format: http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 +cro: + biocontext: + is_identifiers: false + is_obo: true + prefix: CRO + uri_format: http://purl.obolibrary.org/obo/CRO_$1 + bioportal: + name: Contributor Role Ontology + prefix: CRO + download_obo: https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo + example: '0000038' + mappings: + biocontext: CRO + bioportal: CRO + obofoundry: cro + ols: cro + ontobee: CRO + obofoundry: + contact: whimar@ohsu.edu + contact.github: marijane + contact.label: Marijane White + contact.orcid: 0000-0001-5059-4132 + deprecated: false + description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. + download.owl: http://purl.obolibrary.org/obo/cro.owl + homepage: https://github.com/data2health/contributor-role-ontology + license: CC BY 2.0 + license.url: https://creativecommons.org/licenses/by/2.0/ + name: Contributor Role Ontology + preferredPrefix: CRO + prefix: cro + repository: https://github.com/data2health/contributor-role-ontology + ols: + description: A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. + download: http://purl.obolibrary.org/obo/cro.owl + homepage: https://github.com/data2health/contributor-role-ontology + name: Contributor Role Ontology + prefix: cro + version: 2019-12-11 + version.iri: http://purl.obolibrary.org/obo/cro/releases/2019-12-11/cro.owl + ontobee: + library: Library + name: Contributor Role Ontology + prefix: CRO + pattern: ^\d{7}$ +cryoem: + bioportal: + name: Cryo Electron Microscopy + prefix: CRYOEM + example: '0000052' + mappings: + bioportal: CRYOEM + ols: cryoem + ols: + contact: isanchez@cnb.csic.es + description: Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles + download: http://scipion.i2pc.es/ontology/cryoem.owl + homepage: http://scipion.i2pc.es/ontology/cryoem + name: Cryo Electron Microscopy ontology + prefix: cryoem + version: 2021-03-09 + version.iri: http://scipion.i2pc.es/ontology/cryoem/releases/2021-03-09/cryoem.owl + pattern: ^\d{7}$ +cryptodb: + biocontext: + is_identifiers: true + is_obo: false + prefix: CRYPTODB + uri_format: http://identifiers.org/cryptodb/$1 + fairsharing: + abbreviation: CryptoDB + description: CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology profiles across organisms. It also includes supplemental bioinformatics analyses and a web interface for data-mining. + id: '1878' + name: CryptoDB + prefix: FAIRsharing.t3nprm + subjects: + - Functional Genomics + - Genomics + - Parasitology + mappings: + biocontext: CRYPTODB + fairsharing: FAIRsharing.t3nprm + miriam: cryptodb + n2t: cryptodb + prefixcommons: cryptodb + miriam: + deprecated: false + description: CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: https://cryptodb.org/cryptodb/ + id: '00000149' + name: CryptoDB + namespaceEmbeddedInLui: false + pattern: ^\w+ + prefix: cryptodb + sampleId: cgd7_230 + uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1 + n2t: + description: CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: cgd7_230 + homepage: https://cryptodb.org/cryptodb/ + name: CryptoDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^\w+ + prefix: cryptodb + uri_format: https://cryptodb.org/cryptodb/app/record/gene/$1 + prefixcommons: + description: CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers, it also includes supplemental bioinformatics analyses and a web interface for data-mining. + example: cgd7_230 + homepage: http://cryptodb.org/cryptodb/ + keywords: + - genome + name: Cryptosporidum Genomics Resource + pattern: ^\w+$ + prefix: cryptodb + pubmed_ids: + - '16381902' + uri_format: http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +csa: + biocontext: + is_identifiers: true + is_obo: false + prefix: CSA + uri_format: http://identifiers.org/csa/$1 + fairsharing: + abbreviation: CSA + description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. + id: '1849' + name: Catalytic Site Atlas + prefix: FAIRsharing.2ajtcf + subjects: + - Life Science + mappings: + biocontext: CSA + fairsharing: FAIRsharing.2ajtcf + miriam: csa + n2t: csa + prefixcommons: csa + miriam: + deprecated: false + description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. + homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ + id: '00000144' + name: CSA + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: csa + sampleId: 1a05 + uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 + n2t: + description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. + example: 1a05 + homepage: https://www.ebi.ac.uk/thornton-srv/databases/CSA/ + name: CSA at EBI + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: csa + uri_format: https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 + name: Catalytic Site Atlas + prefixcommons: + description: The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. + example: 1a05 + homepage: http://www.ebi.ac.uk/thornton-srv/databases/CSA/ + keywords: + - enzyme + - structure + name: Catalytic Site Atlas + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: csa + pubmed_ids: + - '14681376' + uri_format: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/CSA/CSA_Site_Wrapper.pl?pdb=$1 +csd: + fairsharing: + abbreviation: CSD + description: Established in 1965, the Cambridge Structural Database (CSD) is the a repository for small-molecule organic and metal-organic crystal 3D structures. Database records are automatically checked and manually curated by one of our expert in-house scientific editors. Every structure is enriched with chemical representations, as well as bibliographic, chemical and physical property information, adding further value to the raw structural data. + id: '1796' + name: The Cambridge Structural Database + prefix: FAIRsharing.vs7865 + subjects: + - Organic Chemistry + - Biochemistry + - Organic Molecular Chemistry + - Chemistry + mappings: + fairsharing: FAIRsharing.vs7865 + miriam: csd + miriam: + deprecated: false + description: The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode. + homepage: https://www.ccdc.cam.ac.uk/ + id: '00000820' + name: Cambridge Structural Database + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{6}(\d{2})?$ + prefix: csd + sampleId: PELNAW + uri_format: https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG +csp: + bioportal: + name: Computer Retrieval of Information on Scientific Projects Thesaurus + prefix: CRISP + deprecated: true + example: 2004-2820 + homepage: https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm + mappings: + bioportal: CRISP + name: Computer Retrieval of Information on Science Projects Thesaurus + synonyms: + - CRISP + - CRISP Thesaurus + - CRISP Thesaurus, 2006 + - CSP2005 +cst: + biocontext: + is_identifiers: true + is_obo: false + prefix: CST + uri_format: http://identifiers.org/cst/$1 + bioportal: + name: Cancer Staging Terms + prefix: CST + fairsharing: + abbreviation: CST + description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein. + id: '1800' + name: Cell Signaling Technology Pathway Database + prefix: FAIRsharing.n8pxvx + subjects: + - Life Science + - Biomedical Science + mappings: + biocontext: CST + bioportal: CST + fairsharing: FAIRsharing.n8pxvx + miriam: cst + n2t: cst + prefixcommons: cst + miriam: + deprecated: false + description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. + homepage: http://www.cellsignal.com/pathways/index.html + id: '00000429' + name: Cell Signaling Technology Pathways + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9_-]+$ + prefix: cst + sampleId: Akt_PKB + uri_format: http://www.cellsignal.com/reference/pathway/$1.html + n2t: + description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. + example: Akt_PKB + homepage: http://www.cellsignal.com/pathways/index.html + name: CST Pathways at Cell Signaling Technology + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9_-]+$ + prefix: cst + uri_format: http://www.cellsignal.com/reference/pathway/$1.html + prefixcommons: + description: A small pathway portal for showcasing Cell Signaling Technology phospho-antibody products. Contains pathway diagrams that are clickable and link to more information about each protein and the commercial products that are available for that protein. + example: '3762' + homepage: http://www.cellsignal.com/ + keywords: + - pathway + name: Cell Signaling Technology Pathway Database + pattern: ^\d+$ + prefix: cst + uri_format: http://www.cellsignal.com/products/$1.html +cst.ab: + biocontext: + is_identifiers: true + is_obo: false + prefix: CST.AB + uri_format: http://identifiers.org/cst.ab/$1 + mappings: + biocontext: CST.AB + miriam: cst.ab + n2t: cst.ab + miriam: + deprecated: false + description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. + homepage: http://www.cellsignal.com/catalog/index.html + id: '00000430' + name: Cell Signaling Technology Antibody + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cst.ab + sampleId: '3305' + uri_format: http://www.cellsignal.com/products/$1.html + n2t: + description: Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. + example: '3305' + homepage: http://www.cellsignal.com/catalog/index.html + name: CST Antibody at Cell Signaling Technology + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: cst.ab + uri_format: http://www.cellsignal.com/products/$1.html +ctd.chemical: + biocontext: + is_identifiers: true + is_obo: false + prefix: CTD.CHEMICAL + uri_format: http://identifiers.org/ctd.chemical/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: CTD.CHEMICAL + uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 + mappings: + biocontext: CTD.CHEMICAL + biolink: CTD.CHEMICAL + miriam: ctd.chemical + n2t: ctd.chemical + miriam: + deprecated: false + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + homepage: http://ctdbase.org/ + id: '00000098' + name: CTD Chemical + namespaceEmbeddedInLui: false + pattern: ^[CD]\d+$ + prefix: ctd.chemical + sampleId: D001151 + uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 + n2t: + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + example: D001151 + homepage: http://ctdbase.org/ + name: Comparative Toxicogenomics Database (Chemical) + namespaceEmbeddedInLui: false + pattern: ^[CD]\d+$ + prefix: ctd.chemical + uri_format: http://ctdbase.org/detail.go?type=chem&acc=$1 + part_of: ctd + provides: mesh +ctd.disease: + biocontext: + is_identifiers: true + is_obo: false + prefix: CTD.DISEASE + uri_format: http://identifiers.org/ctd.disease/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: CTD.DISEASE + uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 + mappings: + biocontext: CTD.DISEASE + biolink: CTD.DISEASE + miriam: ctd.disease + n2t: ctd.disease + miriam: + deprecated: false + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + homepage: http://ctdbase.org/ + id: '00000099' + name: CTD Disease + namespaceEmbeddedInLui: false + pattern: ^D\d+$ + prefix: ctd.disease + sampleId: D053716 + uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 + n2t: + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + example: D053716 + homepage: http://ctdbase.org/ + name: Comparative Toxicogenomics Database (Disease) + namespaceEmbeddedInLui: false + pattern: ^D\d+$ + prefix: ctd.disease + uri_format: http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 + part_of: ctd + provides: mesh +ctd.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: CTD.GENE + uri_format: http://identifiers.org/ctd.gene/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: CTD.GENE + uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 + mappings: + biocontext: CTD.GENE + biolink: CTD.GENE + miriam: ctd.gene + n2t: ctd.gene + miriam: + deprecated: false + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + homepage: http://ctdbase.org/ + id: '00000100' + name: CTD Gene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ctd.gene + sampleId: '101' + uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 + n2t: + description: The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. + example: '101' + homepage: http://ctdbase.org/ + name: Comparative Toxicogenomics Database (Gene) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ctd.gene + uri_format: http://ctdbase.org/detail.go?type=gene&acc=$1 + part_of: ctd + provides: ncbigene +cteno: + biocontext: + is_identifiers: false + is_obo: true + prefix: CTENO + uri_format: http://purl.obolibrary.org/obo/CTENO_$1 + bioportal: + name: Ctenophore Ontology + prefix: CTENO + download_obo: https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo + example: '0000047' + fairsharing: + abbreviation: CTENO + description: An anatomical and developmental ontology for ctenophores (Comb Jellies) + id: '529' + name: Ctenophore Ontology + prefix: FAIRsharing.mgxgza + subjects: [] + mappings: + biocontext: CTENO + bioportal: CTENO + fairsharing: FAIRsharing.mgxgza + obofoundry: cteno + ols: cteno + ontobee: CTENO + obofoundry: + contact: cjmungall@lbl.gov + contact.github: cmungall + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + depends_on: + - ro + - uberon + deprecated: false + description: An anatomical and developmental ontology for ctenophores (Comb Jellies) + download.owl: http://purl.obolibrary.org/obo/cteno.owl + homepage: https://github.com/obophenotype/ctenophore-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Ctenophore Ontology + preferredPrefix: CTENO + prefix: cteno + repository: https://github.com/obophenotype/ctenophore-ontology + ols: + description: An anatomical and developmental ontology for ctenophores (Comb Jellies) + download: http://purl.obolibrary.org/obo/cteno.owl + homepage: https://github.com/obophenotype/ctenophore-ontology + name: Ctenophore Ontology + prefix: cteno + version: 2016-10-19 + version.iri: http://purl.obolibrary.org/obo/cteno/releases/2016-10-19/cteno.owl + ontobee: + library: Library + name: Ctenophore Ontology + prefix: CTENO + pattern: ^\d{7}$ +cto: + bioportal: + name: Clinical Trials Ontology + prefix: CTO + example: '0000022' + fairsharing: + abbreviation: CTO + description: The Clinical Trials Ontology (CTO) is also known as the Clinical Trial Ontology-Neurodegenerative Diseases (CTO-NDD), and describes clinical trials in the field of neurodegeneration. This resource has been created for use in the IMI-funded AETIONOMY project (www.aetionomy.org). + id: '421' + name: Clinical Trials Ontology + prefix: FAIRsharing.qp211a + subjects: + - Neurobiology + - Biomedical Science + - Preclinical Studies + mappings: + bioportal: CTO + fairsharing: FAIRsharing.qp211a + obofoundry: cto + ols: cto + ontobee: CTO + name: Clinical Trials Ontology + obofoundry: + contact: alpha.tom.kodamullil@scai.fraunhofer.de + contact.github: akodamullil + contact.label: Dr. Alpha Tom Kodamullil + contact.orcid: 0000-0001-9896-3531 + deprecated: false + description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. + download.owl: http://purl.obolibrary.org/obo/cto.owl + homepage: https://github.com/ClinicalTrialOntology/CTO/ + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: 'CTO: Core Ontology of Clinical Trials' + preferredPrefix: CTO + prefix: cto + repository: https://github.com/ClinicalTrialOntology/CTO + ols: + description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. + download: http://purl.obolibrary.org/obo/cto.owl + homepage: https://github.com/BFO-ontology/BFO + name: 'CTO: Core Ontology of Clinical Trials' + prefix: cto + version: 1.0.0 + ontobee: + library: Library + name: 'CTO: Core Ontology of Clinical Trials' + prefix: CTO + pattern: ^\d{7}$ +cubedb: + biocontext: + is_identifiers: true + is_obo: false + prefix: CUBEDB + uri_format: http://identifiers.org/cubedb/$1 + comment: website down as of 2021-10-04 + deprecated: true + mappings: + biocontext: CUBEDB + miriam: cubedb + n2t: cubedb + miriam: + deprecated: false + description: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. + homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html + id: '00000397' + name: Cube db + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: cubedb + sampleId: AKR + uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ + n2t: + description: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. + example: AKR + homepage: http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html + name: Cube db at Bioinformatics Institute (Singapore) + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: cubedb + uri_format: http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ +cvdo: + biocontext: + is_identifiers: false + is_obo: true + prefix: CVDO + uri_format: http://purl.obolibrary.org/obo/CVDO_$1 + bioportal: + name: Cardiovascular Disease Ontology + prefix: CVDO + example: '0000546' + fairsharing: + abbreviation: CVDO + description: CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes). + id: '371' + name: Cardiovascular Disease Ontology + prefix: FAIRsharing.2basyz + subjects: + - Cardiology + mappings: + biocontext: CVDO + bioportal: CVDO + fairsharing: FAIRsharing.2basyz + obofoundry: cvdo + ols: cvdo + ontobee: CVDO + obofoundry: + contact: paul.fabry@usherbrooke.ca + contact.github: pfabry + contact.label: Paul Fabry + contact.orcid: 0000-0002-3336-2476 + deprecated: false + description: An ontology to describe entities related to cardiovascular diseases + download.owl: http://purl.obolibrary.org/obo/cvdo.owl + homepage: https://github.com/OpenLHS/CVDO + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Cardiovascular Disease Ontology + preferredPrefix: CVDO + prefix: cvdo + repository: https://github.com/OpenLHS/CVDO + ols: + description: An ontology to describe entities related to cardiovascular diseases + download: http://purl.obolibrary.org/obo/cvdo.owl + homepage: https://github.com/OpenLHS/CVDO + name: Cardiovascular Disease Ontology + prefix: cvdo + version: 2020-03-05 + version.iri: http://purl.obolibrary.org/obo/2020-03-05/cvdo.owl + ontobee: + library: Library + name: Cardiovascular Disease Ontology + prefix: CVDO + pattern: ^\d{7}$ +d1id: + biocontext: + is_identifiers: true + is_obo: false + prefix: D1ID + uri_format: http://identifiers.org/d1id/$1 + mappings: + biocontext: D1ID + miriam: d1id + n2t: d1id + miriam: + deprecated: false + description: DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. + homepage: https://www.dataone.org + id: '00000611' + name: DataONE + namespaceEmbeddedInLui: false + pattern: \S+ + prefix: d1id + sampleId: 00030692-0FE1-4A1B-955E-A2E55D659267 + uri_format: https://cn.dataone.org/cn/v2/resolve/{$1} + n2t: + description: DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. + example: 00030692-0FE1-4A1B-955E-A2E55D659267 + homepage: https://www.dataone.org + name: DataONE + namespaceEmbeddedInLui: false + pattern: \S+ + prefix: d1id + uri_format: https://cn.dataone.org/cn/v2/resolve/{$1} +dailymed: + biocontext: + is_identifiers: true + is_obo: false + prefix: DAILYMED + uri_format: http://identifiers.org/dailymed/$1 + mappings: + biocontext: DAILYMED + miriam: dailymed + n2t: dailymed + prefixcommons: dailymed + miriam: + deprecated: false + description: DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. + homepage: https://dailymed.nlm.nih.gov/dailymed/ + id: '00000434' + name: DailyMed + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+ + prefix: dailymed + sampleId: 973a9333-fec7-46dd-8eb5-25738f06ee54 + uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 + n2t: + description: DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. + example: 973a9333-fec7-46dd-8eb5-25738f06ee54 + homepage: https://dailymed.nlm.nih.gov/dailymed/ + name: DailyMed at NLM + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+ + prefix: dailymed + uri_format: https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 + prefixcommons: + description: DailyMed provides high quality information about marketed drugs including FDA labels (package inserts). + example: 3be94523-f6d6-4b25-82b0-3e0d021594c5 + homepage: http://dailymed.nlm.nih.gov/dailymed/ + name: Dailymed + pattern: ^[A-Za-z0-9]{8}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{4}-[A-Za-z0-9]{12}$ + prefix: dailymed + uri_format: http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$1 +dandi: + mappings: + miriam: dandi + miriam: + deprecated: false + description: >- + DANDI works with BICCN and other BRAIN Initiative awardees to curate data + using community data standards such as NWB and BIDS, and to make data and + software for cellular neurophysiology FAIR (Findable, Accessible, + Interoperable, and Reusable). + + DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. + + These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders. + homepage: https://dandiarchive.org/ + id: '00000786' + name: 'DANDI: Distributed Archives for Neurophysiology Data Integration' + namespaceEmbeddedInLui: false + pattern: ^\d{6}(\/\d+\.\d+\.\d+)?$ + prefix: dandi + sampleId: '000017' + uri_format: https://dandiarchive.org/dandiset/$1 + name: Distributed Archives for Neurophysiology Data Integration +darc: + biocontext: + is_identifiers: true + is_obo: false + prefix: DARC + uri_format: http://identifiers.org/darc/$1 + fairsharing: + abbreviation: DARC + description: The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes. + id: '1566' + name: Database of Aligned Ribosomal Complexes + prefix: FAIRsharing.evfe2s + subjects: + - Life Science + mappings: + biocontext: DARC + fairsharing: FAIRsharing.evfe2s + miriam: darc + n2t: darc + miriam: + deprecated: false + description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. + homepage: http://darcsite.genzentrum.lmu.de/darc/index.php + id: '00000366' + name: DARC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: darc + sampleId: '1250' + uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1 + n2t: + description: DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. + example: '1250' + homepage: http://darcsite.genzentrum.lmu.de/darc/index.php + name: DARC at University of Munich + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: darc + uri_format: http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1 + name: Database of Aligned Ribosomal Complexes +dashr: + biocontext: + is_identifiers: true + is_obo: false + prefix: DASHR + uri_format: http://identifiers.org/dashr/$1 + fairsharing: + abbreviation: DASHR + description: Integrated annotation and sequencing-based expression data for all major classes of human small non-coding RNAs (sncRNAs) for both full sncRNA transcripts and mature sncRNA products derived from these larger RNAs. + id: '2248' + name: Database of small human non-coding RNAs + prefix: FAIRsharing.ztvs34 + subjects: + - Life Science + mappings: + biocontext: DASHR + fairsharing: FAIRsharing.ztvs34 + miriam: dashr + n2t: dashr + miriam: + deprecated: false + description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. + homepage: http://lisanwanglab.org/DASHR/ + id: '00000564' + name: DASHR + namespaceEmbeddedInLui: false + pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ + prefix: dashr + sampleId: hsa-mir-200a + uri_format: http://lisanwanglab.org/DASHR/entry/$1 + n2t: + description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. + example: hsa-mir-200a + homepage: http://lisanwanglab.org/DASHR/ + name: DASHR at University of Pennsylvania + namespaceEmbeddedInLui: false + pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ + prefix: dashr + uri_format: http://lisanwanglab.org/DASHR/entry/$1 + name: Database of small human noncoding RNAs +dashr.expression: + biocontext: + is_identifiers: true + is_obo: false + prefix: DASHR.EXPRESSION + uri_format: http://identifiers.org/dashr.expression/$1 + mappings: + biocontext: DASHR.EXPRESSION + miriam: dashr.expression + n2t: dashr.expression + miriam: + deprecated: false + description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. + homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 + id: '00000565' + name: DASHR expression + namespaceEmbeddedInLui: false + pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ + prefix: dashr.expression + sampleId: hsa-mir-200a + uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable + n2t: + description: DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. + example: hsa-mir-200a + homepage: https://dashr1.lisanwanglab.org/show-expression-table.php?start=0 + name: DASHR expression at University of Pennsylvania + namespaceEmbeddedInLui: false + pattern: ^(hsa-(let|mir)-\w+(-\w+)?)|(piR-\d+)|(chr\w+.tRNA\d+-\w+)|(chr\w+.tRNA\d+-\w+-tRF\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\w+)|(HY\d\+(-L\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\d+)?)$ + prefix: dashr.expression + uri_format: https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable +datanator.gene: + mappings: + miriam: datanator.gene + miriam: + deprecated: false + description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. + homepage: https://datanator.info/ + id: '00000720' + name: Datanator Gene + namespaceEmbeddedInLui: false + pattern: ^K[0-9]+$ + prefix: datanator.gene + sampleId: K00973 + uri_format: https://www.datanator.info/gene/$1 + part_of: datanator +datanator.metabolite: + mappings: + miriam: datanator.metabolite + miriam: + deprecated: false + description: Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. + homepage: https://datanator.info/ + id: '00000718' + name: Datanator Metabolite + namespaceEmbeddedInLui: false + pattern: ^[A-Z\-]+$ + prefix: datanator.metabolite + sampleId: OUYCCCASQSFEME-MRVPVSSYSA-N + uri_format: https://www.datanator.info/metabolite/$1 + part_of: datanator +datanator.reaction: + mappings: + miriam: datanator.reaction + miriam: + deprecated: false + description: "\tDatanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms." + homepage: https://icahn.mssm.edu/ + id: '00000855' + name: Datanator Reaction + namespaceEmbeddedInLui: false + pattern: ^.*?--%3E.*?$ + prefix: datanator.reaction + sampleId: XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N + uri_format: https://datanator.info/reaction/$1 +datf: + biocontext: + is_identifiers: true + is_obo: false + prefix: DATF + uri_format: http://identifiers.org/datf/$1 + deprecated: true + mappings: + biocontext: DATF + miriam: datf + n2t: datf + prefixcommons: datf + miriam: + deprecated: false + description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. + homepage: http://datf.cbi.pku.edu.cn/ + id: '00000456' + name: DATF + namespaceEmbeddedInLui: false + pattern: ^AT[1-5]G\d{5}(\.\d+)?$ + prefix: datf + sampleId: AT1G01030.1 + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1 + n2t: + description: DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. + example: AT1G01030.1 + homepage: http://datf.cbi.pku.edu.cn/ + name: DATF through PlantTFDB + namespaceEmbeddedInLui: false + pattern: ^AT[1-5]G\d{5}(\.\d+)?$ + prefix: datf + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1 + name: Database of Arabidopsis Transcription Factors + prefixcommons: + description: The Database of Arabidopsis Transcription Factors (DATF) collects all Arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.The Version 2 of DATF was updated at July 2006. It is based on the Arabidopsis Sequence of TAIR http://www.pdb.org, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference. + example: AT1G08970.3 + homepage: http://datf.cbi.pku.edu.cn + keywords: + - regulation + name: Database of Arabidopsis Transcription Factors + pattern: ^AT\d[A-Z]\d+$ + prefix: datf + uri_format: http://datf.cbi.pku.edu.cn/entry-display.php?id=$1 +dbd: + biocontext: + is_identifiers: true + is_obo: false + prefix: DBD + uri_format: http://identifiers.org/dbd/$1 + mappings: + biocontext: DBD + miriam: dbd + n2t: dbd + prefixcommons: dbd + miriam: + deprecated: false + description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. + homepage: http://www.transcriptionfactor.org/ + id: '00000455' + name: DBD + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dbd + sampleId: '0045310' + uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD + n2t: + description: The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. + example: '0045310' + homepage: http://www.transcriptionfactor.org/ + name: DBD at MRC Laboratory of Molecular Biology + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dbd + uri_format: http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD + name: Transcription Factor Database + prefixcommons: + description: DBD provides transcription factor predictions for more than 150 completely sequenced genomes available for browsing and download. Predictions are based on presence of sequence specific DNA binding domain assignments using hidden Markov models from the SUPERFAMILY and PFAM databases + example: '0035306' + homepage: http://www.transcriptionfactor.org + keywords: + - regulation + - genome + name: DBD + pattern: ^\d+$ + prefix: dbd + uri_format: http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Search/Domain+domain:$1 +dbest: + biocontext: + is_identifiers: true + is_obo: false + prefix: DBEST + uri_format: http://identifiers.org/dbest/$1 + fairsharing: + abbreviation: dbEST + description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is expected to be completed 2019. Accession.version and GI identifiers will not change during this process. For more information please see https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/30/upcoming-changes-est-gss-databases/ + id: '1969' + name: Expressed Sequence Tags database + prefix: FAIRsharing.v9fya8 + subjects: + - Bioinformatics + - Life Science + mappings: + biocontext: DBEST + fairsharing: FAIRsharing.v9fya8 + miriam: dbest + n2t: dbest + ncbi: dbEST + prefixcommons: dbest + miriam: + deprecated: false + description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. + homepage: https://www.ncbi.nlm.nih.gov/nucest + id: '00000159' + name: dbEST + namespaceEmbeddedInLui: false + pattern: ^([A-Z]+)?\d+(\.\d+)?$ + prefix: dbest + providers: + - code: ebi + description: dbEST through European Nucleotide Archive (ENA) + homepage: https://www.ebi.ac.uk/ena + name: dbEST through European Nucleotide Archive (ENA) + uri_format: https://www.ebi.ac.uk/ena/data/view/$1 + - code: CURATOR_REVIEW + description: dbEST through DNA Data Bank of Japan (DDBJ) + homepage: http://www.ddbj.nig.ac.jp/ + name: dbEST through DNA Data Bank of Japan (DDBJ) + uri_format: http://getentry.ddbj.nig.ac.jp/getentry/na/$1 + sampleId: BP100000 + uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 + n2t: + description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. + example: BP100000 + homepage: https://www.ncbi.nlm.nih.gov/nucest + name: dbEST at NCBI + namespaceEmbeddedInLui: false + pattern: ^([A-Z]+)?\d+(\.\d+)?$ + prefix: dbest + uri_format: https://www.ncbi.nlm.nih.gov/nucest/$1 + ncbi: + example: '123456' + homepage: https://www.ncbi.nlm.nih.gov/genbank/dbest + name: EST database maintained at the NCBI. + prefix: dbEST + prefixcommons: + description: The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. + example: BP100000.1 + homepage: http://www.ncbi.nlm.nih.gov/dbEST/index.html + keywords: + - DNA + name: EST database maintained at the NCBI. + pattern: ^BP\d+(\.\d+)?$ + prefix: dbest + uri_format: http://www.ncbi.nlm.nih.gov/nucest/$1 +dbg2introns: + biocontext: + is_identifiers: true + is_obo: false + prefix: DBG2INTRONS + uri_format: http://identifiers.org/dbg2introns/$1 + mappings: + biocontext: DBG2INTRONS + miriam: dbg2introns + n2t: dbg2introns + miriam: + deprecated: false + description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. + homepage: http://webapps2.ucalgary.ca/~groupii/ + id: '00000318' + name: DBG2 Introns + namespaceEmbeddedInLui: false + pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ + prefix: dbg2introns + sampleId: Cu.me.I1 + uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 + n2t: + description: The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. + example: Cu.me.I1 + homepage: http://webapps2.ucalgary.ca/~groupii/ + name: Bacterial Group II Introns at University of Calgary + namespaceEmbeddedInLui: false + pattern: ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ + prefix: dbg2introns + uri_format: http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 +dbgap: + biocontext: + is_identifiers: true + is_obo: false + prefix: DBGAP + uri_format: http://identifiers.org/dbgap/$1 + fairsharing: + abbreviation: dbGaP + description: The Database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. + id: '1996' + name: Database of Genotypes and Phenotypes + prefix: FAIRsharing.88v2k0 + subjects: + - Epigenetics + - Genetics + - Biomedical Science + mappings: + biocontext: DBGAP + fairsharing: FAIRsharing.88v2k0 + miriam: dbgap + n2t: dbgap + miriam: + deprecated: false + description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. + homepage: https://www.ncbi.nlm.nih.gov/projects/gap + id: '00000602' + name: dbGaP + namespaceEmbeddedInLui: false + pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ + prefix: dbgap + sampleId: phs000768.v2.p1 + uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 + n2t: + description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. + example: phs000768.v2.p1 + homepage: https://www.ncbi.nlm.nih.gov/projects/gap + name: dbGaP through NCBI + namespaceEmbeddedInLui: false + pattern: ^phs[0-9]{6}(.v\d+.p\d+)?$ + prefix: dbgap + uri_format: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 + name: Database of Genotypes and Phenotypes +dbmhc: + appears_in: + - cellosaurus + cellosaurus: + category: Cell line databases/resources + homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/ + name: dbMHC database + prefix: dbMHC + deprecated: true + example: '48439' + mappings: + cellosaurus: dbMHC + name: Database of human Major Histocompatibility Complex + pattern: ^\d+$ +dbprobe: + biocontext: + is_identifiers: true + is_obo: false + prefix: DBPROBE + uri_format: http://identifiers.org/dbprobe/$1 + mappings: + biocontext: DBPROBE + miriam: dbprobe + n2t: dbprobe + ncbi: dbProbe + prefixcommons: dbprobe + miriam: + deprecated: false + description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe + id: '00000160' + name: dbProbe + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dbprobe + sampleId: '1000000' + uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1 + n2t: + description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. + example: '1000000' + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe + name: dbProbe at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dbprobe + uri_format: https://www.ncbi.nlm.nih.gov/probe/?term=$1 + ncbi: + example: '38' + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe + name: NCBI Probe database Public registry of nucleic acid reagents + prefix: dbProbe + prefixcommons: + description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. + example: '1000000' + homepage: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe + keywords: + - nucleotide + name: NCBI Probe database Public registry of nucleic acid reagents + pattern: ^\d+$ + prefix: dbprobe + uri_format: http://www.ncbi.nlm.nih.gov/genome/probe/reports/probereport.cgi?uid=$1 +dbsnp: + biocontext: + is_identifiers: false + is_obo: false + prefix: dbSNP + uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1 + cellosaurus: + category: Polymorphism and mutation databases + homepage: https://www.ncbi.nlm.nih.gov/snp/ + name: Single Nucleotide Polymorphism database + prefix: dbSNP + uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 + fairsharing: + abbreviation: dbSNP + description: dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. + id: '1972' + name: Database of Single Nucleotide Polymorphism + prefix: FAIRsharing.edxb58 + subjects: + - Life Science + go: + homepage: http://www.ncbi.nlm.nih.gov/projects/SNP + name: NCBI dbSNP + prefix: dbSNP + uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1 + mappings: + biocontext: dbSNP + cellosaurus: dbSNP + fairsharing: FAIRsharing.edxb58 + go: dbSNP + miriam: dbsnp + n2t: dbsnp + ncbi: dbSNP + prefixcommons: dbsnp + uniprot: dbSNP + miriam: + deprecated: false + description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. + homepage: https://www.ncbi.nlm.nih.gov/snp/ + id: '00000161' + name: dbSNP + namespaceEmbeddedInLui: false + pattern: ^rs\d+$ + prefix: dbsnp + providers: + - code: sib + description: SNP2TFBS + homepage: https://ccg.epfl.ch/snp2tfbs/ + name: SNP2TFBS + uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 + sampleId: rs121909098 + uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 + n2t: + description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. + example: rs121909098 + homepage: https://www.ncbi.nlm.nih.gov/snp/ + name: dbSNP at NCBI + namespaceEmbeddedInLui: false + pattern: ^rs\d+$ + prefix: dbsnp + uri_format: https://www.ncbi.nlm.nih.gov/snp/$1 + ncbi: + example: '4647' + homepage: https://www.ncbi.nlm.nih.gov/snp + name: Variation database maintained at the NCBI. + prefix: dbSNP + prefixcommons: + description: The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. + example: rs199422184 + homepage: http://www.ncbi.nlm.nih.gov/SNP/ + keywords: + - genome + name: Database of single nucleotide polymorphism + pattern: ^rs\d+$ + prefix: dbsnp + pubmed_ids: + - '11125122' + uri_format: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$1 + uniprot: + category: Genetic variation databases + identifier: '13' + link_is_explicit: 'true' + name: Database of single nucleotide polymorphism + prefix: dbSNP + uri_format: https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$1 +dbvar.study: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Studies in dbVar. + example: nstd102 + homepage: https://www.ncbi.nlm.nih.gov/dbvar + name: Database of Genomic Structural Variation - Study + synonyms: + - dbvar.studies + uri_format: https://www.ncbi.nlm.nih.gov/dbvar/studies/$1 +dbvar.variant: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Variants in dbVar. + example: nsv3875336 + homepage: https://www.ncbi.nlm.nih.gov/dbvar + name: Database of Genomic Structural Variation - Variant + synonyms: + - dbvar.variants + uri_format: https://www.ncbi.nlm.nih.gov/dbvar/variants/$1 +dc: + biocontext: + is_identifiers: false + is_obo: false + prefix: dc + uri_format: http://purl.org/dc/elements/1.1/$1 + bioportal: + name: Dublin Core + prefix: DC + description: Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. + example: contributor + fairsharing: + abbreviation: DC + description: The Dublin Metadata Element Set, which is often called Dublin Core (DC), is a standardized metadata scheme for description of any kind of resource such as documents in electronic and non-electronic form, digital materials (such as video, sound, images, etc) and composite media like web pages. Dublin Core Metadata may be used for multiple purposes, from simple resource description, to combining metadata vocabularies of different metadata standards, to providing interoperability for metadata vocabularies in the Linked Data cloud and Semantic Web implementations. Please note that this version of the specification for the Dublin Core Element Set 1.1 is somewhat out of date, although it is not officially deprecated. The DCMI Metadata Terms specification is linked to this record and is the current documentation that should be used for the Dublin Core Element Set 1.1. + id: '1245' + name: Dublin Core Metadata Element Set + prefix: FAIRsharing.3nx7t + subjects: + - Life Science + - Subject Agnostic + - Biomedical Science + has_canonical: dcterms + homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ + mappings: + biocontext: dc + bioportal: DC + fairsharing: FAIRsharing.3nx7t + name: Dublin Core + uri_format: http://purl.org/dc/terms/$1 +dc_cl: + biocontext: + is_identifiers: false + is_obo: true + prefix: DC_CL + uri_format: http://purl.obolibrary.org/obo/DC_CL_$1 + example: '0000003' + mappings: + biocontext: DC_CL + obofoundry: dc_cl + obofoundry: + contact: Lindsay.Cowell@utsouthwestern.edu + contact.label: Lindsay Cowell + contact.orcid: 0000-0003-1617-8244 + deprecated: true + homepage: http://www.dukeontologygroup.org/Projects.html + name: Dendritic cell + prefix: dc_cl + pattern: ^\d{7}$ +dcat: + biocontext: + is_identifiers: false + is_obo: false + prefix: dcat + uri_format: http://www.w3.org/ns/dcat#$1 + biolink: + is_identifiers: false + is_obo: false + prefix: dcat + uri_format: http://www.w3.org/ns/dcat#$1 + bioportal: + name: Data Catalog Vocabulary + prefix: DCAT + description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web + example: Dataset + fairsharing: + abbreviation: DCAT + description: An RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. By using DCAT to describe datasets in data catalogs, publishers increase discoverability and enable applications easily to consume metadata from multiple catalogs. It further enables decentralized publishing of catalogs and facilitates federated dataset search across sites. Aggregated DCAT metadata can serve as a manifest file to facilitate digital preservation. + id: '747' + name: Data Catalog Vocabulary + prefix: FAIRsharing.h4j3qm + subjects: + - Data Management + - Subject Agnostic + homepage: https://www.w3.org/ns/dcat + mappings: + biocontext: dcat + biolink: dcat + bioportal: DCAT + fairsharing: FAIRsharing.h4j3qm + name: Data Catalog + uri_format: http://www.w3.org/ns/dcat#$1 +dcterms: + biocontext: + is_identifiers: false + is_obo: false + prefix: dcterms + uri_format: http://purl.org/dc/terms/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: dct + uri_format: http://purl.org/dc/terms/$1 + bioportal: + name: 'DCMI Metadata Terms: properties in /terms/ namespace' + prefix: DCTERMS + description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. + example: title + fairsharing: + abbreviation: DCTERMS + description: This document is an up-to-date, authoritative specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. Included are the fifteen terms of the Dublin Core Metadata Element Set, which have also been published as a separate specification. + id: '905' + name: Dublin Core Metadata Initiative (DCMI) Metadata Terms + prefix: FAIRsharing.9vtwjs + subjects: + - Subject Agnostic + homepage: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ + mappings: + biocontext: dcterms + biolink: dct + bioportal: DCTERMS + fairsharing: FAIRsharing.9vtwjs + name: Dublin Core Metadata Vocabulary + synonyms: + - dc.terms + uri_format: http://purl.org/dc/terms/$1 +dctypes: + biocontext: + is_identifiers: false + is_obo: false + prefix: dctypes + uri_format: http://purl.org/dc/dcmitype/$1 + description: This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. + example: Collection + homepage: https://dublincore.org/specifications/dublin-core/dcmi-terms/ + mappings: + biocontext: dctypes + name: Dublin Core Types + uri_format: http://purl.org/dc/dcmitype/$1 +ddanat: + biocontext: + is_identifiers: false + is_obo: true + prefix: DDANAT + uri_format: http://purl.obolibrary.org/obo/DDANAT_$1 + bioportal: + name: Dictyostelium Discoideum Anatomy Ontology + prefix: DDANAT + example: '0000006' + fairsharing: + abbreviation: DDANAT + description: 'The Dictyostelium Anatomy Ontology ontology describes the anatomy of the slime mold. It defines the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle. It has two main goals: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes and gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning.' + id: '928' + name: Dictyostelium Anatomy Ontology + prefix: FAIRsharing.z656ab + subjects: + - Anatomy + - Life Science + go: + homepage: http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html + name: Dictyostelium discoideum anatomy + prefix: DDANAT + mappings: + biocontext: DDANAT + bioportal: DDANAT + fairsharing: FAIRsharing.z656ab + go: DDANAT + obofoundry: ddanat + ols: ddanat + ontobee: DDANAT + prefixcommons: ddanat + obofoundry: + contact: pfey@northwestern.edu + contact.github: pfey03 + contact.label: Petra Fey + contact.orcid: 0000-0002-4532-2703 + deprecated: false + description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum + download.obo: http://purl.obolibrary.org/obo/ddanat.obo + download.owl: http://purl.obolibrary.org/obo/ddanat.owl + homepage: http://dictybase.org/ + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Dictyostelium discoideum anatomy + preferredPrefix: DDANAT + prefix: ddanat + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/18366659 + title: An anatomy ontology to represent biological knowledge in Dictyostelium discoideum + repository: https://github.com/dictyBase/migration-data + twitter: dictybase + ols: + description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum + download: http://purl.obolibrary.org/obo/ddanat.owl + homepage: http://dictybase.org/ + name: Dictyostelium discoideum anatomy + prefix: ddanat + version: 2020-04-13 + version.iri: http://purl.obolibrary.org/obo/ddanat/releases/2020-04-13/ddanat.owl + ontobee: + library: Library + name: Dictyostelium discoideum anatomy + prefix: DDANAT + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1008' + description: A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. + example: DDANAT_0010081 + homepage: http://dictybase.org/ + keywords: + - obo + - anatomy + - slime-mould + name: Dictyostelium discoideum anatomy + pattern: ^DDANAT_\d+$ + prefix: ddanat +ddpheno: + biocontext: + is_identifiers: false + is_obo: true + prefix: DDPHENO + uri_format: http://purl.obolibrary.org/obo/DDPHENO_$1 + bioportal: + name: Dictyostelium Discoideum Phenotype Ontology + prefix: DDPHENO + download_obo: https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo + example: '0001417' + fairsharing: + abbreviation: DDPHENO + description: 'A structured controlled vocabulary of phenotypes of the social amoeba Dictyostelium discoideum. The Dicty Phenotype Ontology is a hierarchical controlled vocabulary used for annotating strains with phenotypes. Terms from the Dicty Phenotype Ontology are required when annotating phenotypes within dictyBase. The phenotype ontology consists of two composite terms: (1) the anatomical part or the biological process changed in the mutant, and (2) a quality describing that modification. For example, a ‘delayed aggregation’ phenotype qualifies the ‘aggregation’ (biological process) as being ‘delayed’, or the ‘decreased spore size’ qualifies the ‘spore’ to be of ‘decreased size’.' + id: '867' + name: Dictyostelium Phenotype Ontology + prefix: FAIRsharing.9c1p18 + subjects: + - Life Science + mappings: + biocontext: DDPHENO + bioportal: DDPHENO + fairsharing: FAIRsharing.9c1p18 + obofoundry: ddpheno + ols: ddpheno + ontobee: DDPHENO + obofoundry: + contact: pfey@northwestern.edu + contact.github: pfey03 + contact.label: Petra Fey + contact.orcid: 0000-0002-4532-2703 + deprecated: false + description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. + download.obo: http://purl.obolibrary.org/obo/ddpheno.obo + download.owl: http://purl.obolibrary.org/obo/ddpheno.owl + homepage: http://dictybase.org/ + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Dictyostelium discoideum phenotype ontology + preferredPrefix: DDPHENO + prefix: ddpheno + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/31840793 + title: dictyBase and the Dicty Stock Center (version 2.0) - a progress report + repository: https://github.com/obophenotype/dicty-phenotype-ontology + twitter: dictybase + ols: + description: A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. + download: http://purl.obolibrary.org/obo/ddpheno.owl + homepage: http://dictybase.org/ + name: Dicty Phenotype Ontology (DDPHENO) + prefix: ddpheno + version: 2020-06-19 + version.iri: http://purl.obolibrary.org/obo/ddpheno/releases/2020-06-19/ddpheno.owl + ontobee: + library: Library + name: Dictyostelium discoideum phenotype ontology + prefix: DDPHENO + pattern: ^\d{7}$ +decipher: + biocontext: + is_identifiers: false + is_obo: true + prefix: DECIPHER + uri_format: http://purl.obolibrary.org/obo/DECIPHER_$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms + example: '1' + fairsharing: + abbreviation: DECIPHER + description: DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) is an interactive web-based resource that incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. + id: '2636' + name: DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources + prefix: FAIRsharing.l8Sf5x + subjects: + - Life Science + - Biomedical Science + homepage: https://www.deciphergenomics.org/ + mappings: + biocontext: DECIPHER + fairsharing: FAIRsharing.l8Sf5x + name: DECIPHER CNV Syndromes + pattern: ^\d+$ + references: + - https://www.deciphergenomics.org/redirect?to=https%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.ajhg.2009.03.010 + uri_format: https://www.deciphergenomics.org/syndrome/$1 +degradome: + biocontext: + is_identifiers: true + is_obo: false + prefix: DEGRADOME + uri_format: http://identifiers.org/degradome/$1 + mappings: + biocontext: DEGRADOME + miriam: degradome + n2t: degradome + miriam: + deprecated: false + description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. + homepage: http://degradome.uniovi.es/ + id: '00000454' + name: Degradome Database + namespaceEmbeddedInLui: false + pattern: ^[AMCST][0-9x][0-9]$ + prefix: degradome + sampleId: Ax1 + uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1 + n2t: + description: The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. + example: Ax1 + homepage: http://degradome.uniovi.es/ + name: Degradome Database at + namespaceEmbeddedInLui: false + pattern: ^[AMCST][0-9x][0-9]$ + prefix: degradome + uri_format: http://degradome.uniovi.es/cgi-bin/protease/$1 +depmap: + cellosaurus: + category: Cell line databases/resources + homepage: https://depmap.org/portal/ + name: Cancer Dependency Map + prefix: DepMap + uri_format: https://depmap.org/portal/cell_line/$1 + description: Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells. + example: ACH-000001 + homepage: https://depmap.org/portal + mappings: + cellosaurus: DepMap + name: DepMap Cell Lines + pattern: ^ACH-\d+$ + uri_format: https://depmap.org/portal/cell_line/$1 +depod: + biocontext: + is_identifiers: true + is_obo: false + prefix: DEPOD + uri_format: http://identifiers.org/depod/$1 + fairsharing: + abbreviation: DEPOD + description: DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. + id: '2178' + name: The human DEPhOsphorylation Database + prefix: FAIRsharing.q9j2e3 + subjects: + - Life Science + mappings: + biocontext: DEPOD + fairsharing: FAIRsharing.q9j2e3 + miriam: depod + n2t: depod + uniprot: DEPOD + miriam: + deprecated: false + description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. + homepage: http://www.depod.bioss.uni-freiburg.de + id: '00000428' + name: DEPOD + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: depod + sampleId: PTPN1 + uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 + n2t: + description: The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. + example: PTPN1 + homepage: http://www.depod.bioss.uni-freiburg.de + name: DEPOD at EMBL + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: depod + uri_format: http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1 + name: Human Dephosphorylation Database + provides: hgnc.symbol + uniprot: + category: PTM databases + identifier: '190' + link_is_explicit: 'true' + name: DEPOD human dephosphorylation database + prefix: DEPOD + uri_format: http://depod.bioss.uni-freiburg.de/showp.php?name=$1 +dermo: + bioportal: + name: Human Dermatological Disease Ontology + prefix: DERMO + description: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders + example: '0000000' + fairsharing: + abbreviation: DERMO + description: Ontology of human dermatologic disease + id: '808' + name: Human Dermatological Disease Ontology + prefix: FAIRsharing.k008w7 + subjects: [] + homepage: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x + mappings: + bioportal: DERMO + fairsharing: FAIRsharing.k008w7 + name: Human Dermatological Disease Ontology + pattern: ^\d{7}$ +dev.ga4ghdos: + biocontext: + is_identifiers: true + is_obo: false + prefix: DEV.GA4GHDOS + uri_format: http://identifiers.org/dev.ga4ghdos/$1 + mappings: + biocontext: DEV.GA4GHDOS + miriam: dev.ga4ghdos + n2t: dev.ga4ghdos + miriam: + deprecated: false + description: Assists in resolving data across cloud resources. + homepage: http://github.com/ga4gh/data-object-service-schemas + id: '00000656' + name: Development Data Object Service + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9\-:#\.]+$ + prefix: dev.ga4ghdos + sampleId: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 + uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1 + n2t: + description: Assists in resolving data across cloud resources. + example: 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 + homepage: http://github.com/ga4gh/data-object-service-schemas + name: Data Object Service + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9\-:#\.]+$ + prefix: dev.ga4ghdos + uri_format: https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1 +dg.4503: + mappings: + miriam: dg.4503 + miriam: + deprecated: false + description: Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org + homepage: https://gen3.biodatacatalyst.nhlbi.nih.gov + id: '00000869' + name: BioData Catalyst + namespaceEmbeddedInLui: false + pattern: '[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}' + prefix: dg.4503 + sampleId: 0000ffeb-36e0-4a29-b21d-84423bda979d + uri_format: https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1 +dg.4dfc: + mappings: + miriam: dg.4dfc + miriam: + deprecated: false + description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org + homepage: https://nci-crdc.datacommons.io/ + id: '00000857' + name: NCI Data Commons Framework Services + namespaceEmbeddedInLui: false + pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}' + prefix: dg.4dfc + sampleId: 81944ba1-81d0-436e-8552-33d77a27834b + uri_format: https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1 +dg.6vts: + mappings: + miriam: dg.6vts + miriam: + deprecated: false + description: Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org + homepage: https://jcoin.datacommons.io + id: '00000876' + name: JCOIN + namespaceEmbeddedInLui: false + pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}' + prefix: dg.6vts + sampleId: 2afacf00-9a1d-4d80-8c32-69d3923d3913 + uri_format: https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1 +dg.anv0: + mappings: + miriam: dg.anv0 + miriam: + deprecated: false + description: DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org + homepage: https://gen3.theanvil.io + id: '00000871' + name: Anvil + namespaceEmbeddedInLui: false + pattern: '[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}' + prefix: dg.anv0 + sampleId: 00077f1c-c45a-47ba-8e6c-1bf6b6b43fce + uri_format: https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1 +dg.f82a1a: + mappings: + miriam: dg.f82a1a + miriam: + deprecated: false + description: Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org + homepage: https://kidsfirstdrc.org + id: '00000887' + name: Kids First + namespaceEmbeddedInLui: false + pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}' + prefix: dg.f82a1a + sampleId: 00026f50-858a-446b-8ed9-b0e3ecd7b20e + uri_format: https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1 +dg5b0d: + mappings: + miriam: dg.5b0d + miriam: + deprecated: false + description: The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources. + homepage: https://data.bloodpac.org/. + id: '00000895' + name: BloodPAC + namespaceEmbeddedInLui: false + pattern: '[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}' + prefix: dg.5b0d + sampleId: 00000d53-99bc-4d3e-8ed7-6dc358baccb7 + uri_format: https://data.bloodpac.org/ga4gh/drs/v1/objects/$1 +dgrc: + cellosaurus: + category: Cell line collections + homepage: https://dgrc.bio.indiana.edu/cells/Catalog + name: Drosophila Genomics Resource Center + prefix: DGRC + uri_format: https://dgrc.bio.indiana.edu/product/View?product=$1 + example: '215' + mappings: + cellosaurus: DGRC + pattern: ^\d+$ +dhba: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A controlled vocabulary to support the study of transcription in the developing human brain + download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dhba.obo + example: '10153' + homepage: https://www.brainspan.org/ + name: Developing Human Brain Atlas + pattern: ^\d+$ + preferred_prefix: DHBA +dicom: + bioportal: + name: DICOM Controlled Terminology + prefix: DCM + example: '109082' + fairsharing: + abbreviation: DICOM + description: DICOM — Digital Imaging and Communications in Medicine — is the international standard for medical images and related information (ISO 12052). It defines the formats for medical images that can be exchanged with the data and quality necessary for clinical use. DICOM is implemented in almost every radiology, cardiology imaging, and radiotherapy device (X-ray, CT, MRI, ultrasound, etc.), and increasingly in devices in other medical domains such as ophthalmology and dentistry. With tens of thousands of imaging devices in use, DICOM is one of the most widely deployed healthcare messaging standards in the world. There are literally billions of DICOM images currently in use for clinical care. Since its first publication in 1993, DICOM has revolutionized the practice of radiology, allowing the replacement of X-ray film with a fully digital workflow. Much as the Internet has become the platform for new consumer information applications, DICOM has enabled advanced medical imaging applications that have “changed the face of clinical medicine”. From the emergency department, to cardiac stress testing, to breast cancer detection, DICOM is the standard that makes medical imaging work — for doctors and for patients. + id: '84' + name: Digital Imaging and COmmunications in Medicine + prefix: FAIRsharing.b7z8by + subjects: + - Anatomy + - Medicine + - Biomedical Science + mappings: + bioportal: DCM + fairsharing: FAIRsharing.b7z8by + ols: dicom + ols: + contact: dclunie@dclunie.com + description: DICOM Controlled Terminology + download: ftp://medical.nema.org/MEDICAL/Dicom/Resources/Ontology/DCM/dcm.owl + homepage: http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html + name: DICOM Controlled Terminology + prefix: dicom + version: 2021e_20211122 + pattern: ^\d+$ +dictybase: + biocontext: + is_identifiers: false + is_obo: false + prefix: dictyBase + uri_format: http://dictybase.org/gene/$1 + description: A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics + fairsharing: + abbreviation: dictyBase + description: dictyBase is a single-access database for the complete genome sequence and expression data of four Dictyostelid species providing information on research, genome and annotations. There is also a repository of plasmids and strains held at the Dicty Stock Centre. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. + id: '2293' + name: dictyBase + prefix: FAIRsharing.4shj9c + subjects: + - Anatomy + - Life Science + - Comparative Genomics + go: + homepage: http://dictybase.org + name: dictyBase + prefix: dictyBase + synonyms: + - DDB + - DictyBase + uri_format: http://dictybase.org/gene/$1 + mappings: + biocontext: dictyBase + fairsharing: FAIRsharing.4shj9c + go: dictyBase + ncbi: dictyBase + prefixcommons: dictybase + uniprot: dictyBase + name: dictyBase + ncbi: + example: DDB0191090 + homepage: http://dictybase.org/ + name: Dictyostelium genome database + prefix: dictyBase + prefixcommons: + description: Genome information, literature and experimental resources for Dictyostelium discoideum + example: DBS0237308 + homepage: http://dictybase.org/ + keywords: + - genome + name: Dictyostelium discoideum online informatics resource + pattern: ^DBS\d{7}$ + prefix: dictybase + synonyms: + - dictyBase + uniprot: + category: Organism-specific databases + comment: Replacement for DictyBase + identifier: '15' + link_is_explicit: 'true' + name: Dictyostelium discoideum online informatics resource + prefix: dictyBase + uri_format: http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=$1 +dictybase.est: + biocontext: + is_identifiers: true + is_obo: false + prefix: DICTYBASE.EST + uri_format: http://identifiers.org/dictybase.est/$1 + mappings: + biocontext: DICTYBASE.EST + miriam: dictybase.est + n2t: dictybase.est + miriam: + deprecated: false + description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. + homepage: http://dictybase.org/ + id: '00000330' + name: Dictybase EST + namespaceEmbeddedInLui: false + pattern: ^DDB\d+$ + prefix: dictybase.est + sampleId: DDB0016567 + uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 + n2t: + description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. + example: DDB0016567 + homepage: http://dictybase.org/ + name: Dictybase Gene at Northwestern University + namespaceEmbeddedInLui: false + pattern: ^DDB\d+$ + prefix: dictybase.est + uri_format: http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 + name: dictyBase Expressed Sequence Tag + part_of: dictybase +dictybase.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: DICTYBASE.GENE + uri_format: http://identifiers.org/dictybase.gene/$1 + mappings: + biocontext: DICTYBASE.GENE + miriam: dictybase.gene + n2t: dictybase.gene + miriam: + deprecated: false + description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. + homepage: http://dictybase.org/ + id: '00000286' + name: Dictybase Gene + namespaceEmbeddedInLui: false + pattern: ^DDB_G\d+$ + prefix: dictybase.gene + sampleId: DDB_G0267522 + uri_format: http://dictybase.org/gene/$1 + n2t: + description: The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. + example: DDB_G0267522 + homepage: http://dictybase.org/ + name: Dictybase Gene at Northwestern University + namespaceEmbeddedInLui: false + pattern: ^DDB_G\d+$ + prefix: dictybase.gene + uri_format: http://dictybase.org/gene/$1 + part_of: dictybase +did: + banana: did + mappings: + miriam: did + n2t: did + miriam: + deprecated: false + description: DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. + homepage: https://w3c-ccg.github.io/did-spec/ + id: '00000691' + name: Decentralized Identifiers (DIDs) + namespaceEmbeddedInLui: true + pattern: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$ + prefix: did + sampleId: sov:WRfXPg8dantKVubE3HX8pw + uri_format: https://uniresolver.io/#did:$1 + n2t: + description: DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. + example: sov:WRfXPg8dantKVubE3HX8pw + homepage: https://w3c-ccg.github.io/did-spec/ + name: Decentralized Identifiers (DIDs) + namespaceEmbeddedInLui: true + pattern: ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$ + prefix: did + uri_format: https://uniresolver.io/#did:$1 + name: Decentralized Identifier + pattern: ^[a-z0-9]+:[A-Za-z0-9.\-:]+$ +dideo: + biocontext: + is_identifiers: false + is_obo: true + prefix: DIDEO + uri_format: http://purl.obolibrary.org/obo/DIDEO_$1 + bioportal: + name: Drug Interaction and Evidence Ontology + prefix: DIDEO + example: '00000180' + fairsharing: + abbreviation: DIDEO + description: 'A domain ontology for potential drug-drug interactions (PDDIs) that covers the material entities and processes in the domain of discourse for PDDI evidence and knowledge claims. The representation enables the integration of drug interaction mechanisms, effects, risk factors, severity, and management options with the chemical and pharmacological properties (e.g., chemical structure, function, pharmacokinetic and pharmacodynamic properties) of the interacting drugs. It also has a rich and detailed set evidence entities related to pharmacology. See below for publications about DIDEO. A description of the goals of the project can be found in the following workshop paper located in the docs/DIDEO-discussion-ICBO-Brochhausen-2014.pdf: Brochhausen, M., Schneider, J., Malone, D., Empey, PE., Hogan WR., and Boyce, RD. Towards a foundational representation of potential drug-drug interaction knowledge. The 1st International Drug-Drug Interaction Knowledge Representation Workshop (DIKR 2014). Collocated with the 2014 International Conference on Biomedical Ontology (ICBO 2014). October 6th, Houston, Texas. United States.' + id: '295' + name: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology + prefix: FAIRsharing.9y8f0n + subjects: [] + mappings: + biocontext: DIDEO + bioportal: DIDEO + fairsharing: FAIRsharing.9y8f0n + obofoundry: dideo + ols: dideo + ontobee: DIDEO + obofoundry: + contact: mbrochhausen@gmail.com + contact.github: mbrochhausen + contact.label: Mathias Brochhausen + contact.orcid: 0000-0003-1834-3856 + deprecated: false + description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology + download.owl: http://purl.obolibrary.org/obo/dideo.owl + homepage: https://github.com/DIDEO/DIDEO + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology + preferredPrefix: DIDEO + prefix: dideo + repository: https://github.com/DIDEO/DIDEO + ols: + description: The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology + download: http://purl.obolibrary.org/obo/dideo.owl + homepage: https://github.com/DIDEO/DIDEO + name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology + prefix: dideo + version: 2021-06-11 + version.iri: http://purl.obolibrary.org/obo/dideo/release/2021-06-11/dideo.owl + ontobee: + library: Library + name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology + prefix: DIDEO + pattern: ^\d{8}$ +dinto: + biocontext: + is_identifiers: false + is_obo: true + prefix: DINTO + uri_format: http://purl.obolibrary.org/obo/DINTO_$1 + bioportal: + name: The Drug-Drug Interactions Ontology + prefix: DINTO + mappings: + biocontext: DINTO + bioportal: DINTO + obofoundry: dinto + ontobee: DINTO + obofoundry: + contact: maria.herrero@kcl.ac.uk + contact.label: Maria Herrero + deprecated: true + description: A formal represention for drug-drug interactions knowledge. + download.owl: http://purl.obolibrary.org/obo/dinto.owl + homepage: http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: The Drug-Drug Interactions Ontology + prefix: dinto + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/26147071 + title: 'DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.' + repository: https://github.com/labda/DINTO + ontobee: + library: Library + name: The Drug-Drug Interactions Ontology + prefix: DINTO +dip: + biocontext: + is_identifiers: true + is_obo: false + prefix: DIP + uri_format: http://identifiers.org/dip/$1 + fairsharing: + abbreviation: DIP + description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the core DIP data. + id: '2089' + name: Database of Interacting Proteins + prefix: FAIRsharing.qje0v8 + subjects: + - Biology + mappings: + biocontext: DIP + fairsharing: FAIRsharing.qje0v8 + miriam: dip + n2t: dip + prefixcommons: dip + uniprot: DIP + miriam: + deprecated: false + description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions + homepage: https://dip.doe-mbi.ucla.edu/ + id: '00000044' + name: Database of Interacting Proteins + namespaceEmbeddedInLui: false + pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ + prefix: dip + sampleId: DIP-743N + uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 + n2t: + description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions + example: DIP-743N + homepage: https://dip.doe-mbi.ucla.edu/ + name: Database of interacting proteins + namespaceEmbeddedInLui: false + pattern: ^DIP(\:)?\-\d{1,}[ENXS]$ + prefix: dip + uri_format: https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 + prefixcommons: + description: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions + example: DIP-743N + homepage: http://dip.doe-mbi.ucla.edu + keywords: + - interaction + - protein + name: Database of Interacting Proteins + pattern: ^DIP[\:\-]\d{3}[EN]$ + prefix: dip + pubmed_ids: + - '14681454' + uri_format: http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 + uniprot: + category: Protein-protein interaction databases + identifier: '16' + link_is_explicit: 'true' + name: Database of interacting proteins + prefix: DIP + uri_format: https://dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=$1 +discoverx: + cellosaurus: + category: Cell line collections + homepage: https://www.discoverx.com/products-applications/cell-lines + name: DiscoverX cell line products + prefix: DiscoverX + uri_format: https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact + example: 95-0166C6 + mappings: + cellosaurus: DiscoverX +disdriv: + bioportal: + name: Disease Drivers Ontology + prefix: DISDRIV + example: '0000000' + mappings: + bioportal: DISDRIV + obofoundry: disdriv + ols: disdriv + obofoundry: + contact: lynn.schriml@gmail.com + contact.github: lschriml + contact.label: Lynn Schriml + contact.orcid: 0000-0001-8910-9851 + deprecated: false + description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI. + download.owl: http://purl.obolibrary.org/obo/disdriv.owl + homepage: http://www.disease-ontology.org + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Disease Drivers Ontology + preferredPrefix: DISDRIV + prefix: disdriv + repository: https://github.com/DiseaseOntology/DiseaseDriversOntology + twitter: diseaseontology + ols: + description: Drivers of human diseases including environmental, maternal and social exposures. + download: http://purl.obolibrary.org/obo/disdriv.owl + homepage: http://www.disease-ontology.org + name: Disease Drivers + prefix: disdriv + pattern: ^\d+$ +diseaseclass: + appears_in: + - efo + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + description: Legacy disease classes that later became MONDO + download_obo: https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo + example: '0000598' + name: Disease Class + pattern: ^\d{7}$ +diseasesdb: + description: 'The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities.' + example: '1784' + homepage: http://www.diseasesdatabase.com/ + name: Diseases Database + pattern: ^\d+$ + wikidata: + database: Q213103 + prefix: P557 +disprot: + biocontext: + is_identifiers: true + is_obo: false + prefix: DISPROT + uri_format: http://identifiers.org/disprot/$1 + fairsharing: + abbreviation: DisProt + description: The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions are manually curated from literature. DisProt annotations cover both structural and functional aspects of disorder detected by specific experimental methods. + id: '1904' + name: Database of Protein Disorder + prefix: FAIRsharing.dt9z89 + subjects: + - Biomedical Science + mappings: + biocontext: DISPROT + fairsharing: FAIRsharing.dt9z89 + miriam: disprot + n2t: disprot + prefixcommons: disprot + uniprot: DisProt + miriam: + deprecated: false + description: DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. + homepage: https://disprot.org/ + id: '00000199' + name: DisProt + namespaceEmbeddedInLui: false + pattern: ^DP\d{5}$ + prefix: disprot + sampleId: DP00003 + uri_format: https://disprot.org/$1 + n2t: + description: The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. + example: DP00003 + homepage: http://www.disprot.org/ + name: DisProt at Indiana University + namespaceEmbeddedInLui: false + pattern: ^DP\d{5}$ + prefix: disprot + uri_format: http://www.disprot.org/$1 + prefixcommons: + description: The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. + example: DP00001 + homepage: http://www.disprot.org/ + keywords: + - protein + - structure + name: Database of protein disorder + pattern: ^DP\d{5}$ + prefix: disprot + pubmed_ids: + - '17145717' + uri_format: http://www.disprot.org/protein.php?id=$1 + uniprot: + category: Family and domain databases + identifier: '17' + link_is_explicit: 'true' + name: Database of protein disorder + prefix: DisProt + uri_format: https://disprot.org/$1 +disprot.region: + mappings: + miriam: disprot.region + miriam: + deprecated: false + description: DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature. + homepage: https://www.disprot.org + id: '00000745' + name: DisProt region + namespaceEmbeddedInLui: false + pattern: ^DP\d{5}r\d{3}$ + prefix: disprot.region + sampleId: DP00086r013 + uri_format: https://www.disprot.org/$1 +dlxb: + mappings: + miriam: dlxb + miriam: + deprecated: false + description: DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences. + homepage: https://doulix.com + id: '00000747' + name: Linear double stranded DNA sequences + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]{6,7}$ + prefix: dlxb + sampleId: 6VDC956 + uri_format: https://doulix.com/biomodules/$1/ + part_of: dlx + uri_format: https://doulix.com/biomodules/$1 +dlxc: + mappings: + miriam: dlxc + miriam: + deprecated: false + description: DOULIX lab-tested standard biological parts, in this case, full length constructs. + homepage: https://doulix.com + id: '00000742' + name: Circular double stranded DNA sequences composed + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]{6,7}$ + prefix: dlxc + sampleId: M77F7JM + uri_format: https://doulix.com/constructs/$1/ + part_of: dlx + uri_format: https://doulix.com/constructs/$1 +dmba: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A controlled vocabulary to support the study of transcription in the developing mouse brain + download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo + example: '688' + homepage: https://developingmouse.brain-map.org/ + name: Developing Mouse Brain Atlas + pattern: ^\d+$ + preferred_prefix: DMBA +doi: + biocontext: + is_identifiers: false + is_obo: false + prefix: DOI + uri_format: http://dx.doi.org/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: doi + uri_format: https://doi.org/$1 + cellosaurus: + category: Reference resources + homepage: https://dx.doi.org + name: Digital Object Identifier + prefix: DOI + uri_format: https://dx.doi.org/$1 + comment: >- + The [DOI resolution factsheet](https://www.doi.org/factsheets/DOIProxy.html) + specifies that `https://doi.org/DOI` is the preferred format: + + + > Users may resolve DOI names that are structured to use the DOI system Proxy Server (https://doi.org (preferred)). The resolution of the DOI name in this case depends on the use of URL syntax: the example DOI name doi:10.10.123/456 would be resolved from the address: "https://doi.org/10.123/456". Any standard browser encountering a DOI name in this form will be able to resolve it. The proxy service (both doi.org and the **earlier but no longer preferred** dx.doi.org) is accessible over IPv6, and supports DNSSEC. The proxy servers respond to HTTPS (**preferred**) as well as HTTP requests. + contributor_extras: + - email: cjmungall@lbl.gov + github: cmungall + name: Chris Mungall + orcid: 0000-0002-6601-2165 + - github: dhimmel + name: Daniel Himmelstein + orcid: 0000-0002-3012-7446 + fairsharing: + abbreviation: DOI + description: The digital object identifier (DOI) system originated in a joint initiative of three trade associations in the publishing industry (International Publishers Association; International Association of Scientific, Technical and Medical Publishers; Association of American Publishers). The system was announced at the Frankfurt Book Fair 1997. The International DOI® Foundation (IDF) was created to develop and manage the DOI system, also in 1997. The DOI system was adopted as International Standard ISO 26324 in 2012. The DOI system implements the Handle System and adds a number of new features. The DOI system provides an infrastructure for persistent unique identification of objects of any type. The DOI system is designed to work over the Internet. A DOI name is permanently assigned to an object to provide a resolvable persistent network link to current information about that object, including where the object, or information about it, can be found on the Internet. While information about an object can change over time, its DOI name will not change. A DOI name can be resolved within the DOI system to values of one or more types of data relating to the object identified by that DOI name, such as a URL, an e-mail address, other identifiers and descriptive metadata. The DOI system enables the construction of automated services and transactions. Applications of the DOI system include but are not limited to managing information and documentation location and access; managing metadata; facilitating electronic transactions; persistent unique identification of any form of any data; and commercial and non-commercial transactions. The content of an object associated with a DOI name is described unambiguously by DOI metadata, based on a structured extensible data model that enables the object to be associated with metadata of any desired degree of precision and granularity to support description and services. The data model supports interoperability between DOI applications. The scope of the DOI system is not defined by reference to the type of content (format, etc.) of the referent, but by reference to the functionalities it provides and the context of use. The DOI system provides, within networks of DOI applications, for unique identification, persistence, resolution, metadata and semantic interoperability. + id: '1332' + name: Digital Object Identifier + prefix: FAIRsharing.hFLKCn + subjects: + - Knowledge and Information Systems + go: + homepage: http://dx.doi.org/ + name: Digital Object Identifier + prefix: DOI + uri_format: http://dx.doi.org/$1 + mappings: + biocontext: DOI + biolink: doi + cellosaurus: DOI + fairsharing: FAIRsharing.hFLKCn + go: DOI + miriam: doi + n2t: doi + prefixcommons: doi + scholia: doi + miriam: + deprecated: false + description: The Digital Object Identifier System is for identifying content objects in the digital environment. + homepage: https://www.doi.org/ + id: '00000019' + name: DOI + namespaceEmbeddedInLui: false + pattern: ^(doi\:)?\d{2}\.\d{4}.*$ + prefix: doi + providers: + - code: scholia + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + homepage: https://scholia.toolforge.org/ + name: Scholia + uri_format: https://scholia.toolforge.org/doi/$1 + sampleId: 10.1038/nbt1156 + uri_format: https://doi.org/$1 + n2t: + description: The Digital Object Identifier System is for identifying content objects in the digital environment. + example: 10.1038/nbt1156 + homepage: https://www.doi.org/ + name: Digital Object Identifier + namespaceEmbeddedInLui: false + pattern: ^(doi\:)?\d{2}\.\d{4}.*$ + prefix: doi + uri_format: https://doi.org/$1 + prefixcommons: + description: The Digital Object Identifier System is for identifying content objects in the digital environment. + example: 10.1038/nbt1156 + homepage: http://www.doi.org/ + keywords: + - bibliography + name: Digital Object Identifier + pattern: ^(doi\:)?\d{2}\.\d{4}.*$ + prefix: doi + uri_format: http://dx.doi.org/$1 + providers: + - code: dx_doi_http + description: An alternate provider from the DOI website using HTTP + homepage: https://www.doi.org + name: Digital Object Identifier + uri_format: http://dx.doi.org/$1 + - code: dx_doi_https + description: An alternate provider from the DOI website using HTTPS + homepage: https://www.doi.org + name: Digital Object Identifier + uri_format: https://dx.doi.org/$1 + - code: doi_http + description: An alternate provider from the DOI website using HTTP + homepage: https://www.doi.org + name: Digital Object Identifier + uri_format: http://doi.org/$1 + references: + - https://github.com/biopragmatics/bioregistry/issues/287 + - https://github.com/biopragmatics/bioregistry/pull/316 + uri_format: https://doi.org/$1 +doid: + biocontext: + is_identifiers: false + is_obo: true + prefix: DOID + uri_format: http://purl.obolibrary.org/obo/DOID_$1 + bioportal: + name: Human Disease Ontology + prefix: DOID + download_obo: https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo + example: '0110974' + fairsharing: + abbreviation: DOID + description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics, underlying mechanisms and related medical vocabulary disease concepts. + id: '870' + name: Disease Ontology + prefix: FAIRsharing.8b6wfq + subjects: + - Life Science + - Biomedical Science + mappings: + biocontext: DOID + bioportal: DOID + fairsharing: FAIRsharing.8b6wfq + miriam: doid + n2t: doid + obofoundry: doid + ols: doid + ontobee: DOID + prefixcommons: do + wikidata: P699 + miriam: + deprecated: false + description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. + homepage: https://www.ebi.ac.uk/ols/ontologies/doid + id: '00000233' + name: Human Disease Ontology + namespaceEmbeddedInLui: true + pattern: ^DOID:\d+$ + prefix: doid + providers: + - code: hdo + description: Human Disease Ontology at Northwestern University + homepage: http://disease-ontology.org/ + name: Human Disease Ontology at Northwestern University + uri_format: http://disease-ontology.org/term/DOID:$1 + sampleId: '11337' + uri_format: https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1 + n2t: + description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. + example: '11337' + homepage: http://disease-ontology.org/ + name: Human Disease Ontology at Northwestern University + namespaceEmbeddedInLui: true + pattern: ^DOID\:\d+$ + prefix: doid + uri_format: http://disease-ontology.org/term/DOID:$1 + obofoundry: + appears_in: + - clo + - scdo + contact: lynn.schriml@gmail.com + contact.github: lschriml + contact.label: Lynn Schriml + contact.orcid: 0000-0001-8910-9851 + deprecated: false + description: An ontology for describing the classification of human diseases organized by etiology. + download.obo: http://purl.obolibrary.org/obo/doid.obo + download.owl: http://purl.obolibrary.org/obo/doid.owl + homepage: http://www.disease-ontology.org + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Human Disease Ontology + preferredPrefix: DOID + prefix: doid + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/25348409 + title: 'Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data' + - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 + title: The Human Disease Ontology 2022 update + repository: https://github.com/DiseaseOntology/HumanDiseaseOntology + twitter: diseaseontology + ols: + description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. + download: http://purl.obolibrary.org/obo/doid.owl + name: Human Disease Ontology + prefix: doid + version: 2022-04-28 + version.iri: http://purl.obolibrary.org/obo/doid/releases/2022-04-28/doid.owl + ontobee: + library: Foundry + name: Human Disease Ontology + prefix: DOID + pattern: ^\d+$ + prefixcommons: + bioportal: '1009' + description: The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. + example: DOID:11337 + homepage: http://diseaseontology.sourceforge.net/ + keywords: + - obo + - disease + - human + - ontology + name: Human disease ontology + pattern: ^DOID\:\d+$ + prefix: do + uri_format: http://disease-ontology.org/term/$1 + synonyms: + - do + wikidata: + database: Q5282129 + database.homepage: http://disease-ontology.org/ + database.label: Disease Ontology + homepage: http://disease-ontology.org + name: Disease Ontology ID + pattern: DOID:([0-9]{7}|[1-9][0-9]{0,4}) + prefix: P699 + uri_format: http://www.disease-ontology.org/?id=$1 +dommino: + biocontext: + is_identifiers: true + is_obo: false + prefix: DOMMINO + uri_format: http://identifiers.org/dommino/$1 + homepage: http://korkinlab.org/dommino + mappings: + biocontext: DOMMINO + miriam: dommino + n2t: dommino + miriam: + deprecated: false + description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. + homepage: http://dommino.org/ + id: '00000373' + name: DOMMINO + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: dommino + sampleId: 2GC4 + uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 + n2t: + description: DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. + example: 2GC4 + homepage: http://dommino.org/ + name: DOMMINO at University of Missouri + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: dommino + uri_format: http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 + name: Database of Macromolecular Interactions +door: + biocontext: + is_identifiers: true + is_obo: false + prefix: DOOR + uri_format: http://identifiers.org/door/$1 + mappings: + biocontext: DOOR + miriam: door + n2t: door + prefixcommons: door + miriam: + deprecated: false + description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. + homepage: http://csbl.bmb.uga.edu/DOOR/operon.php + id: '00000453' + name: DOOR + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: door + sampleId: '1398574' + uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 + n2t: + description: DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. + example: '1398574' + homepage: http://csbl.bmb.uga.edu/DOOR/operon.php + name: DOOR v1 at University of Georgia + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: door + uri_format: http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 + name: Database for Prokaryotic Operons + prefixcommons: + description: DOOR (Database of prOkaryotic OpeRons) is an operon database developed by Computational Systems Biology Lab (CSBL) at University of Georgia. The operons in the database are based on prediction. + example: '607986' + homepage: http://csbl1.bmb.uga.edu/OperonDB/ + keywords: + - DNA + name: Database of prOkaryotic OpeRons + pattern: ^\d+$ + prefix: door + uri_format: http://csbl1.bmb.uga.edu/OperonDB/genedetail.php?id=$1 +doqcs.model: + biocontext: + is_identifiers: true + is_obo: false + prefix: DOQCS.MODEL + uri_format: http://identifiers.org/doqcs.model/$1 + mappings: + biocontext: DOQCS.MODEL + miriam: doqcs.model + n2t: doqcs.model + prefixcommons: doqcs.model + miriam: + deprecated: false + description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. + homepage: http://doqcs.ncbs.res.in/ + id: '00000134' + name: 'Database of Quantitative Cellular Signaling: Model' + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: doqcs.model + sampleId: '57' + uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 + n2t: + description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. + example: '57' + homepage: http://doqcs.ncbs.res.in/ + name: Database of Quantitative Cellular Signaling (DOQCS) - Model Access + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: doqcs.model + uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 + part_of: doqcs + prefixcommons: + description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. + example: '57' + homepage: http://doqcs.ncbs.res.in/ + keywords: + - model + name: 'Database of Quantitative Cellular Signaling: Model' + pattern: ^\d+$ + prefix: doqcs.model + pubmed_ids: + - '12584128' + uri_format: http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 +doqcs.pathway: + biocontext: + is_identifiers: true + is_obo: false + prefix: DOQCS.PATHWAY + uri_format: http://identifiers.org/doqcs.pathway/$1 + mappings: + biocontext: DOQCS.PATHWAY + miriam: doqcs.pathway + n2t: doqcs.pathway + prefixcommons: doqcs.pathway + miriam: + deprecated: false + description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. + homepage: http://doqcs.ncbs.res.in/ + id: '00000135' + name: 'Database of Quantitative Cellular Signaling: Pathway' + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: doqcs.pathway + sampleId: '131' + uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 + n2t: + description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. + example: '131' + homepage: http://doqcs.ncbs.res.in/ + name: Database of Quantitative Cellular Signaling (DOQCS) - Pathway Access + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: doqcs.pathway + uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 + part_of: doqcs + prefixcommons: + description: The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. + example: '38' + homepage: http://doqcs.ncbs.res.in/ + keywords: + - pathway + name: 'Database of Quantitative Cellular Signaling: Pathway' + pattern: ^\d+$ + prefix: doqcs.pathway + pubmed_ids: + - '12584128' + uri_format: http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 +dpo: + bioportal: + name: Drosophila Phenotype Ontology + prefix: DPO + comment: DPO is a subset of terms from FBcv + mappings: + bioportal: DPO + obofoundry: dpo + ols: dpo + ontobee: DPO + no_own_terms: true + obofoundry: + contact: cp390@cam.ac.uk + contact.github: Clare72 + contact.label: Clare Pilgrim + contact.orcid: 0000-0002-1373-1705 + deprecated: false + description: An ontology of commonly encountered and/or high level Drosophila phenotypes. + download.json: http://purl.obolibrary.org/obo/dpo.json + download.obo: http://purl.obolibrary.org/obo/dpo.obo + download.owl: http://purl.obolibrary.org/obo/dpo.owl + homepage: http://purl.obolibrary.org/obo/fbcv + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Drosophila Phenotype Ontology + preferredPrefix: FBcv + prefix: dpo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/24138933 + title: The Drosophila phenotype ontology. + repository: https://github.com/FlyBase/drosophila-phenotype-ontology + ols: + description: An ontology for the description of Drosophila melanogaster phenotypes. + download: http://purl.obolibrary.org/obo/dpo.owl + homepage: http://purl.obolibrary.org/obo/fbcv + name: Drosophila Phenotype Ontology (DPO) + prefix: dpo + version: 2022-04-13 + version.iri: http://purl.obolibrary.org/obo/dpo/releases/2022-04-13/dpo.owl + ontobee: + library: Library + name: Drosophila Phenotype Ontology + prefix: DPO + part_of: fbcv + preferred_prefix: DPO +dpv: + biocontext: + is_identifiers: true + is_obo: false + prefix: DPV + uri_format: http://identifiers.org/dpv/$1 + mappings: + biocontext: DPV + miriam: dpv + n2t: dpv + miriam: + deprecated: false + description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. + homepage: http://www.dpvweb.net/ + id: '00000280' + name: DPV + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dpv + sampleId: '100' + uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 + n2t: + description: Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. + example: '100' + homepage: http://www.dpvweb.net/ + name: DPV at Rothamsted + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: dpv + uri_format: http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 + name: Description of Plant Viruses +dragondb.allele: + biocontext: + is_identifiers: true + is_obo: false + prefix: DRAGONDB.ALLELE + uri_format: http://identifiers.org/dragondb.allele/$1 + comment: Deprecated because the website is dead + deprecated: true + mappings: + biocontext: DRAGONDB.ALLELE + miriam: dragondb.allele + n2t: dragondb.allele + miriam: + deprecated: false + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. + homepage: http://www.antirrhinum.net/ + id: '00000300' + name: DragonDB Allele + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.allele + sampleId: cho + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele + n2t: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. + example: cho + homepage: http://www.antirrhinum.net/ + name: DragonDB Allele at University of British Columbia + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.allele + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele + part_of: dragondb +dragondb.dna: + biocontext: + is_identifiers: true + is_obo: false + prefix: DRAGONDB.DNA + uri_format: http://identifiers.org/dragondb.dna/$1 + comment: Deprecated because the website is dead + deprecated: true + mappings: + biocontext: DRAGONDB.DNA + miriam: dragondb.dna + n2t: dragondb.dna + miriam: + deprecated: false + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. + homepage: http://www.antirrhinum.net/ + id: '00000297' + name: DragonDB DNA + namespaceEmbeddedInLui: false + pattern: ^\d\w+$ + prefix: dragondb.dna + sampleId: 3hB06 + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA + n2t: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. + example: 3hB06 + homepage: http://www.antirrhinum.net/ + name: DragonDB DNA at University of British Columbia + namespaceEmbeddedInLui: false + pattern: ^\d\w+$ + prefix: dragondb.dna + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA + part_of: dragondb +dragondb.locus: + biocontext: + is_identifiers: true + is_obo: false + prefix: DRAGONDB.LOCUS + uri_format: http://identifiers.org/dragondb.locus/$1 + comment: Deprecated because the website is dead + deprecated: true + mappings: + biocontext: DRAGONDB.LOCUS + miriam: dragondb.locus + n2t: dragondb.locus + miriam: + deprecated: false + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. + homepage: http://www.antirrhinum.net/ + id: '00000299' + name: DragonDB Locus + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.locus + sampleId: DEF + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus + n2t: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. + example: DEF + homepage: http://www.antirrhinum.net/ + name: DragonDB Locus at University of British Columbia + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.locus + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus + part_of: dragondb +dragondb.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: DRAGONDB.PROTEIN + uri_format: http://identifiers.org/dragondb.protein/$1 + comment: Deprecated because the website is dead + deprecated: true + mappings: + biocontext: DRAGONDB.PROTEIN + miriam: dragondb.protein + n2t: dragondb.protein + miriam: + deprecated: false + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. + homepage: http://www.antirrhinum.net/ + id: '00000298' + name: DragonDB Protein + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.protein + sampleId: AMDEFA + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide + n2t: + description: DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. + example: AMDEFA + homepage: http://www.antirrhinum.net/ + name: DragonDB Protein at University of British Columbia + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: dragondb.protein + uri_format: http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide + part_of: dragondb +dron: + biocontext: + is_identifiers: false + is_obo: true + prefix: DRON + uri_format: http://purl.obolibrary.org/obo/DRON_$1 + bioportal: + name: The Drug Ontology + prefix: DRON + example: '00023232' + fairsharing: + abbreviation: DrOn + description: An ontology of drug products and packaged drug products. + id: '641' + name: The Drug Ontology + prefix: FAIRsharing.w5ntfd + subjects: + - Biomedical Science + mappings: + biocontext: DRON + bioportal: DRON + fairsharing: FAIRsharing.w5ntfd + obofoundry: dron + ols: dron + ontobee: DRON + obofoundry: + appears_in: + - scdo + contact: hoganwr@gmail.com + contact.github: hoganwr + contact.label: William Hogan + contact.orcid: 0000-0002-9881-1017 + deprecated: false + description: An ontology to support comparative effectiveness researchers studying claims data. + download.owl: http://purl.obolibrary.org/obo/dron.owl + homepage: https://github.com/ufbmi/dron + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: The Drug Ontology + preferredPrefix: DRON + prefix: dron + publications: + - id: https://doi.org/10.1186/s13326-017-0121-5 + title: 'Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request' + repository: https://github.com/ufbmi/dron + ols: + description: We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). + download: http://purl.obolibrary.org/obo/dron.owl + homepage: https://github.com/ufbmi/dron + name: The Drug Ontology + prefix: dron + version: 2022-04-22 + version.iri: http://purl.obolibrary.org/obo/dron/releases/2022-04-22/dron.owl + ontobee: + library: Library + name: The Drug Ontology + prefix: DRON + pattern: ^\d{8}$ +drsc: + biocontext: + is_identifiers: true + is_obo: false + prefix: DRSC + uri_format: http://identifiers.org/drsc/$1 + mappings: + biocontext: DRSC + miriam: drsc + n2t: drsc + miriam: + deprecated: false + description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. + homepage: http://flyrnai.org/ + id: '00000367' + name: DRSC + namespaceEmbeddedInLui: false + pattern: ^DRSC\d+$ + prefix: drsc + sampleId: DRSC05221 + uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 + n2t: + description: The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. + example: DRSC05221 + homepage: http://flyrnai.org/ + name: DRSC at Harvard Medical School + namespaceEmbeddedInLui: false + pattern: ^DRSC\d+$ + prefix: drsc + uri_format: http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 + name: Drosophila RNAi Screening Center +drugbank: + biocontext: + is_identifiers: false + is_obo: false + prefix: DrugBank + uri_format: http://www.drugbank.ca/drugs/$1 + cellosaurus: + category: Chemistry resources + homepage: https://go.drugbank.com/ + name: DrugBank database + prefix: DrugBank + uri_format: https://go.drugbank.com/drugs/$1 + cheminf: + description: Database identifier used by DrugBank. + name: DrugBank + obsolete: false + prefix: '000406' + example: DB14938 + fairsharing: + abbreviation: DrugBank + description: The DrugBank database is a freely available bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. + id: '1844' + name: DrugBank + prefix: FAIRsharing.353yat + subjects: + - Life Science + - Biomedical Science + homepage: http://www.drugbank.ca + mappings: + biocontext: DrugBank + cellosaurus: DrugBank + cheminf: '000406' + fairsharing: FAIRsharing.353yat + miriam: drugbank + n2t: drugbank + prefixcommons: drugbank + uniprot: DrugBank + wikidata: P715 + miriam: + deprecated: false + description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. + homepage: http://www.drugbank.ca/ + id: '00000102' + name: DrugBank + namespaceEmbeddedInLui: false + pattern: ^DB\d{5}$ + prefix: drugbank + sampleId: DB00001 + uri_format: http://www.drugbank.ca/drugs/$1 + n2t: + description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. + example: DB00001 + homepage: http://www.drugbank.ca/ + name: DrugBank drug information + namespaceEmbeddedInLui: false + pattern: ^DB\d{5}$ + prefix: drugbank + uri_format: http://www.drugbank.ca/drugs/$1 + name: DrugBank + prefixcommons: + description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. + example: DB00001 + homepage: http://www.drugbank.ca/ + keywords: + - drug + - protein + name: DrugBank + pattern: ^DB\d{5}$ + prefix: drugbank + pubmed_ids: + - '24203711' + - '21059682' + - '18048412' + - '16381955' + uri_format: http://www.drugbank.ca/drugs/$1 + synonyms: + - DRUGBANK_ID + - DrugBank + uniprot: + category: Chemistry databases + identifier: '19' + link_is_explicit: 'true' + name: Drug and drug target database + prefix: DrugBank + uri_format: https://www.drugbank.ca/drugs/$1 + wikidata: + database: Q1122544 + database.homepage: http://www.drugbank.ca/ + database.label: DrugBank + homepage: https://www.drugbank.ca + name: DrugBank ID + pattern: (SALT\d{1}|CAT\d{1})?\d{5} + prefix: P715 + uri_format: https://go.drugbank.com/drugs/DB$1 +drugbank.salt: + biocontext: + is_identifiers: true + is_obo: false + prefix: DRUGBANK.TARGET + uri_format: http://identifiers.org/drugbank.target/$1 + description: DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. + example: DBSALT001211 + homepage: http://www.drugbank.ca + mappings: + biocontext: DRUGBANK.TARGET + name: DrugBank Salts + part_of: drugbank + pattern: ^DBSALT\d{6}$ + synonyms: + - drugbank.target + uri_format: https://go.drugbank.com/salts/$1 +drugbankv4.target: + biocontext: + is_identifiers: true + is_obo: false + prefix: DRUGBANKV4.TARGET + uri_format: http://identifiers.org/drugbankv4.target/$1 + mappings: + biocontext: DRUGBANKV4.TARGET + miriam: drugbankv4.target + n2t: drugbankv4.target + miriam: + deprecated: false + description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. + homepage: http://www.drugbank.ca/targets + id: '00000528' + name: DrugBank Target v4 + namespaceEmbeddedInLui: false + pattern: ^BE\d{7}$ + prefix: drugbankv4.target + sampleId: BE0000048 + uri_format: http://www.drugbank.ca/biodb/bio_entities/$1 + n2t: + description: The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. + example: BE0000048 + homepage: http://www.drugbank.ca/targets + name: DrugBank Target information version 4 + namespaceEmbeddedInLui: false + pattern: ^BE\d{7}$ + prefix: drugbankv4.target + uri_format: http://www.drugbank.ca/biodb/bio_entities/$1 + part_of: drugbank +drugcentral: + biolink: + is_identifiers: false + is_obo: false + prefix: DrugCentral + uri_format: http://drugcentral.org/drugcard/$1 + description: DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. + example: '307' + fairsharing: + abbreviation: DrugCentral + description: DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource. This resource was created and is maintained by the Division of Translational Informatics at the University of New Mexico School of Medicine. + id: '2363' + name: DrugCentral + prefix: FAIRsharing.3me82d + subjects: + - Drug Discovery + - Drug Repositioning + - Drug Development + - Pharmacy + - Pharmacology + - Biomedical Science + homepage: http://drugcentral.org + mappings: + biolink: DrugCentral + fairsharing: FAIRsharing.3me82d + uniprot: DrugCentral + name: Drug Central + pattern: ^\d+$ + synonyms: + - Drug_Central + uniprot: + category: Chemistry databases + identifier: '239' + link_is_explicit: 'true' + name: DrugCentral + prefix: DrugCentral + uri_format: https://drugcentral.org/target/$1 + uri_format: http://drugcentral.org/drugcard/$1 +dsmz: + cellosaurus: + category: Cell line collections + homepage: https://www.dsmz.de/collection/catalogue/human-and-animal-cell-lines/catalogue + name: Deutsche Sammlung von Mikroorganismen und Zellkulturen + prefix: DSMZ + uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). + example: ACC-1 + homepage: https://www.dsmz.de + mappings: + cellosaurus: DSMZ + name: Deutsche Sammlung von Mikroorganismen und Zellkulturen + uri_format: https://www.dsmz.de/collection/catalogue/details/culture/$1 +dto: + appears_in: + - pr + bioportal: + name: Drug Target Ontology + prefix: DTO + description: 'DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.' + example: '90000018' + fairsharing: + abbreviation: DTO + description: Drug Target Ontology (DTO) is developed as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families, GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO also contains drug target development classifications, a large collection of cell lines from the LINCS project and relevant cell-disease and cell-tissue relations. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a modularization approach. DTO will serve as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov). + id: '1469' + name: Drug Target Ontology + prefix: FAIRsharing.tke3y2 + subjects: + - Drug Discovery + - Biomedical Science + homepage: https://github.com/DrugTargetOntology/DTO + mappings: + bioportal: DTO + fairsharing: FAIRsharing.tke3y2 + name: Drug Target Ontology + pattern: ^\d+$ + repository: https://github.com/DrugTargetOntology/DTO +duo: + biocontext: + is_identifiers: false + is_obo: true + prefix: DUO + uri_format: http://purl.obolibrary.org/obo/DUO_$1 + bioportal: + name: The Data Use Ontology + prefix: DUO + example: '0000046' + fairsharing: + abbreviation: DUO + description: The Data Use Ontology (DUO) describes data use requirements and limitations. DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. This resource is based on the OBO Foundry principles, and developed using the W3C Web Ontology Language. It is used in production by the European Genome-phenome Archive (EGA) at EMBL-EBI and CRG as well as the Broad Institute for the Data Use Oversight System (DUOS). + id: '256' + name: The Data Use Ontology + prefix: FAIRsharing.5dnjs2 + subjects: + - Data Management + - Subject Agnostic + mappings: + biocontext: DUO + bioportal: DUO + fairsharing: FAIRsharing.5dnjs2 + obofoundry: duo + ols: duo + ontobee: DUO + obofoundry: + appears_in: + - scdo + contact: mcourtot@gmail.com + contact.github: mcourtot + contact.label: Melanie Courtot + contact.orcid: 0000-0002-9551-6370 + depends_on: + - bfo + - iao + deprecated: false + description: DUO is an ontology which represent data use conditions. + download.owl: http://purl.obolibrary.org/obo/duo.owl + homepage: https://github.com/EBISPOT/DUO + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Data Use Ontology + preferredPrefix: DUO + prefix: duo + repository: https://github.com/EBISPOT/DUO + ols: + download: http://purl.obolibrary.org/obo/duo.owl + name: duo + prefix: duo + version: 2021-02-23 + version.iri: http://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl + ontobee: + library: Library + name: Data Use Ontology + prefix: DUO + pattern: ^\d{7}$ +eaglei: + cellosaurus: + category: Biological sample resources + homepage: https://www.eagle-i.net/ + name: eagle-i resource discovery tool + prefix: eagle-i + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Discovery tool for biomedical research resources available at institutions throughout the U.S. + example: 0000012b-5661-2f63-2f73-b43980000000 + homepage: https://hawaii.eagle-i.net + mappings: + cellosaurus: eagle-i + name: eagle-i + uri_format: http://hawaii.eagle-i.net/i/$1 +ebisc: + cellosaurus: + category: Cell line collections + homepage: https://www.ebisc.org + name: European Bank for induced pluripotent Stem Cells + prefix: EBiSC + uri_format: https://cells.ebisc.org/$1 + example: ESi007-A + mappings: + cellosaurus: EBiSC +ecacc: + cellosaurus: + category: Cell line collections + homepage: https://www.phe-culturecollections.org.uk/products/celllines/index.aspx + name: European Collection of Cell Cultures + prefix: ECACC + uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?refId=$1&collection=ecacc_gc + description: The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs). + example: '90062901' + homepage: https://www.phe-culturecollections.org.uk/collections/ecacc.aspx + mappings: + cellosaurus: ECACC + name: European Collection of Authenticated Cell Culture + pattern: ^\d+$ + uri_format: https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1 +ecao: + bioportal: + name: The Echinoderm Anatomy and Development Ontology + prefix: ECAO + example: '0107180' + mappings: + bioportal: ECAO + obofoundry: ecao + ols: ecao + ontobee: ECAO + obofoundry: + contact: ettensohn@cmu.edu + contact.github: ettensohn + contact.label: Charles Ettensohn + contact.orcid: 0000-0002-3625-0955 + depends_on: + - cl + - ro + - uberon + deprecated: false + description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586). + download.obo: http://purl.obolibrary.org/obo/ecao.obo + download.owl: http://purl.obolibrary.org/obo/ecao.owl + homepage: https://github.com/echinoderm-ontology/ecao_ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: The Echinoderm Anatomy and Development Ontology + preferredPrefix: ECAO + prefix: ecao + repository: https://github.com/echinoderm-ontology/ecao_ontology + ols: + description: None + download: http://purl.obolibrary.org/obo/ecao.owl + homepage: https://github.com/echinoderm-ontology/ecao_ontology + name: Echinoderm Anatomy and Development Ontology + prefix: ecao + version: 2020-05-22 + version.iri: http://purl.obolibrary.org/obo/ecao/releases/2020-05-22/ecao.owl + ontobee: + library: Library + name: The Echinoderm Anatomy and Development Ontology + prefix: ECAO + pattern: ^\d{7}$ +eccode: + biocontext: + is_identifiers: false + is_obo: false + prefix: EC + uri_format: http://www.enzyme-database.org/query.php?ec=$1 + example_decoys: + - '100' + - '2.' + - 2.n1 + - 2.3. + - 2.3.n1 + - 2.3.1. + - 2.3.1.n + - 2.3.4.1. + example_extras: + - '2' + - '2.3' + - 2.3.1 + - 2.3.1.n12 + - 3.1.26.n2 + fairsharing: + abbreviation: IntEnz + description: IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. + id: '1853' + name: Integrated relational Enzyme database + prefix: FAIRsharing.q1fdkc + subjects: + - Bioinformatics + - Enzymology + go: + homepage: http://enzyme.expasy.org/ + name: Enzyme Commission + prefix: EC + uri_format: https://enzyme.expasy.org/EC/$1 + mappings: + biocontext: EC + fairsharing: FAIRsharing.q1fdkc + go: EC + miriam: ec-code + n2t: ec-code + prefixcommons: intenz + miriam: + deprecated: false + description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. + homepage: https://www.ebi.ac.uk/intenz/ + id: '00000004' + name: Enzyme Nomenclature + namespaceEmbeddedInLui: false + pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ + prefix: ec-code + providers: + - code: CURATOR_REVIEW + description: KEGG Ligand Database for Enzyme Nomenclature + homepage: https://www.genome.jp/dbget-bin/www_bfind?enzyme + name: KEGG Ligand Database for Enzyme Nomenclature + uri_format: https://www.genome.jp/dbget-bin/www_bget?ec:$1 + - code: expenz + description: ExploreEnz at Trinity College + homepage: http://www.enzyme-database.org/ + name: ExploreEnz at Trinity College + uri_format: http://www.enzyme-database.org/query.php?ec=$1 + - code: enzymeportal + description: Enzyme Portal through EMBL-EBI + homepage: https://www.ebi.ac.uk/enzymeportal + name: Enzyme Portal through EMBL-EBI + uri_format: https://www.ebi.ac.uk/enzymeportal/ec/$1 + - code: expasy + description: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) + homepage: https://enzyme.expasy.org/ + name: Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) + uri_format: https://enzyme.expasy.org/EC/$1 + sampleId: 1.1.1.1 + uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 + n2t: + description: The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. + example: 1.1.1.1 + homepage: https://www.ebi.ac.uk/intenz/ + name: IntEnZ (Integrated relational Enzyme database) + namespaceEmbeddedInLui: false + pattern: ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ + prefix: ec-code + uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 + name: Enzyme Nomenclature + pattern: ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$ + prefixcommons: + description: IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. + example: '17854' + homepage: http://www.ebi.ac.uk/intenz + keywords: + - classification + - enzyme + name: Integrated relational Enzyme database + pattern: ^\d+$ + prefix: intenz + uri_format: http://www.ebi.ac.uk/intenz/query?cmd=SearchID&id=$1 + synonyms: + - EC + - EC-CODE + - ECCODE + - EC_CODE + - ec-code + - intenz + uri_format: https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 + wikidata: + prefix: P591 +ecg: + bioportal: + name: Electrocardiography Ontology + prefix: ECG + description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. + example: '000000159' + fairsharing: + abbreviation: ECG + description: The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. This ontology was developed and is being maintained by the CardioVascular Research Grid (www.cvrg.org). + id: '19' + name: ElectroCardioGraphy Ontology + prefix: FAIRsharing.azr389 + subjects: + - Biomedical Science + homepage: https://bioportal.bioontology.org/ontologies/ECG + mappings: + bioportal: ECG + fairsharing: FAIRsharing.azr389 + name: Electrocardiogram Ontology + pattern: ^\d+$ + synonyms: + - ECGOntology +echobase: + biocontext: + is_identifiers: true + is_obo: false + prefix: ECHOBASE + uri_format: http://identifiers.org/echobase/$1 + go: + homepage: https://www.york.ac.uk/res/thomas/ + name: EchoBASE post-genomic database for Escherichia coli + prefix: EchoBASE + uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?&recordID=$1 + mappings: + biocontext: ECHOBASE + go: EchoBASE + miriam: echobase + n2t: echobase + prefixcommons: echobase + uniprot: EchoBASE + miriam: + deprecated: false + description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. + homepage: http://www.york.ac.uk/ + id: '00000200' + name: EchoBASE + namespaceEmbeddedInLui: false + pattern: ^EB\d+$ + prefix: echobase + sampleId: EB0170 + uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 + n2t: + description: EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. + example: EB0170 + homepage: http://www.york.ac.uk/ + name: EchoBASE at the University of York + namespaceEmbeddedInLui: false + pattern: ^EB\d+$ + prefix: echobase + uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 + prefixcommons: + description: EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. + example: EB0170 + homepage: http://www.ecoli-york.org/ + keywords: + - gene + - gene expression + name: EchoBASE - an integrated post-genomic database for E. coli + pattern: ^EB\d+$ + prefix: echobase + pubmed_ids: + - '15608209' + uri_format: http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 + uniprot: + category: Organism-specific databases + identifier: '20' + link_is_explicit: 'true' + name: EchoBASE - an integrated post-genomic database for E. coli + prefix: EchoBASE + uri_format: https://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 +ecmdb: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes. + example: ECMDB00005 + homepage: https://ecmdb.ca + name: E. coli Metabolite Database + pattern: ^ECMDB\d+$ + synonyms: + - ECMDB + uri_format: http://ecmdb.ca/compounds/$1 + wikidata: + database: Q17052437 +eco: + biocontext: + is_identifiers: false + is_obo: true + prefix: ECO + uri_format: http://purl.obolibrary.org/obo/ECO_$1 + bioportal: + name: Evidence and Conclusion Ontology + prefix: ECO + example: '0007807' + fairsharing: + abbreviation: ECO + description: The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures, and query of eviden + id: '1483' + name: Evidence and Conclusion Ontology + prefix: FAIRsharing.wvpgwn + subjects: + - Computational Biology + - Life Science + go: + homepage: http://www.evidenceontology.org/ + name: Evidence Code Ontology + prefix: ECO + uri_format: http://www.evidenceontology.org/browse/#ECO_$1 + mappings: + biocontext: ECO + bioportal: ECO + fairsharing: FAIRsharing.wvpgwn + go: ECO + miriam: eco + n2t: eco + obofoundry: eco + ols: eco + ontobee: ECO + prefixcommons: eco + miriam: + deprecated: false + description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. + homepage: https://www.ebi.ac.uk/ols/ontologies/eco + id: '00000055' + name: Evidence Code Ontology + namespaceEmbeddedInLui: true + pattern: ECO:\d{7}$ + prefix: eco + sampleId: '0000006' + uri_format: https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1 + n2t: + description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. + example: '0000006' + homepage: http://bioportal.bioontology.org/ontologies/ECO + name: Evidence Code Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ECO:\d{7}$ + prefix: eco + uri_format: http://purl.bioontology.org/ontology/ECO/ECO:$1 + obofoundry: + contact: mgiglio@som.umaryland.edu + contact.github: mgiglio99 + contact.label: Michelle Giglio + contact.orcid: 0000-0001-7628-5565 + deprecated: false + description: An ontology for experimental and other evidence statements. + download.obo: http://purl.obolibrary.org/obo/eco.obo + download.owl: http://purl.obolibrary.org/obo/eco.owl + homepage: https://github.com/evidenceontology/evidenceontology/ + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Evidence ontology + preferredPrefix: ECO + prefix: eco + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/30407590 + title: 'ECO, the Evidence & Conclusion Ontology: community standard for evidence information.' + - id: https://www.ncbi.nlm.nih.gov/pubmed/25052702 + title: Standardized description of scientific evidence using the Evidence Ontology (ECO) + repository: https://github.com/evidenceontology/evidenceontology + ols: + description: The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means. + download: http://purl.obolibrary.org/obo/eco.owl + homepage: https://github.com/evidenceontology/evidenceontology/ + name: Evidence & Conclusion Ontology (ECO) + prefix: eco + version: 2022-04-11 + version.iri: http://purl.obolibrary.org/obo/eco/releases/2022-04-11/eco.owl + ontobee: + library: Library + name: Evidence ontology + prefix: ECO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1012' + description: Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. + example: ECO:0000006 + keywords: + - obo + - ontology + name: Evidence Code Ontology + pattern: ^ECO:\d{7}$ + prefix: eco + uri_format: http://www.ebi.ac.uk/ontology-lookup/?termId=$1 +ecocore: + biocontext: + is_identifiers: false + is_obo: true + prefix: ECOCORE + uri_format: http://purl.obolibrary.org/obo/ECOCORE_$1 + bioportal: + name: An ontology of core ecological entities + prefix: ECOCORE + example: '00000001' + mappings: + biocontext: ECOCORE + bioportal: ECOCORE + obofoundry: ecocore + ols: ecocore + ontobee: ECOCORE + obofoundry: + contact: p.buttigieg@gmail.com + contact.github: pbuttigieg + contact.label: Pier Luigi Buttigieg + contact.orcid: 0000-0002-4366-3088 + depends_on: + - bfo + - chebi + - envo + - go + - iao + - pato + - pco + - po + - ro + - uberon + deprecated: false + description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. + download.obo: http://purl.obolibrary.org/obo/ecocore.obo + download.owl: http://purl.obolibrary.org/obo/ecocore.owl + homepage: https://github.com/EcologicalSemantics/ecocore + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: An ontology of core ecological entities + preferredPrefix: ECOCORE + prefix: ecocore + repository: https://github.com/EcologicalSemantics/ecocore + ols: + description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. + download: http://purl.obolibrary.org/obo/ecocore.owl + homepage: https://github.com/EcologicalSemantics/ecocore + name: An ontology of core ecological entities + prefix: ecocore + version: 2022-03-09 + version.iri: http://purl.obolibrary.org/obo/ecocore/releases/2022-03-09/ecocore.owl + ontobee: + library: Library + name: An ontology of core ecological entities + prefix: ECOCORE + pattern: ^\d+$ +ecocyc: + description: EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways. + example: AICARTRANSIMPCYCLO-CPLX + fairsharing: + abbreviation: EcoCyc + description: EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc has been curated from 37,000 publications as of 2019. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc. + id: '2054' + name: EcoCyc E. coli Database + prefix: FAIRsharing.65dmtr + subjects: + - Biology + go: + homepage: http://ecocyc.org/ + name: Encyclopedia of E. coli metabolism + prefix: EcoCyc + uri_format: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=$1 + mappings: + fairsharing: FAIRsharing.65dmtr + go: EcoCyc + ncbi: ECOCYC + name: EcoCyc + ncbi: + example: sroC + homepage: https://ecocyc.org/ + name: E. coli database + prefix: ECOCYC + uri_format: https://biocyc.org/gene?id=$1 +ecogene: + biocontext: + is_identifiers: false + is_obo: false + prefix: EcoGene + uri_format: http://ecogene.org/gene/$1 + fairsharing: + abbreviation: EcoGene + description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. + id: '1869' + name: Escherichia coli strain K12 genome database + prefix: FAIRsharing.3q3kvn + subjects: [] + mappings: + biocontext: EcoGene + fairsharing: FAIRsharing.3q3kvn + miriam: ecogene + n2t: ecogene + ncbi: EcoGene + prefixcommons: ecogene + miriam: + deprecated: false + description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. + homepage: http://ecogene.org/ + id: '00000163' + name: EcoGene + namespaceEmbeddedInLui: false + pattern: ^EG\d+$ + prefix: ecogene + sampleId: EG10173 + uri_format: http://www.ecogene.org/gene/$1 + n2t: + description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. + example: EG10173 + homepage: http://ecogene.org/ + name: EcoGene at University of Miami + namespaceEmbeddedInLui: false + pattern: ^EG\d+$ + prefix: ecogene + uri_format: http://www.ecogene.org/gene/$1 + ncbi: + example: EG11277 + homepage: http://ecogene.org + name: Database of Escherichia coli Sequence and Function + prefix: EcoGene + prefixcommons: + description: The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. + example: EG10173 + homepage: http://ecogene.org/ + keywords: + - genome + - protein + name: Escherichia coli strain K12 genome database + pattern: ^EG\d+$ + prefix: ecogene + pubmed_ids: + - '10592181' + uri_format: http://ecogene.org/geneInfo.php?eg_id=$1 +ecolexicon: + comment: No resolution - everything is in a single page app + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology. + example: canal + homepage: http://ecolexicon.ugr.es/en/index.htm + name: EcoLexicon +ecoliwiki: + biocontext: + is_identifiers: true + is_obo: false + prefix: ECOLIWIKI + uri_format: http://identifiers.org/ecoliwiki/$1 + fairsharing: + abbreviation: EcoliWiki + description: EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. + id: '1576' + name: EcoliWiki + prefix: FAIRsharing.tx95wa + subjects: + - Genomics + - Bioinformatics + - Life Science + - Ontology and Terminology + go: + description: EcoliHub\'s subsystem for community annotation of E. coli K-12 + homepage: http://ecoliwiki.net/ + name: EcoliWiki from EcoliHub + prefix: EcoliWiki + mappings: + biocontext: ECOLIWIKI + fairsharing: FAIRsharing.tx95wa + go: EcoliWiki + miriam: ecoliwiki + n2t: ecoliwiki + miriam: + deprecated: false + description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. + homepage: http://ecoliwiki.net/colipedia/ + id: '00000442' + name: EcoliWiki + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+$ + prefix: ecoliwiki + sampleId: aaeA + uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene + n2t: + description: EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. + example: aaeA + homepage: http://ecoliwiki.net/colipedia/ + name: EcoliWiki at Texas Agrilife Research + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9-]+$ + prefix: ecoliwiki + uri_format: http://ecoliwiki.net/colipedia/index.php/$1:Gene +ecto: + biolink: + is_identifiers: false + is_obo: true + prefix: ECTO + uri_format: http://purl.obolibrary.org/obo/ECTO_$1 + bioportal: + name: Environmental conditions, treatments and exposures ontology + prefix: ECTO + example: '0000001' + mappings: + biolink: ECTO + bioportal: ECTO + obofoundry: ecto + ols: ecto + ontobee: ECTO + obofoundry: + contact: annethessen@gmail.com + contact.github: diatomsRcool + contact.label: Anne Thessen + contact.orcid: 0000-0002-2908-3327 + depends_on: + - chebi + - envo + - exo + - go + - iao + - maxo + - nbo + - ncbitaxon + - ncit + - pato + - ro + - uberon + - xco + deprecated: false + description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). + download.json: http://purl.obolibrary.org/obo/ecto.json + download.obo: http://purl.obolibrary.org/obo/ecto.obo + download.owl: http://purl.obolibrary.org/obo/ecto.owl + homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Environmental conditions, treatments and exposures ontology + preferredPrefix: ECTO + prefix: ecto + repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology + ols: + description: ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). + download: http://purl.obolibrary.org/obo/ecto.owl + homepage: https://github.com/EnvironmentOntology/environmental-exposure-ontology + name: Environment Exposure Ontology + prefix: ecto + version: 2021-08-25 + version.iri: http://purl.obolibrary.org/obo/ecto/releases/2021-08-25/ecto.owl + ontobee: + library: Library + name: Environmental conditions, treatments and exposures ontology + prefix: ECTO + pattern: ^\d{7}$ +ecyano.entity: + biocontext: + is_identifiers: true + is_obo: false + prefix: ECYANO.ENTITY + uri_format: http://identifiers.org/ecyano.entity/$1 + mappings: + biocontext: ECYANO.ENTITY + miriam: ecyano.entity + n2t: ecyano.entity + miriam: + deprecated: false + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. + homepage: http://www.e-cyanobacterium.org/bcs/entity/ + id: '00000585' + name: E-cyanobacterium entity + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.entity + sampleId: '23' + uri_format: http://e-cyanobacterium.org/bcs/entity/$1/ + n2t: + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. + example: '23' + homepage: http://www.e-cyanobacterium.org/bcs/entity/ + name: e-cyanobacterium entity at Masaryk University Brno + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.entity + uri_format: http://e-cyanobacterium.org/bcs/entity/$1/ + part_of: ecyano + uri_format: https://www.e-cyanobacterium.org/bcs/entity/$1 +ecyano.experiment: + mappings: + miriam: ecyano.experiment + miriam: + deprecated: false + description: E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments. + homepage: https://www.e-cyanobacterium.org/experiments-repository/ + id: '00000760' + name: E-cyanobacterium Experimental Data + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.experiment + sampleId: '18' + uri_format: https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1 + part_of: ecyano +ecyano.model: + biocontext: + is_identifiers: true + is_obo: false + prefix: ECYANO.MODEL + uri_format: http://identifiers.org/ecyano.model/$1 + mappings: + biocontext: ECYANO.MODEL + miriam: ecyano.model + n2t: ecyano.model + miriam: + deprecated: false + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. + homepage: http://e-cyanobacterium.org/models/ + id: '00000586' + name: E-cyanobacterium model + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.model + sampleId: '26' + uri_format: http://e-cyanobacterium.org/models/model/$1/ + n2t: + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. + example: '26' + homepage: http://e-cyanobacterium.org/models/ + name: e-cyanobacterium entity at Masaryk University Brno + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.model + uri_format: http://e-cyanobacterium.org/models/model/$1/ + uri_format: https://e-cyanobacterium.org/models/model/$1 +ecyano.rule: + biocontext: + is_identifiers: true + is_obo: false + prefix: ECYANO.RULE + uri_format: http://identifiers.org/ecyano.rule/$1 + mappings: + biocontext: ECYANO.RULE + miriam: ecyano.rule + n2t: ecyano.rule + miriam: + deprecated: false + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. + homepage: http://www.e-cyanobacterium.org/bcs/rule/ + id: '00000587' + name: E-cyanobacterium rule + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.rule + sampleId: '56' + uri_format: http://e-cyanobacterium.org/bcs/rule/$1/ + n2t: + description: E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. + example: '56' + homepage: http://www.e-cyanobacterium.org/bcs/rule/ + name: e-cyanobacterium entity at Masaryk University Brno + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ecyano.rule + uri_format: http://e-cyanobacterium.org/bcs/rule/$1/ + part_of: ecyano + uri_format: https://e-cyanobacterium.org/bcs/rule/$1 +edam: + biocontext: + is_identifiers: true + is_obo: false + prefix: EDAM + uri_format: http://identifiers.org/edam/$1 + bioportal: + name: EDAM - Bioscientific data analysis ontology + prefix: EDAM + fairsharing: + abbreviation: EDAM + description: EDAM (originally from “EMBRACE Data and Methods”) is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. + id: '1205' + name: EMBRACE Data and Methods Ontology + prefix: FAIRsharing.a6r7zs + subjects: + - Bioinformatics + - Life Science + mappings: + biocontext: EDAM + bioportal: EDAM + fairsharing: FAIRsharing.a6r7zs + miriam: edam + n2t: edam + ols: edam + ontobee: EDAM + prefixcommons: edam + miriam: + deprecated: false + description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' + homepage: http://bioportal.bioontology.org/ontologies/EDAM + id: '00000189' + name: EDAM Ontology + namespaceEmbeddedInLui: false + pattern: ^(data|topic|operation|format)\_\d{4}$ + prefix: edam + sampleId: data_1664 + uri_format: http://purl.bioontology.org/ontology/EDAM/$1 + n2t: + description: 'EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).' + example: data_1664 + homepage: http://bioportal.bioontology.org/ontologies/EDAM + name: EDAM through BioPortal + namespaceEmbeddedInLui: false + pattern: ^(data|topic|operation|format)\_\d{4}$ + prefix: edam + uri_format: http://purl.bioontology.org/ontology/EDAM/$1 + ols: + contact: edam@elixir-dk.org + description: EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use. + download: https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl + homepage: http://edamontology.org + name: Bioinformatics operations, data types, formats, identifiers and topics + prefix: edam + version: 2019-07-17 + ontobee: + library: Not Specified/No + name: EMBRACE Data and Methods + prefix: EDAM + prefixcommons: + bioportal: '1498' + description: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. + example: EDAM_data:1664 + homepage: https://sourceforge.net/projects/edamontology/ + keywords: + - obo + - ontology + name: Bioinformatics operations, types of data, data formats and topics + pattern: ^EDAM_(data|topic)\:\d{4}$ + prefix: edam + uri_format: http://www.ebi.ac.uk/ontology-lookup/?termId=$1 + uri_format: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1 +edda: + bioportal: + name: EDDA Study Designs Taxonomy + prefix: EDDA + description: Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries. + example: health_care_quality_assessment + fairsharing: + abbreviation: EDDA + description: 'Terminology of study designs and publication types (beta version). Developed by the Evidence in Documents, Discovery, and Analysis (EDDA) Group. Tanja Bekhuis (PI); Eugene Tseytlin (Systems Developer); Ashleigh Faith (Taxonomist). Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pennsylvania, US. This work was made possible, in part, by the US National Library of Medicine, National Institutes of Health, grant no. R00LM010943. Based on research described in Bekhuis T, Demner-Fushman D, Crowley RS. Comparative effectiveness research designs: an analysis of terms and coverage in Medical Subject Headings (MeSH) and Emtree. Journal of the Medical Library Association (JMLA). 2013 April;101(2):92-100. PMC3634392. The terminology appearing in JMLA has been enriched with terms from MeSH, NCI Thesaurus (NCIT), and Emtree, the controlled vocabularies for MEDLINE, the National Cancer Institute, and Embase, respectively, as well as from published research literature. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCIT, Emtree, and medical dictionaries. A class for Publication Type is included because investigators consider type and design when screening reports for inclusion in comparative effectiveness research. EDDA Study Designs and Publications by Tanja Bekhuis is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.' + id: '1289' + name: EDDA Study Designs Taxonomy + prefix: FAIRsharing.2ffmsb + subjects: [] + homepage: https://bioportal.bioontology.org/ontologies/EDDA + mappings: + bioportal: EDDA + fairsharing: FAIRsharing.2ffmsb +efo: + biocontext: + is_identifiers: false + is_obo: true + prefix: EFO + uri_format: http://purl.obolibrary.org/obo/EFO_$1 + biolink: + is_identifiers: false + is_obo: false + prefix: EFO + uri_format: http://www.ebi.ac.uk/efo/EFO_$1 + bioportal: + name: Experimental Factor Ontology + prefix: EFO + cellosaurus: + category: Experimental variables resources + homepage: https://www.ebi.ac.uk/efo/ + name: Experimental Factor Ontology + prefix: EFO + uri_format: https://www.ebi.ac.uk/efo/$1 + contact: + email: plwhetzel@gmail.com + github: twhetzel + name: Trish Whetzel + orcid: 0000-0002-3458-4839 + download_obo: http://www.ebi.ac.uk/efo/efo.obo + example: '0005147' + fairsharing: + abbreviation: EFO + description: The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and the Centre for Therapeutic Target Validation. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype. + id: '1498' + name: Experimental Factor Ontology + prefix: FAIRsharing.1gr4tz + subjects: + - Functional Genomics + mappings: + biocontext: EFO + biolink: EFO + bioportal: EFO + cellosaurus: EFO + fairsharing: FAIRsharing.1gr4tz + miriam: efo + n2t: efo + ols: efo + ontobee: EFO + miriam: + deprecated: false + description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. + homepage: https://www.ebi.ac.uk/ols/ontologies/efo + id: '00000391' + name: Experimental Factor Ontology + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: efo + providers: + - code: ebi + description: EFO through Functional Genomics Group (EBI) + homepage: https://www.ebi.ac.uk/efo/ + name: EFO through Functional Genomics Group (EBI) + uri_format: https://www.ebi.ac.uk/efo/EFO_$1 + sampleId: '0004859' + uri_format: https://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=EFO:$1 + n2t: + description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. + example: '0004859' + homepage: http://bioportal.bioontology.org/ontologies/EFO + name: EFO through BioPortal + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: efo + uri_format: http://purl.bioontology.org/ontology/EFO/efo:EFO_$1 + ols: + contact: efo-users@lists.sourceforge.net + description: The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org + download: http://www.ebi.ac.uk/efo/efo.owl + homepage: http://www.ebi.ac.uk/efo + name: Experimental Factor Ontology + prefix: efo + version: 3.42.0 + version.iri: http://www.ebi.ac.uk/efo/releases/v3.42.0/efo.owl + ontobee: + library: Not Specified/No + name: Experimental Factor Ontology + prefix: EFO + preferred_prefix: EFO + repository: https://github.com/EBISPOT/efo/ + uri_format: http://www.ebi.ac.uk/efo/EFO_$1 +ega.dataset: + biocontext: + is_identifiers: true + is_obo: false + prefix: EGA.DATASET + uri_format: http://identifiers.org/ega.dataset/$1 + fairsharing: + abbreviation: EGA + description: The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. Access to data must be approved by the specified Data Access Committee (DAC). + id: '1865' + name: The European Genome-phenome Archive + prefix: FAIRsharing.mya1ff + subjects: + - Genomics + - Phenomics + - Biomedical Science + - Biology + homepage: https://ega-archive.org/ + mappings: + biocontext: EGA.DATASET + fairsharing: FAIRsharing.mya1ff + miriam: ega.dataset + n2t: ega.dataset + miriam: + deprecated: false + description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. + homepage: https://www.ebi.ac.uk/ega/dataset + id: '00000512' + name: European Genome-phenome Archive Dataset + namespaceEmbeddedInLui: false + pattern: ^EGAD\d{11}$ + prefix: ega.dataset + providers: + - code: omicsdi + description: EGA Dataset through OmicsDI + homepage: https://www.omicsdi.org/ + name: EGA Dataset through OmicsDI + uri_format: https://www.omicsdi.org/dataset/ega/$1 + sampleId: EGAD00000000001 + uri_format: https://www.ebi.ac.uk/ega/datasets/$1 + n2t: + description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. + example: EGAD00000000001 + homepage: https://www.ebi.ac.uk/ega/dataset + name: EGA Dataset at European Bioinformatics Institute + namespaceEmbeddedInLui: false + pattern: ^EGAD\d{11}$ + prefix: ega.dataset + uri_format: https://www.ebi.ac.uk/ega/datasets/$1 +ega.study: + biocontext: + is_identifiers: true + is_obo: false + prefix: EGA.STUDY + uri_format: http://identifiers.org/ega.study/$1 + mappings: + biocontext: EGA.STUDY + miriam: ega.study + n2t: ega.study + miriam: + deprecated: false + description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. + homepage: https://www.ebi.ac.uk/ega/studies + id: '00000511' + name: European Genome-phenome Archive Study + namespaceEmbeddedInLui: false + pattern: ^EGAS\d{11}$ + prefix: ega.study + providers: + - code: omicsdi + description: EGA Study through OmicsDI + homepage: https://www.omicsdi.org/ + name: EGA Study through OmicsDI + uri_format: https://www.omicsdi.org/dataset/ega/$1 + sampleId: EGAS00000000001 + uri_format: https://www.ebi.ac.uk/ega/studies/$1 + n2t: + description: The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. + example: EGAS00000000001 + homepage: https://www.ebi.ac.uk/ega/studies + name: EGA Study at European Bioinformatics Institute + namespaceEmbeddedInLui: false + pattern: ^EGAS\d{11}$ + prefix: ega.study + uri_format: https://www.ebi.ac.uk/ega/studies/$1 +eggnog: + biocontext: + is_identifiers: true + is_obo: false + prefix: EGGNOG + uri_format: http://identifiers.org/eggnog/$1 + fairsharing: + abbreviation: eggNOG + description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' + id: '1577' + name: 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups' + prefix: FAIRsharing.j1wj7d + subjects: + - Life Science + mappings: + biocontext: EGGNOG + fairsharing: FAIRsharing.j1wj7d + miriam: eggnog + n2t: eggnog + prefixcommons: eggnog + uniprot: eggNOG + miriam: + deprecated: false + description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' + homepage: http://eggnog.embl.de/version_3.0/ + id: '00000201' + name: eggNOG + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: eggnog + sampleId: veNOG12876 + uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 + n2t: + description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' + example: veNOG12876 + homepage: http://eggnog.embl.de/version_3.0/ + name: eggNOG Version 3 at European Molecular Biology Laboratory + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: eggnog + uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 + prefixcommons: + description: 'eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).' + example: NOG80852 + homepage: http://eggnog.embl.de + keywords: + - gene + name: 'Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups' + pattern: ^\w+$ + prefix: eggnog + pubmed_ids: + - '19900971' + uri_format: http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 + uniprot: + category: Phylogenomic databases + identifier: '152' + link_is_explicit: 'true' + name: 'evolutionary genealogy of genes: Non-supervised Orthologous Groups' + prefix: eggNOG + uri_format: http://eggnogdb.embl.de/#/app/results?seqid=%u&target_nogs=%s +ehda: + biocontext: + is_identifiers: false + is_obo: true + prefix: EHDA + uri_format: http://purl.obolibrary.org/obo/EHDA_$1 + bioportal: + name: Human Developmental Anatomy Ontology, timed version + prefix: EHDA + example: '1' + mappings: + biocontext: EHDA + bioportal: EHDA + obofoundry: ehda + prefixcommons: ehda + obofoundry: + contact: J.Bard@ed.ac.uk + contact.label: Jonathan Bard + deprecated: true + homepage: http://genex.hgu.mrc.ac.uk/ + name: Human developmental anatomy, timed version + prefix: ehda + pattern: ^\d+$ + prefixcommons: + bioportal: '1022' + description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). + example: EHDAA_1 + homepage: http://genex.hgu.mrc.ac.uk/ + keywords: + - obo + - anatomy + - development + - human + name: Human developmental anatomy, timed version + pattern: ^EHDA_\d+$ + prefix: ehda +ehdaa: + biocontext: + is_identifiers: false + is_obo: true + prefix: EHDAA + uri_format: http://purl.obolibrary.org/obo/EHDAA_$1 + bioportal: + name: Human Developmental Anatomy Ontology, abstract version 1 + prefix: EHDAA + example: '1' + mappings: + biocontext: EHDAA + bioportal: EHDAA + obofoundry: ehdaa + prefixcommons: ehdaa + obofoundry: + contact: J.Bard@ed.ac.uk + contact.label: Jonathan Bard + deprecated: true + name: Human developmental anatomy, abstract version + prefix: ehdaa + pattern: ^\d+$ + prefixcommons: + bioportal: '1021' + description: A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). + example: EHDAA_573 + homepage: http://genex.hgu.mrc.ac.uk/ + keywords: + - obo + - anatomy + - development + - human + name: Human developmental anatomy, abstract version + pattern: ^EHDAA_\d+$ + prefix: ehdaa +ehdaa2: + biocontext: + is_identifiers: false + is_obo: true + prefix: EHDAA2 + uri_format: http://purl.obolibrary.org/obo/EHDAA2_$1 + bioportal: + name: Human Developmental Anatomy Ontology, abstract version 2 + prefix: EHDAA2 + example: '0000000' + fairsharing: + abbreviation: EHDAA2 + description: The EHDAA2 ontology is a human developmental anatomy covering the first 49 days [Carnegie stages (CS)1–20], primarily structured around the parts of organ systems and their development. The ontology includes more than 2000 anatomical entities (AEs) that range from the whole embryo, through organ systems and organ parts down to simple or leaf tissues (groups of cells with the same morphological phenotype), as well as features such as cavities. It represents a complete rebuilding of the EHDA intended to meet current standards. The intention has been to include as much information about human developmental anatomy as is practical and as is available in the literature. + id: '199' + name: Edinburgh human developmental anatomy abstract version 2 + prefix: FAIRsharing.7zxrs6 + subjects: + - Anatomy + - Life Science + - Biomedical Science + mappings: + biocontext: EHDAA2 + bioportal: EHDAA2 + fairsharing: FAIRsharing.7zxrs6 + obofoundry: ehdaa2 + ols: ehdaa2 + ontobee: EHDAA2 + obofoundry: + contact: J.Bard@ed.ac.uk + contact.label: Jonathan Bard + depends_on: + - aeo + - caro + - cl + deprecated: true + description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. + download.obo: http://purl.obolibrary.org/obo/ehdaa2.obo + download.owl: http://purl.obolibrary.org/obo/ehdaa2.owl + homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Human developmental anatomy, abstract + prefix: ehdaa2 + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22973865 + title: A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20). + repository: https://github.com/obophenotype/human-developmental-anatomy-ontology + ols: + description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human. + download: http://purl.obolibrary.org/obo/ehdaa2.owl + homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology + name: Human developmental anatomy, abstract + prefix: ehdaa2 + version: 2013-07-04 + version.iri: http://purl.obolibrary.org/obo/ehdaa2/releases/2013-07-04/ehdaa2.owl + ontobee: + library: Library + name: Human developmental anatomy, abstract + prefix: EHDAA2 + pattern: ^\d{7}$ + synonyms: + - EHDAA2_RETIRED + - HDAA2 + - RETIRED_EHDAA2 +elm: + biocontext: + is_identifiers: true + is_obo: false + prefix: ELM + uri_format: http://identifiers.org/elm/$1 + fairsharing: + abbreviation: ELM + description: This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs), are compact protein interaction sites composed of short stretches of adjacent amino acids. + id: '1578' + name: Eukaryotic Linear Motifs + prefix: FAIRsharing.rj3kj5 + subjects: + - Life Science + mappings: + biocontext: ELM + fairsharing: FAIRsharing.rj3kj5 + miriam: elm + n2t: elm + uniprot: ELM + miriam: + deprecated: false + description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. + homepage: http://elm.eu.org/ + id: '00000250' + name: ELM + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: elm + sampleId: CLV_MEL_PAP_1 + uri_format: http://elm.eu.org/elms/elmPages/$1.html + n2t: + description: Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. + example: CLV_MEL_PAP_1 + homepage: http://elm.eu.org/ + name: ELM at EMBL (Germany) + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: elm + uri_format: http://elm.eu.org/elms/elmPages/$1.html + name: Eukaryotic Linear Motif Resource + uniprot: + category: Protein-protein interaction databases + identifier: '223' + link_is_explicit: 'true' + name: The Eukaryotic Linear Motif resource for Functional Sites in Proteins + prefix: ELM + uri_format: http://elm.eu.org/instances.html?q=$1 +emap: + biocontext: + is_identifiers: false + is_obo: true + prefix: EMAP + uri_format: http://purl.obolibrary.org/obo/EMAP_$1 + bioportal: + name: Mouse Gross Anatomy and Development Ontology + prefix: EMAP + example: '1' + mappings: + biocontext: EMAP + bioportal: EMAP + obofoundry: emap + obofoundry: + contact: Terry.Hayamizu@jax.org + contact.github: tfhayamizu + contact.label: Terry Hayamizu + contact.orcid: 0000-0002-0956-8634 + deprecated: true + description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). + download.owl: http://purl.obolibrary.org/obo/emap.owl + homepage: http://emouseatlas.org + name: Mouse gross anatomy and development, timed + prefix: emap + pattern: ^\d+$ +emapa: + biocontext: + is_identifiers: false + is_obo: true + prefix: EMAPA + uri_format: http://purl.obolibrary.org/obo/EMAPA_$1 + bioportal: + name: Mouse gross anatomy and development, timed + prefix: EMAPA + example: '26753' + fairsharing: + abbreviation: EMAPA + description: Abstract (i.e. non-stage specific) stage-specific anatomical structures of the mouse. + id: '513' + name: Mouse gross anatomy and development, timed + prefix: FAIRsharing.j0fa1d + subjects: [] + go: + description: A time-independent Mouse Anatomical Dictionary; part of Gene Expression Database + homepage: http://emouseatlas.org/ + name: Mouse gross anatomy and development, abstract + prefix: EMAPA + uri_format: http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1 + mappings: + biocontext: EMAPA + bioportal: EMAPA + fairsharing: FAIRsharing.j0fa1d + go: EMAPA + obofoundry: emapa + ols: emapa + ontobee: EMAPA + obofoundry: + contact: Terry.Hayamizu@jax.org + contact.github: tfhayamizu + contact.label: Terry Hayamizu + contact.orcid: 0000-0002-0956-8634 + deprecated: false + description: An ontology for mouse anatomy covering embryonic development and postnatal stages. + download.obo: http://purl.obolibrary.org/obo/emapa.obo + download.owl: http://purl.obolibrary.org/obo/emapa.owl + homepage: http://www.informatics.jax.org/expression.shtml + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Mouse Developmental Anatomy Ontology + preferredPrefix: EMAPA + prefix: emapa + repository: https://github.com/obophenotype/mouse-anatomy-ontology + ols: + description: An ontology for mouse anatomy covering embryonic development and postnatal stages. + download: http://purl.obolibrary.org/obo/emapa.owl + homepage: http://www.informatics.jax.org/expression.shtml + name: Mouse Developmental Anatomy Ontology + prefix: emapa + version: 2021-09-01 + version.iri: http://purl.obolibrary.org/obo/emapa/releases/2021-09-01/emapa.owl + ontobee: + library: Library + name: Mouse Developmental Anatomy Ontology + prefix: EMAPA + pattern: ^\d+$ + synonyms: + - EMAPA_RETIRED +emdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: EMDB + uri_format: http://identifiers.org/emdb/$1 + fairsharing: + abbreviation: EMDB + description: Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB was founded at EBI in 2002, under the leadership of Kim Henrick. Since 2007 it has been operated jointly by the PDBe, and the Research Collaboratory for Structural Bioinformatics (RCSB PDB) as a part of EMDataBank which is funded by a joint NIH grant to PDBe, the RCSB and the National Center for Macromolecular Imaging (NCMI). + id: '2126' + name: Electron Microscopy Data Bank + prefix: FAIRsharing.651n9j + subjects: + - Virology + - Biology + - Epidemiology + mappings: + biocontext: EMDB + fairsharing: FAIRsharing.651n9j + miriam: emdb + n2t: emdb + miriam: + deprecated: false + description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. + homepage: https://www.ebi.ac.uk/pdbe/emdb/ + id: '00000561' + name: Electron Microscopy Data Bank + namespaceEmbeddedInLui: false + pattern: ^EMD-\d{4}$ + prefix: emdb + sampleId: EMD-1001 + uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1 + n2t: + description: The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. + example: EMD-1001 + homepage: https://www.ebi.ac.uk/pdbe/emdb/ + name: EMDB at Protein Data Bank in Europe + namespaceEmbeddedInLui: false + pattern: ^EMD-\d{4}$ + prefix: emdb + uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1 +emolecules: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Catalog of purchasable reagents and building blocks + example: '491187' + homepage: https://reaxys.emolecules.com + name: Reaxys eMolecules + pattern: ^\d+$ + uri_format: https://reaxys.emolecules.com/cgi-bin/more?vid=$1 +empiar: + description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure + example: '10595' + fairsharing: + abbreviation: EMPIAR + description: EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored. + id: '2649' + name: Electron Microscopy Public Image Archive + prefix: FAIRsharing.dff3ef + subjects: + - Bioinformatics + - Biology + homepage: https://www.ebi.ac.uk/pdbe/emdb + mappings: + fairsharing: FAIRsharing.dff3ef + name: Electron Microscopy Public Image Archive + pattern: ^\d+$ + uri_format: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1 +ena.embl: + biocontext: + is_identifiers: true + is_obo: false + prefix: ENA.EMBL + uri_format: http://identifiers.org/ena.embl/$1 + fairsharing: + abbreviation: ENA + description: The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data, the ENA provides a portfolio of services for submission, data management, search and retrieval across web and programmatic interfaces. The ENA is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis. + id: '1850' + name: European Nucleotide Archive + prefix: FAIRsharing.dj8nt8 + subjects: + - Functional Genomics + - Metagenomics + - Genomics + - Bioinformatics + - Data Management + - Biodiversity + - Transcriptomics + go: + description: ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive. International nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank + homepage: http://www.ebi.ac.uk/ena/ + name: European Nucleotide Archive + prefix: ENA + uri_format: http://www.ebi.ac.uk/ena/data/view/$1 + mappings: + biocontext: ENA.EMBL + fairsharing: FAIRsharing.dj8nt8 + go: ENA + miriam: ena.embl + n2t: ena.embl + prefixcommons: ena + miriam: + deprecated: false + description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. + homepage: https://www.ebi.ac.uk/ena/ + id: '00000372' + name: ENA + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+(\.\d+)?$ + prefix: ena.embl + providers: + - code: CURATOR_REVIEW + description: ENA through GenBank + homepage: https://www.ncbi.nlm.nih.gov/Genbank/ + name: ENA through GenBank + uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 + sampleId: BN000065 + uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 + n2t: + description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. + example: BN000065 + homepage: https://www.ncbi.nlm.nih.gov/Genbank/ + name: ENA through GenBank + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+(\.\d+)?$ + prefix: ena.embl + uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 + prefixcommons: + description: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. + example: BN000065 + homepage: http://www.ebi.ac.uk/ena/ + keywords: + - DNA + name: European Nucleotide Archive + pattern: ^[A-Z]+[0-9]+$ + prefix: ena + uri_format: http://www.ebi.ac.uk/ena/data/view/$1 + synonyms: + - ena + uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 +encode: + biocontext: + is_identifiers: true + is_obo: false + prefix: ENCODE + uri_format: http://identifiers.org/encode/$1 + cellosaurus: + category: Biological sample resources + homepage: https://www.encodeproject.org + name: Encyclopedia of DNA Elements + prefix: ENCODE + uri_format: https://www.encodeproject.org/biosamples/$1 + fairsharing: + abbreviation: ENCODE + description: Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database. + id: '1579' + name: Encyclopedia of DNA Elements at UCSC + prefix: FAIRsharing.v0hbjs + subjects: + - Life Science + homepage: https://www.encodeproject.org + mappings: + biocontext: ENCODE + cellosaurus: ENCODE + fairsharing: FAIRsharing.v0hbjs + miriam: encode + n2t: encode + miriam: + deprecated: false + description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. + homepage: www.encodeproject.org + id: '00000662' + name: 'ENCODE: Encyclopedia of DNA Elements' + namespaceEmbeddedInLui: false + pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ + prefix: encode + sampleId: ENCSR163RYW + uri_format: https://www.encodeproject.org/$1 + n2t: + description: The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. + example: ENCSR163RYW + homepage: www.encodeproject.org + name: 'ENCODE: Encyclopedia of DNA Elements' + namespaceEmbeddedInLui: false + pattern: ^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$ + prefix: encode + uri_format: https://www.encodeproject.org/$1 + name: Encyclopedia of DNA Elements +enm: + bioportal: + name: eNanoMapper + prefix: ENM + example: '8000221' + fairsharing: + abbreviation: ENM + description: The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology. + id: '493' + name: eNanoMapper Ontology + prefix: FAIRsharing.2gpf81 + subjects: + - Health Science + mappings: + bioportal: ENM + fairsharing: FAIRsharing.2gpf81 + ols: enm + ols: + description: 'The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ' + download: http://enanomapper.github.io/ontologies/enanomapper.owl + homepage: http://www.enanomapper.net/ + name: eNanoMapper Ontology + prefix: enm + version: '7.3' + pattern: ^\d+$ +ensembl: + biocontext: + is_identifiers: false + is_obo: false + prefix: ENSEMBL + uri_format: http://ensembl.org/id/$1 + example_extras: + - ENSG00000049246.14 + - ENSG00000109819.9 + - ENSG00000132326.12 + - ENSG00000179094.16 + - ENST00000264867.7 + fairsharing: + abbreviation: Ensembl + description: Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. + id: '1867' + name: Ensembl + prefix: FAIRsharing.fx0mw7 + subjects: + - Genomics + - Biomedical Science + - Comparative Genomics + go: + homepage: http://www.ensembl.org/ + name: Ensembl database of automatically annotated genomic data + prefix: ENSEMBL + synonyms: + - Ensembl + - ensembl + mappings: + biocontext: ENSEMBL + fairsharing: FAIRsharing.fx0mw7 + go: ENSEMBL + miriam: ensembl + n2t: ensembl + ncbi: ENSEMBL + prefixcommons: ensembl + uniprot: Ensembl + wikidata: P594 + miriam: + deprecated: false + description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. + homepage: https://www.ensembl.org/ + id: '00000003' + name: Ensembl + namespaceEmbeddedInLui: false + pattern: ^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$ + prefix: ensembl + providers: + - code: CURATOR_REVIEW + description: Ensembl US West mirror + homepage: http://uswest.ensembl.org/ + name: Ensembl US West mirror + uri_format: http://uswest.ensembl.org/id/$1 + - code: CURATOR_REVIEW + description: Ensembl US East mirror + homepage: http://useast.ensembl.org/ + name: Ensembl US East mirror + uri_format: http://useast.ensembl.org/id/$1 + - code: CURATOR_REVIEW + description: Ensembl Asia mirror + homepage: http://asia.ensembl.org/ + name: Ensembl Asia mirror + uri_format: http://asia.ensembl.org/id/$1 + sampleId: ENSG00000139618 + uri_format: https://www.ensembl.org/id/$1 + n2t: + description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. + example: ENSG00000139618 + homepage: https://www.ensembl.org/ + name: Ensembl at Sanger/EMBL-EBI + namespaceEmbeddedInLui: false + pattern: ^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$ + prefix: ensembl + uri_format: https://www.ensembl.org/id/$1 + name: Ensembl Gene + ncbi: + example: HUMAN-Clone-AC005612 + homepage: http://useast.ensembl.org/index.html + name: Database of automatically annotated genomic data + prefix: ENSEMBL + pattern: ^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$ + prefixcommons: + description: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. + example: ENSG00000139618 + homepage: http://www.ensembl.org/ + keywords: + - genome + name: Ensembl + pattern: ^ENS[A-Z]*[FPTG]\d{11}(\.\d+)?$ + prefix: ensembl + pubmed_ids: + - '16381931' + uri_format: http://www.ensembl.org/id/$1 + providers: + - code: bgee + description: Gene expression in various tissues + homepage: https://bgee.org + name: Bgee + uri_format: https://bgee.org/?page=gene&gene_id=$1 + - code: gnomad + description: The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community. + homepage: https://gnomad.broadinstitute.org + name: Genome Aggregation database + uri_format: https://gnomad.broadinstitute.org/gene/$1 + - code: opentargets.genetics + description: Open Targets Genetics is a comprehensive tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets. + homepage: https://genetics.opentargets.org + name: OpenTargets Genetics + uri_format: https://genetics.opentargets.org/gene/$1 + synonyms: + - Ensembl + uniprot: + category: Genome annotation databases + identifier: '23' + link_is_explicit: 'true' + name: Ensembl eukaryotic genome annotation project + prefix: Ensembl + uri_format: https://www.ensembl.org/id/$1 + wikidata: + database: Q1344256 + database.homepage: http://www.ensembl.org/ + database.label: Ensembl genome database project + format.rdf: http://rdf.ebi.ac.uk/resource/ensembl/$1 + homepage: https://www.ensembl.org + name: Ensembl gene ID + pattern: (ENS(|MUS|RNO)G\d{11})|(Y[A-P][LR]\d{3}[CW](-[A-G])?) + prefix: P594 + uri_format: https://identifiers.org/ensembl/$1 +ensembl.bacteria: + biocontext: + is_identifiers: true + is_obo: false + prefix: ENSEMBL.BACTERIA + uri_format: http://identifiers.org/ensembl.bacteria/$1 + fairsharing: + abbreviation: Ensembl Bacteria + description: Ensembl Bacteria is a browser for bacterial and archaeal genomes. These are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan). + id: '2402' + name: Ensembl Bacteria + prefix: FAIRsharing.zsgmvd + subjects: + - Genomics + - Comparative Genomics + mappings: + biocontext: ENSEMBL.BACTERIA + fairsharing: FAIRsharing.zsgmvd + miriam: ensembl.bacteria + n2t: ensembl.bacteria + prefixcommons: ensembl.bacteria + uniprot: EnsemblBacteria + miriam: + deprecated: false + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + homepage: https://bacteria.ensembl.org/ + id: '00000202' + name: Ensembl Bacteria + namespaceEmbeddedInLui: false + pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ + prefix: ensembl.bacteria + sampleId: MU9_3181 + uri_format: https://bacteria.ensembl.org/id/$1 + n2t: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + example: MU9_3181 + homepage: https://bacteria.ensembl.org/ + name: Ensembl Bacteria at EBI + namespaceEmbeddedInLui: false + pattern: ^((EB\w+)|([A-Z0-9]+\_[A-Z0-9]+))$ + prefix: ensembl.bacteria + uri_format: https://bacteria.ensembl.org/id/$1 + prefixcommons: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + example: EBESCT00000015660 + homepage: http://bacteria.ensembl.org/ + keywords: + - genome + name: Ensembl Bacteria + pattern: ^EB\w+$ + prefix: ensembl.bacteria + pubmed_ids: + - '19884133' + uri_format: http://bacteria.ensembl.org/[?species_name]/Gene/Summary?g=$1 + uniprot: + category: Genome annotation databases + identifier: '147' + link_is_explicit: 'true' + name: Ensembl bacterial and archaeal genome annotation project + prefix: EnsemblBacteria + uri_format: http://www.ensemblgenomes.org/id/$1 +ensembl.fungi: + biocontext: + is_identifiers: true + is_obo: false + prefix: ENSEMBL.FUNGI + uri_format: http://identifiers.org/ensembl.fungi/$1 + fairsharing: + abbreviation: Ensembl Fungi + description: Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators. + id: '2405' + name: Ensembl Fungi + prefix: FAIRsharing.bg5xqs + subjects: + - Genomics + - Comparative Genomics + go: + homepage: http://fungi.ensembl.org/ + name: Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi. + prefix: EnsemblFungi + uri_format: http://www.ensemblgenomes.org/id/$1 + mappings: + biocontext: ENSEMBL.FUNGI + fairsharing: FAIRsharing.bg5xqs + go: EnsemblFungi + miriam: ensembl.fungi + n2t: ensembl.fungi + prefixcommons: ensembl.fungi + uniprot: EnsemblFungi + miriam: + deprecated: false + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. + homepage: https://fungi.ensembl.org/ + id: '00000206' + name: Ensembl Fungi + namespaceEmbeddedInLui: false + pattern: ^[A-Z-a-z0-9]+$ + prefix: ensembl.fungi + sampleId: CADAFLAT00006211 + uri_format: https://fungi.ensembl.org/id/$1 + n2t: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. + example: CADAFLAT00006211 + homepage: https://fungi.ensembl.org/ + name: Enzembl Fungi at EBI + namespaceEmbeddedInLui: false + pattern: ^[A-Z-a-z0-9]+$ + prefix: ensembl.fungi + uri_format: https://fungi.ensembl.org/id/$1 + prefixcommons: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + example: CADAFLAT00006211 + homepage: http://fungi.ensembl.org/ + keywords: + - genome + name: Ensembl Fungi + pattern: ^\w+$ + prefix: ensembl.fungi + uri_format: http://fungi.ensembl.org/[?species_name]/Gene/Summary?g=$1 + uniprot: + category: Genome annotation databases + identifier: '148' + link_is_explicit: 'true' + name: Ensembl fungal genome annotation project + prefix: EnsemblFungi + uri_format: http://www.ensemblgenomes.org/id/$1 +ensembl.metazoa: + biocontext: + is_identifiers: true + is_obo: false + prefix: ENSEMBL.METAZOA + uri_format: http://identifiers.org/ensembl.metazoa/$1 + fairsharing: + abbreviation: Ensembl Metazoa + description: Ensembl Metazoa provides access to genomes of metazoans of interest in disease, environmental sciences, agriculture and economic concern. Extensive coverage exists of diptera, nematodes, lepidoptera and hymenoptera. + id: '2406' + name: Ensembl Metazoa + prefix: FAIRsharing.c23cqq + subjects: + - Genomics + - Comparative Genomics + go: + homepage: http://metazoa.ensembl.org/ + name: Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa. + prefix: EnsemblMetazoa + uri_format: http://www.ensemblgenomes.org/id/$1 + mappings: + biocontext: ENSEMBL.METAZOA + fairsharing: FAIRsharing.c23cqq + go: EnsemblMetazoa + miriam: ensembl.metazoa + n2t: ensembl.metazoa + prefixcommons: ensembl.metazoa + uniprot: EnsemblMetazoa + miriam: + deprecated: false + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. + homepage: https://metazoa.ensembl.org/ + id: '00000204' + name: Ensembl Metazoa + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?\d+$ + prefix: ensembl.metazoa + sampleId: FBtr0084214 + uri_format: https://metazoa.ensembl.org/id/$1 + n2t: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. + example: FBtr0084214 + homepage: https://metazoa.ensembl.org/ + name: Enzembl Metazoa at EBI + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?\d+$ + prefix: ensembl.metazoa + uri_format: https://metazoa.ensembl.org/id/$1 + prefixcommons: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + example: AGAP006864 + homepage: http://metazoa.ensembl.org/ + keywords: + - genome + name: Ensembl Metazoa + pattern: ^\w+(\.)?\d+$ + prefix: ensembl.metazoa + uri_format: http://metazoa.ensembl.org/[?species_name]/Gene/Summary?g=$1 + uniprot: + category: Genome annotation databases + identifier: '149' + link_is_explicit: 'true' + name: Ensembl metazoan genome annotation project + prefix: EnsemblMetazoa + uri_format: http://www.ensemblgenomes.org/id/$1 +ensembl.plant: + biocontext: + is_identifiers: true + is_obo: false + prefix: ENSEMBL.PLANT + uri_format: http://identifiers.org/ensembl.plant/$1 + mappings: + biocontext: ENSEMBL.PLANT + miriam: ensembl.plant + n2t: ensembl.plant + prefixcommons: ensembl.plant + miriam: + deprecated: false + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. + homepage: https://plants.ensembl.org/ + id: '00000205' + name: Ensembl Plants + namespaceEmbeddedInLui: false + pattern: ^\w+(\.\d+)?(\.\d+)?$ + prefix: ensembl.plant + sampleId: AT1G73965 + uri_format: https://plants.ensembl.org/id/$1 + n2t: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. + example: AT1G73965 + homepage: https://plants.ensembl.org/ + name: Enzembl Plants at EBI + namespaceEmbeddedInLui: false + pattern: ^\w+(\.\d+)?(\.\d+)?$ + prefix: ensembl.plant + uri_format: https://plants.ensembl.org/id/$1 + prefixcommons: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + example: LOC_Os12g44300 + homepage: http://plants.ensembl.org/ + keywords: + - genome + name: Ensembl Plants + pattern: ^\w+$ + prefix: ensembl.plant + uri_format: http://plants.ensembl.org/[?species_name]/Gene/Summary?g=$1 +ensembl.protist: + biocontext: + is_identifiers: true + is_obo: false + prefix: ENSEMBL.PROTIST + uri_format: http://identifiers.org/ensembl.protist/$1 + mappings: + biocontext: ENSEMBL.PROTIST + miriam: ensembl.protist + n2t: ensembl.protist + prefixcommons: ensembl.protist + miriam: + deprecated: false + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. + homepage: https://protists.ensembl.org + id: '00000203' + name: Ensembl Protists + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: ensembl.protist + sampleId: PF3D7_1328700 + uri_format: https://protists.ensembl.org/id/$1 + n2t: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. + example: PF3D7_1328700 + homepage: https://protists.ensembl.org + name: Ensembl Protists at EBI + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: ensembl.protist + uri_format: https://protists.ensembl.org/id/$1 + prefixcommons: + description: Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. + example: PFC0120w + homepage: http://protists.ensembl.org/ + keywords: + - genome + name: Ensembl Protists + pattern: ^\w+$ + prefix: ensembl.protist + uri_format: http://protists.ensembl.org/[?species_name]/Gene/Summary?g=$1 +ensemblglossary: + example: '0000198' + mappings: + ols: ensemblglossary + ols: + description: The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. + download: https://raw.githubusercontent.com/Ensembl/ensembl-glossary/master/ensembl-glossary.owl + homepage: http://ensembl.org/glossary + name: Ensembl Glossary + prefix: ensemblglossary + version: 2021-07-14 + version.iri: http://ensembl.org/glossary/ensembl-glossary/releases/2021-07-14/ensembl-glossary.owl + pattern: ^\d{7}$ +envipath: + fairsharing: + abbreviation: enviPath + description: enviPath is both a database and a prediction system, for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways, and supports the annotation of pathways with experimental and environmental conditions. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. + id: '2242' + name: enviPath + prefix: FAIRsharing.g0c5qn + subjects: + - Environmental Science + mappings: + fairsharing: FAIRsharing.g0c5qn + miriam: envipath + miriam: + deprecated: false + description: enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. + homepage: https://envipath.org/ + id: '00000727' + name: enviPath + namespaceEmbeddedInLui: false + pattern: ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ + prefix: envipath + sampleId: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea + uri_format: https://envipath.org/package/$1 +envo: + biocontext: + is_identifiers: false + is_obo: true + prefix: ENVO + uri_format: http://purl.obolibrary.org/obo/ENVO_$1 + bioportal: + name: Environment Ontology + prefix: ENVO + fairsharing: + abbreviation: ENVO + description: The Environment Ontology (EnvO) provides a controlled, structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms ranging from astronomical objects, through planetary scale biomes, to nanomaterials. Further, these terms are interlinked with logical axioms describing their composition, colocalisation, and relationships to environmental and biological processes. Using ENVO terms for an environmental description allows a comprehensive description of environment that is key to machine-assisted integration, archiving and federated searching of environmental data. + id: '919' + name: Environment Ontology + prefix: FAIRsharing.azqskx + subjects: + - Environmental Science + - Ecology + - Life Science + - Nutritional Science + - Epidemiology + mappings: + biocontext: ENVO + bioportal: ENVO + fairsharing: FAIRsharing.azqskx + miriam: envo + n2t: envo + obofoundry: envo + ols: envo + ontobee: ENVO + miriam: + deprecated: false + description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. + homepage: https://www.ebi.ac.uk/ols/ontologies/envo + id: '00000591' + name: Environment Ontology + namespaceEmbeddedInLui: true + pattern: ^ENVO:\d{7,8}$ + prefix: envo + sampleId: '09200010' + uri_format: https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1 + n2t: + description: The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. + example: '09200010' + homepage: http://purl.bioontology.org/ontology/ENVO/ + name: The Environment Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^ENVO:\d{8}$ + prefix: envo + uri_format: http://purl.bioontology.org/ontology/ENVO/ENVO:$1 + obofoundry: + appears_in: + - agro + - cdno + - ecocore + - ecto + - foodon + - ons + - pco + - rbo + - scdo + contact: p.buttigieg@gmail.com + contact.github: pbuttigieg + contact.label: Pier Luigi Buttigieg + contact.orcid: 0000-0002-4366-3088 + depends_on: + - chebi + - foodon + - go + - ncbitaxon + - pco + - po + - ro + - uberon + deprecated: false + description: Ontology of environmental features and habitats + download.json: http://purl.obolibrary.org/obo/envo.json + download.obo: http://purl.obolibrary.org/obo/envo.obo + download.owl: http://purl.obolibrary.org/obo/envo.owl + homepage: http://environmentontology.org/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Environment Ontology + preferredPrefix: ENVO + prefix: envo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/24330602 + title: 'The environment ontology: contextualising biological and biomedical entities' + - id: https://www.ncbi.nlm.nih.gov/pubmed/27664130 + title: 'The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation' + repository: https://github.com/EnvironmentOntology/envo + ols: + description: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities + download: http://purl.obolibrary.org/obo/envo.owl + homepage: http://environmentontology.org/ + name: The Environment Ontology + prefix: envo + version: 2021-05-14 + version.iri: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl + ontobee: + library: Library + name: Environment Ontology + prefix: ENVO + pattern: ^\d{7,8}$ +enzo: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Enzo Life Sciences is an antibody vendor. + example: ALX-210-175 + homepage: https://www.enzolifesciences.com + name: Enzo Life Sciences + synonyms: + - Enzo Life Sciences + uri_format: https://www.enzolifesciences.com/$1 +eo: + banana: EO + biocontext: + is_identifiers: false + is_obo: true + prefix: EO + uri_format: http://purl.obolibrary.org/obo/EO_$1 + mappings: + biocontext: EO + miriam: eo + n2t: eo + obofoundry: eo + prefixcommons: eo + miriam: + deprecated: false + description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. + homepage: http://archive.gramene.org/db/ontology/search_term?id=EO:0007359 + id: '00000518' + name: Plant Environment Ontology + namespaceEmbeddedInLui: true + pattern: ^(P)?EO\:\d{7}$ + prefix: eo + sampleId: '0007404' + uri_format: http://archive.gramene.org/db/ontology/search?query=EO:$1 + n2t: + description: The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. + example: '0007404' + homepage: http://bioportal.bioontology.org/ontologies/PECO + name: Plant Environment Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^(P)?EO\:\d{7}$ + prefix: eo + uri_format: http://purl.bioontology.org/ontology/PECO/EO:$1 + obofoundry: + appears_in: + - foodon + contact: jaiswalp@science.oregonstate.edu + contact.github: jaiswalp + contact.label: Pankaj Jaiswal + contact.orcid: 0000-0002-1005-8383 + deprecated: true + description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. + download.obo: http://purl.obolibrary.org/obo/eo.obo + download.owl: http://purl.obolibrary.org/obo/eo.owl + homepage: http://planteome.org/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Plant Environment Ontology + prefix: eo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22847540 + title: Ontologies as integrative tools for plant science. + repository: https://github.com/Planteome/plant-environment-ontology + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1036' + description: A structured controlled vocabulary for the representation of plant environmental conditions. + example: EO_0007191 + homepage: http://www.gramene.org/plant_ontology/ontology_browse.html#eo + keywords: + - obo + - plant + name: Plant environmental conditions + pattern: ^EO_\d+$ + prefix: eo +eol: + bioportal: + name: Environment Ontology for Livestock + prefix: EOL + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. + download_owl: https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl + example: '0001927' + fairsharing: + abbreviation: EOL + description: The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. + id: '743' + name: Environment Ontology for Livestock + prefix: FAIRsharing.w7bw2y + subjects: + - Environmental Science + - Animal Husbandry + - Agriculture + mappings: + bioportal: EOL + fairsharing: FAIRsharing.w7bw2y + ols: eol + ols: + contact: pylebail@rennes.inra.fr + description: L'ontologie EOL décrit les conditions d'environnement des élevages d'animaux domestiques. Elle décrit plus particulièrement les modalités de l'alimentation, de l'environnement, de la structure des élevages et des systèmes d'élevage + download: http://www.atol-ontology.com/public/telechargement/eol.owl + homepage: http://www.atol-ontology.com + name: Environment Ontology for Livestock + prefix: eol + version: 2018-09-13 + pattern: ^\d{7}$ +eolife: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A collaborative project intended to create an encyclopedia documenting all living species known to science + example: '1044544' + fairsharing: + abbreviation: EOL + description: The Encyclopedia of Life (EOL) is a collaborative encyclopedia to describe all known living species. It identifies sources of biodiversity knowledge that are legally and practically shareable; integrates them with other sources and adds metadata; provides searching and other services; and collaborates with other projects to support data sharing. + id: '2888' + name: Encyclopedia of Life + prefix: FAIRsharing.3J6NYn + subjects: + - Taxonomy + - Ecology + - Biodiversity + - Biology + homepage: https://eol.org + mappings: + fairsharing: FAIRsharing.3J6NYn + wikidata: P830 + name: Encyclopedia of Life + pattern: ^\d+$ + uri_format: https://eol.org/pages/$1 + wikidata: + database: Q82486 + database.homepage: https://eol.org + database.label: Encyclopedia of Life + homepage: http://eol.org/api/docs/pages + name: Encyclopedia of Life ID + pattern: '[1-9]\d{0,7}' + prefix: P830 + uri_format: https://eol.org/ar/pages/$1 +epcc: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Collection of European paediatric cardiac coding files + homepage: https://www.aepc.org/european-paediatric-cardiac-coding + name: European Paediatric Cardiac Codes + proprietary: true + references: + - https://www.cambridge.org/core/journals/cardiology-in-the-young/article/abs/european-paediatric-cardiac-codes-the-long-list-with-icd9-icd10-crossmapping-and-crossmap-to-epcc-short-list/FCA4DFCCB661298294A3D113FC79D5BE +epd: + biocontext: + is_identifiers: true + is_obo: false + prefix: EPD + uri_format: http://identifiers.org/epd/$1 + fairsharing: + abbreviation: EPD + description: The EPD has been created and is maintained by the Lamond group in the University of Dundee. It combines a polyglot persistent database and web-application that provides open access to integrated proteomics data for >30 000 proteins from published studies on human cells and model organisms. It is designed to provide a user-friendly interface, featuring graphical navigation with interactive visualizations that facilitate powerful data exploration in an intuitive manner. The EPD offers a flexible and scalable ecosystem to integrate proteomics data with genomics information, RNA expression and other related, large-scale datasets. + id: '2515' + name: The Encyclopedia of Proteome Dynamics + prefix: FAIRsharing.sym4ne + subjects: + - Proteomics + - Life Science + - Data Visualization + mappings: + biocontext: EPD + fairsharing: FAIRsharing.sym4ne + miriam: epd + n2t: epd + ncbi: EPD + uniprot: EPD + miriam: + deprecated: false + description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. + homepage: http://epd.vital-it.ch/ + id: '00000408' + name: EPD + namespaceEmbeddedInLui: false + pattern: ^[A-Z-_0-9]+$ + prefix: epd + sampleId: TA_H3 + uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1 + n2t: + description: The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. + example: TA_H3 + homepage: http://epd.vital-it.ch/ + name: EPD at Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^[A-Z-_0-9]+$ + prefix: epd + uri_format: http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1 + ncbi: + example: EP00576 + homepage: http://epd.vital-it.ch/ + name: Eukaryotic Promoter Database + prefix: EPD + uniprot: + category: Proteomic databases + identifier: '205' + link_is_explicit: 'true' + name: Encyclopedia of Proteome Dynamics + prefix: EPD + uri_format: https://www.peptracker.com/epd/analytics/?protein_id=$1 +epio: + bioportal: + name: EpilepsyOntology + prefix: EPIO + example: '0000011' + mappings: + bioportal: EPIO + obofoundry: epio + ontobee: EPIO + obofoundry: + contact: alpha.tom.kodamullil@scai.fraunhofer.de + contact.github: akodamullil + contact.label: Alpha Tom Kodamullil + contact.orcid: 0000-0001-9896-3531 + depends_on: + - bfo + deprecated: false + description: A application driven Epilepsy Ontology with official terms from the ILAE. + download.owl: http://purl.obolibrary.org/obo/epio.owl + homepage: https://github.com/SCAI-BIO/EpilepsyOntology + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Epilepsy Ontology + preferredPrefix: EPIO + prefix: epio + repository: https://github.com/SCAI-BIO/EpilepsyOntology + ontobee: + library: Library + name: Epilepsy Ontology + prefix: EPIO + pattern: ^\d{7}$ +epo: + biocontext: + is_identifiers: false + is_obo: true + prefix: EPO + uri_format: http://purl.obolibrary.org/obo/EPO_$1 + bioportal: + name: Early Pregnancy Ontology + prefix: EPO + download_owl: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl + mappings: + biocontext: EPO + bioportal: EPO + obofoundry: epo + ontobee: EPO + obofoundry: + deprecated: true + description: An ontology designed to support the semantic annotation of epidemiology resources + download.owl: http://purl.obolibrary.org/obo/epo.owl + homepage: https://code.google.com/p/epidemiology-ontology/ + name: Epidemiology Ontology + prefix: epo + ontobee: + library: Library + name: Epidemiology Ontology + prefix: EPO +epso: + bioportal: + name: Epilepsy and Seizure Ontology + prefix: EPSO + example: '0000400' + fairsharing: + abbreviation: EPSO + description: 'The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ' + id: '265' + name: Epilepsy and Seizure Ontology + prefix: FAIRsharing.ttprgy + subjects: + - Neurology + homepage: http://prism.case.edu/prism/index.php/EpilepsyOntology + mappings: + bioportal: EPSO + fairsharing: FAIRsharing.ttprgy + ontobee: EPSO + ontobee: + library: Library + name: Epilepsy Ontology + prefix: EPSO + pattern: ^\d{7}$ +erm: + mappings: + miriam: erm + n2t: erm + miriam: + deprecated: false + description: The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. + homepage: https://nanocommons.github.io/identifiers/ + id: '00000763' + name: European Registry of Materials + namespaceEmbeddedInLui: false + pattern: ^ERM[0-9]{8}$ + prefix: erm + sampleId: ERM00000044 + uri_format: https://nanocommons.github.io/identifiers/registry#$1 + n2t: + description: The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. + example: ERM00000044 + homepage: https://nanocommons.github.io/identifiers/ + name: European Registry of Materials + namespaceEmbeddedInLui: false + pattern: ^ERM[0-9]{8}$ + prefix: erm + uri_format: https://nanocommons.github.io/identifiers/registry#$1 +ero: + biocontext: + is_identifiers: false + is_obo: true + prefix: ERO + uri_format: http://purl.obolibrary.org/obo/ERO_$1 + bioportal: + name: Eagle-I Research Resource Ontology + prefix: ERO + example: '0001655' + fairsharing: + abbreviation: ERO + description: A unique feature of the eagle-i software is that the data collection and search tools are completely driven by ontologies. These ontologies are a set of modules that are written in the OWL language and edited and managed using Protégé. Beginning in 2009, the eagle-i Research Resource Ontology (ERO) was developed alongside the eagle-i applications to model various biomedical research resources such as instruments, Core Facilities, protocols, reagents, animal models and biospecimens. It has now been integrated into the VIVO-ISF Ontology, which leverages and expands upon both the eagle-i and VIVO ontologies to create a semantic framework that describes not only scientific resources but research activities and clinical activities. + id: '1166' + name: eagle-i Research Resource Ontology + prefix: FAIRsharing.nwgynk + subjects: + - Life Science + - Biomedical Science + mappings: + biocontext: ERO + bioportal: ERO + fairsharing: FAIRsharing.nwgynk + obofoundry: ero + ols: ero + ontobee: ERO + obofoundry: + contact: Marc_Ciriello@hms.harvard.edu + contact.label: Marc Ciriello + deprecated: true + description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. + download.owl: http://purl.obolibrary.org/obo/ero.owl + homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology + license: CC BY 2.0 + license.url: https://creativecommons.org/licenses/by/2.0/ + name: eagle-i resource ontology + prefix: ero + ols: + description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. + download: http://purl.obolibrary.org/obo/ero.owl + homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology + name: eagle-i resource ontology + prefix: ero + version: 2016-07-27 + ontobee: + library: Library + name: eagle-i resource ontology + prefix: ERO + pattern: ^\d{7}$ +erv: + biocontext: + is_identifiers: true + is_obo: false + prefix: ERV + uri_format: http://identifiers.org/erv/$1 + mappings: + biocontext: ERV + miriam: erv + n2t: erv + miriam: + deprecated: false + description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. + homepage: https://herv.img.cas.cz/ + id: '00000619' + name: Human Endogenous Retrovirus Database + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\-\_]+$ + prefix: erv + sampleId: THE1B + uri_format: https://herv.img.cas.cz/s/$1 + n2t: + description: Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. + example: THE1B + homepage: https://herv.img.cas.cz/ + name: Human Endogenous Retrovirus Database + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\-\_]+$ + prefix: erv + uri_format: https://herv.img.cas.cz/s/$1 +estdab: + cellosaurus: + category: Cell line databases/resources + homepage: https://www.ebi.ac.uk/ipd/estdab/ + name: European Searchable Tumour Line Database + prefix: ESTDAB + uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?$1 + comment: Website is dead + deprecated: true + example: '046' + mappings: + cellosaurus: ESTDAB + pattern: ^\d{3}$ + uri_format: https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1 +eu89h: + biocontext: + is_identifiers: true + is_obo: false + prefix: EU89H + uri_format: http://identifiers.org/eu89h/$1 + mappings: + biocontext: EU89H + miriam: eu89h + n2t: eu89h + miriam: + deprecated: false + description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. + homepage: http://data.jrc.ec.europa.eu/ + id: '00000644' + name: JRC Data Catalogue + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\-_]+$ + prefix: eu89h + sampleId: jrc-eurl-ecvam-chemagora + uri_format: http://data.europa.eu/89h/$1 + n2t: + description: The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. + example: jrc-eurl-ecvam-chemagora + homepage: http://data.jrc.ec.europa.eu/ + name: JRC Data Catalogue + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9\-_]+$ + prefix: eu89h + uri_format: http://data.europa.eu/89h/$1 +euclinicaltrials: + biocontext: + is_identifiers: true + is_obo: false + prefix: EUCLINICALTRIALS + uri_format: http://identifiers.org/euclinicaltrials/$1 + mappings: + biocontext: EUCLINICALTRIALS + miriam: euclinicaltrials + n2t: euclinicaltrials + miriam: + deprecated: false + description: "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population." + homepage: https://www.clinicaltrialsregister.eu/ + id: '00000536' + name: EU Clinical Trials + namespaceEmbeddedInLui: false + pattern: ^\d{4}\-\d{6}\-\d{2}$ + prefix: euclinicaltrials + sampleId: 2008-005144-16 + uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 + n2t: + description: The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population. + example: 2008-005144-16 + homepage: https://www.clinicaltrialsregister.eu/ + name: EU Clinical Trials at European Medicines Agency + namespaceEmbeddedInLui: false + pattern: ^\d{4}\-\d{6}\-\d{2}$ + prefix: euclinicaltrials + uri_format: https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 +eupath: + biocontext: + is_identifiers: false + is_obo: true + prefix: EUPATH + uri_format: http://purl.obolibrary.org/obo/EUPATH_$1 + bioportal: + name: VEuPathDB Ontology + prefix: EUPATH + example: '0010316' + fairsharing: + abbreviation: VEuPathDB Ontology + description: The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource. The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. + id: '1484' + name: Eukaryotic Pathogen, Host & Vector Genomics Resource Ontology + prefix: FAIRsharing.9rhr9j + subjects: + - Functional Genomics + - Biomedical Science + - Epidemiology + - Population Genetics + mappings: + biocontext: EUPATH + bioportal: EUPATH + fairsharing: FAIRsharing.9rhr9j + obofoundry: eupath + ols: eupath + ontobee: EUPATH + obofoundry: + appears_in: + - scdo + contact: jiezheng@pennmedicine.upenn.edu + contact.github: zhengj2007 + contact.label: Jie Zheng + contact.orcid: 0000-0002-2999-0103 + deprecated: false + description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). + download.owl: http://purl.obolibrary.org/obo/eupath.owl + homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: VEuPathDB ontology + preferredPrefix: EUPATH + prefix: eupath + repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology + ols: + description: The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. + download: http://purl.obolibrary.org/obo/eupath.owl + homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology + name: VEuPathDB Ontology + prefix: eupath + version: 2022-02-15 + version.iri: http://purl.obolibrary.org/obo/eupath/2022-02-15/eupath.owl + ontobee: + library: Library + name: VEuPathDB ontology + prefix: EUPATH + pattern: ^\d{7}$ +eurofir: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries. + homepage: https://www.eurofir.org + name: European Food Information Resource Network + proprietary: true +ev: + appears_in: + - cl + biocontext: + is_identifiers: false + is_obo: true + prefix: EV + uri_format: http://purl.obolibrary.org/obo/EV_$1 + mappings: + biocontext: EV + obofoundry: ev + obofoundry: + contact: evoc@sanbi.ac.za + contact.label: eVOC mailing list + deprecated: true + homepage: http://www.evocontology.org/ + name: eVOC (Expressed Sequence Annotation for Humans) + prefix: ev + references: + - https://twitter.com/Bgeedb/status/1350124337815281664 +evm: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + name: eVOC mouse development stage + references: + - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229 +exac.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: EXAC.GENE + uri_format: http://identifiers.org/exac.gene/$1 + mappings: + biocontext: EXAC.GENE + miriam: exac.gene + n2t: exac.gene + miriam: + deprecated: false + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. + homepage: http://exac.broadinstitute.org/ + id: '00000548' + name: ExAC Gene + namespaceEmbeddedInLui: false + pattern: ^ENSG\d{11}$ + prefix: exac.gene + sampleId: ENSG00000169174 + uri_format: http://exac.broadinstitute.org/gene/$1 + n2t: + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. + example: ENSG00000169174 + homepage: http://exac.broadinstitute.org/ + name: ExAC Gene at Exome Aggregation Consortium + namespaceEmbeddedInLui: false + pattern: ^ENSG\d{11}$ + prefix: exac.gene + uri_format: http://exac.broadinstitute.org/gene/$1 +exac.transcript: + biocontext: + is_identifiers: true + is_obo: false + prefix: EXAC.TRANSCRIPT + uri_format: http://identifiers.org/exac.transcript/$1 + mappings: + biocontext: EXAC.TRANSCRIPT + miriam: exac.transcript + n2t: exac.transcript + miriam: + deprecated: false + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. + homepage: http://exac.broadinstitute.org/ + id: '00000547' + name: ExAC Transcript + namespaceEmbeddedInLui: false + pattern: ^ENST\d{11}$ + prefix: exac.transcript + sampleId: ENST00000407236 + uri_format: http://exac.broadinstitute.org/transcript/$1 + n2t: + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. + example: ENST00000407236 + homepage: http://exac.broadinstitute.org/ + name: ExAC Transcript at Exome Aggregation Consortium + namespaceEmbeddedInLui: false + pattern: ^ENST\d{11}$ + prefix: exac.transcript + uri_format: http://exac.broadinstitute.org/transcript/$1 +exac.variant: + biocontext: + is_identifiers: true + is_obo: false + prefix: EXAC.VARIANT + uri_format: http://identifiers.org/exac.variant/$1 + mappings: + biocontext: EXAC.VARIANT + miriam: exac.variant + n2t: exac.variant + miriam: + deprecated: false + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. + homepage: http://exac.broadinstitute.org/ + id: '00000541' + name: ExAC Variant + namespaceEmbeddedInLui: false + pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ + prefix: exac.variant + sampleId: 22-46615880-T-C + uri_format: http://exac.broadinstitute.org/variant/$1 + n2t: + description: The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. + example: 22-46615880-T-C + homepage: http://exac.broadinstitute.org/ + name: ExAC Variant at Exome Aggregation Consortium + namespaceEmbeddedInLui: false + pattern: ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ + prefix: exac.variant + uri_format: http://exac.broadinstitute.org/variant/$1 +exo: + biocontext: + is_identifiers: false + is_obo: true + prefix: EXO + uri_format: http://purl.obolibrary.org/obo/EXO_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: ExO + uri_format: http://purl.obolibrary.org/obo/ExO_$1 + bioportal: + name: Exposure Ontology + prefix: EXO + example: '0000078' + fairsharing: + abbreviation: ExO + description: Exposure Ontology (ExO) is designed to facilitate the centralization and integration of exposure data to inform understanding of environmental health. ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. + id: '512' + name: Exposure Ontology + prefix: FAIRsharing.6hna78 + subjects: + - Environmental Science + - Epigenetics + - Toxicology + mappings: + biocontext: EXO + biolink: ExO + bioportal: EXO + fairsharing: FAIRsharing.6hna78 + obofoundry: exo + ols: exo + ontobee: ExO + obofoundry: + appears_in: + - ecto + - scdo + contact: annethessen@gmail.com + contact.github: diatomsRcool + contact.label: Anne Thessen + contact.orcid: 0000-0002-2908-3327 + deprecated: false + description: Vocabularies for describing exposure data to inform understanding of environmental health. + download.obo: http://purl.obolibrary.org/obo/exo.obo + download.owl: http://purl.obolibrary.org/obo/exo.owl + homepage: https://github.com/CTDbase/exposure-ontology + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Exposure ontology + preferredPrefix: ExO + prefix: exo + repository: https://github.com/CTDbase/exposure-ontology + ols: + description: ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. + download: http://purl.obolibrary.org/obo/exo.owl + homepage: https://github.com/CTDbase/exposure-ontology + name: Exposure ontology (ExO) + prefix: exo + version: 2020-03-10 + version.iri: http://purl.obolibrary.org/obo/exo/2.1/exo.owl + ontobee: + library: Library + name: Exposure ontology + prefix: ExO + pattern: ^\d{7}$ + synonyms: + - ExO +fabio: + biolink: + is_identifiers: false + is_obo: false + prefix: fabio + uri_format: http://purl.org/spar/fabio/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references. + example: d4e2515 + fairsharing: + abbreviation: FaBiO + description: FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web descriptions of entities that are published or potentially publishable, and that contain or are referred to by bibliographic references, or entities used to define such bibliographic references. FaBiO entities are primarily textual publications such as books, magazines, newspapers and journals, and items of their content such as poems, conference papers and editorials. However, they also include blogs, web pages, datasets, computer algorithms, experimental protocols, formal specifications and vocabularies, legal records, governmental papers, technical and commercial reports and similar publications, and also anthologies, catalogues and similar collections. + id: '3628' + name: FRBR-aligned Bibliographic Ontology + prefix: FAIRsharing.2f3180 + subjects: + - Subject Agnostic + homepage: https://github.com/sparontologies/fabio + mappings: + biolink: fabio + fairsharing: FAIRsharing.2f3180 + name: FaBiO, the FRBR-aligned Bibliographic Ontology + repository: https://github.com/sparontologies/fabio + uri_format: https://sparontologies.github.io/fabio/current/fabio.html#$1 +facebase: + biocontext: + is_identifiers: true + is_obo: false + prefix: FACEBASE + uri_format: http://identifiers.org/facebase/$1 + fairsharing: + abbreviation: FaceBase + description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. + id: '2254' + name: FaceBase + prefix: FAIRsharing.mqvqde + subjects: + - Anatomy + - Medicine + - Epigenetics + - Genetics + - Developmental Biology + mappings: + biocontext: FACEBASE + fairsharing: FAIRsharing.mqvqde + miriam: facebase + n2t: facebase + miriam: + deprecated: false + description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. + homepage: https://www.facebase.org + id: '00000642' + name: FaceBase Data Repository + namespaceEmbeddedInLui: false + pattern: ^FB\d{8}$ + prefix: facebase + sampleId: FB00000917 + uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 + n2t: + description: FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. + example: FB00000917 + homepage: https://www.facebase.org + name: FaceBase Data Repository + namespaceEmbeddedInLui: false + pattern: ^FB\d{8}$ + prefix: facebase + uri_format: https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 +fairsharing: + biocontext: + is_identifiers: true + is_obo: false + prefix: FAIRSHARING + uri_format: http://identifiers.org/fairsharing/$1 + fairsharing: + abbreviation: FAIRsharing + description: FAIRsharing is a FAIR-supporting resource that provides an informative and educational registry on data standards, databases, repositories and policy, alongside search and visualization tools and services that interoperate with other FAIR-enabling resources. FAIRsharing guides consumers to discover, select and use standards, databases, repositories and policy with confidence, and producers to make their resources more discoverable, more widely adopted and cited. Each record in FAIRsharing is curated in collaboration with the maintainers of the resource themselves, ensuring that the metadata in the FAIRsharing registry is accurate and timely. Every record is manually reviewed at least once a year. Records can be collated into collections, based on a project, society or organisation, or Recommendations, where they are collated around a policy, such as a journal or funder data policy. + id: '2521' + name: FAIRsharing + prefix: FAIRsharing.2abjs5 + subjects: + - Environmental Science + - Humanities + - Natural Science + - Earth Science + - Agriculture + - Life Science + - Biomedical Science + mappings: + biocontext: FAIRSHARING + fairsharing: FAIRsharing.2abjs5 + miriam: fairsharing + n2t: fairsharing + miriam: + deprecated: false + description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. + homepage: https://fairsharing.org/ + id: '00000364' + name: FAIRsharing + namespaceEmbeddedInLui: false + pattern: ^bsg-[dscp]?\d{6}$ + prefix: fairsharing + sampleId: bsg-000052 + uri_format: https://fairsharing.org/$1 + n2t: + description: The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. + example: bsg-000052 + homepage: https://fairsharing.org/ + name: FAIRSharing at University of Oxford + namespaceEmbeddedInLui: false + pattern: ^bsg-[dscp]?\d{6}$ + prefix: fairsharing + uri_format: https://fairsharing.org/$1 +faldo: + biocontext: + is_identifiers: false + is_obo: false + prefix: faldo + uri_format: http://biohackathon.org/resource/faldo#$1 + bioportal: + name: Feature Annotation Location Description Ontology + prefix: FALDO + description: It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources + example: ForwardStrandPosition + fairsharing: + abbreviation: FALDO + description: The Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences for data resources represented in RDF and/or OWL. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. + id: '478' + name: Feature Annotation Location Description Ontology + prefix: FAIRsharing.haxp7g + subjects: + - Genetics + homepage: http://biohackathon.org/resource/faldo + mappings: + biocontext: faldo + bioportal: FALDO + fairsharing: FAIRsharing.haxp7g + name: 'Feature Annotation Location Description Ontology ' + uri_format: http://biohackathon.org/resource/faldo#$1 +fao: + biocontext: + is_identifiers: false + is_obo: true + prefix: FAO + uri_format: http://purl.obolibrary.org/obo/FAO_$1 + bioportal: + name: Fungal Gross Anatomy Ontology + prefix: FAO + example: '0000001' + fairsharing: + abbreviation: FAO + description: A structured controlled vocabulary for the anatomy of fungi. + id: '168' + name: Fungal Gross Anatomy Ontology + prefix: FAIRsharing.xs6t67 + subjects: + - Anatomy + - Life Science + - Microbiology + mappings: + biocontext: FAO + bioportal: FAO + fairsharing: FAIRsharing.xs6t67 + obofoundry: fao + ols: fao + ontobee: FAO + prefixcommons: fao + obofoundry: + contact: vw253@cam.ac.uk + contact.github: ValWood + contact.label: Val Wood + contact.orcid: 0000-0001-6330-7526 + deprecated: false + description: A structured controlled vocabulary for the anatomy of fungi. + download.obo: http://purl.obolibrary.org/obo/fao.obo + download.owl: http://purl.obolibrary.org/obo/fao.owl + homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Fungal gross anatomy + preferredPrefix: FAO + prefix: fao + repository: https://github.com/obophenotype/fungal-anatomy-ontology + ols: + description: A structured controlled vocabulary for the anatomy of fungi. + download: http://purl.obolibrary.org/obo/fao.owl + homepage: https://github.com/obophenotype/fungal-anatomy-ontology/ + name: Fungal gross anatomy + prefix: fao + version: 2020-05-07 + version.iri: http://purl.obolibrary.org/obo/fao/releases/2020-05-07/fao.owl + ontobee: + library: Library + name: Fungal gross anatomy + prefix: FAO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1019' + description: The project aims to develop a controlled vocabulary to describe the 'anatomy' of fungi and other microbes, called the fungal anatomy ontology (FAO). + example: FAO_0000001 + homepage: http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/ + keywords: + - obo + - anatomy + - fungi + name: Fungal Anatomy Ontology + pattern: ^FAO_\d+$ + prefix: fao +fbbi: + biocontext: + is_identifiers: false + is_obo: true + prefix: FBbi + uri_format: http://purl.obolibrary.org/obo/FBbi_$1 + bioportal: + name: Biological Imaging Methods Ontology + prefix: FBbi + example: '00000268' + fairsharing: + abbreviation: FBbi + description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. + id: '33' + name: Biological Imaging methods Ontology + prefix: FAIRsharing.ny3z9j + subjects: + - Life Science + - Biomedical Science + mappings: + biocontext: FBbi + bioportal: FBbi + fairsharing: FAIRsharing.ny3z9j + obofoundry: fbbi + ols: fbbi + ontobee: FBBI + prefixcommons: fbbi + obofoundry: + contact: wawong@gmail.com + contact.github: wawong + contact.label: Willy Wong + contact.orcid: 0000-0002-8841-5870 + deprecated: false + description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. + download.owl: http://purl.obolibrary.org/obo/fbbi.owl + homepage: http://cellimagelibrary.org/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Biological Imaging Methods Ontology + preferredPrefix: FBbi + prefix: fbbi + repository: https://github.com/CRBS/Biological_Imaging_Methods_Ontology + ols: + description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. + download: http://purl.obolibrary.org/obo/fbbi.owl + homepage: http://cellimagelibrary.org/ + name: Biological Imaging Methods Ontology + prefix: fbbi + version: 2020-11-06 + version.iri: http://purl.obolibrary.org/obo/fbbi/releases/2020-11-06/fbbi.owl + ontobee: + library: Library + name: Biological Imaging Methods Ontology + prefix: FBBI + pattern: ^\d+$ + prefixcommons: + bioportal: '1023' + description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. + example: FBbi_00000222 + homepage: http://cellimagelibrary.org/ + keywords: + - obo + - experiment + - imaging + name: Biological imaging methods + pattern: ^FBbi_\d+$ + prefix: fbbi + synonyms: + - FBbi +fbbt: + biocontext: + is_identifiers: false + is_obo: true + prefix: FBbt + uri_format: http://purl.obolibrary.org/obo/FBbt_$1 + bioportal: + name: Drosophila Gross Anatomy Ontology + prefix: FB-BT + example: '00007294' + fairsharing: + abbreviation: FBbt + description: An ontology of the anatomy of Drosophila melanogaster. It can be used for annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. It was originally developed by FlyBase, who continue to maintain it and use it for curation. + id: '28' + name: Drosophila anatomy ontology + prefix: FAIRsharing.y2qkst + subjects: + - Anatomy + - Developmental Biology + - Life Science + go: + homepage: http://flybase.org/ + name: Drosophila gross anatomy + prefix: FBbt + uri_format: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:$1 + mappings: + biocontext: FBbt + bioportal: FB-BT + fairsharing: FAIRsharing.y2qkst + go: FBbt + obofoundry: fbbt + ols: fbbt + ontobee: FBBT + prefixcommons: fbbt + obofoundry: + contact: cp390@cam.ac.uk + contact.github: Clare72 + contact.label: Clare Pilgrim + contact.orcid: 0000-0002-1373-1705 + deprecated: false + description: An ontology representing the gross anatomy of Drosophila melanogaster. + download.json: http://purl.obolibrary.org/obo/fbbt.json + download.obo: http://purl.obolibrary.org/obo/fbbt.obo + download.owl: http://purl.obolibrary.org/obo/fbbt.owl + homepage: http://purl.obolibrary.org/obo/fbbt + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Drosophila gross anatomy + preferredPrefix: FBbt + prefix: fbbt + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/24139062 + title: The Drosophila anatomy ontology + - id: https://www.ncbi.nlm.nih.gov/pubmed/22402613 + title: A strategy for building neuroanatomy ontologies + - id: https://www.ncbi.nlm.nih.gov/pubmed/22180411 + title: The Virtual Fly Brain Browser and Query Interface + - id: https://www.ncbi.nlm.nih.gov/pubmed/16381917 + title: 'FlyBase: anatomical data, images and queries' + repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology + ols: + description: An ontology of Drosophila melanogaster anatomy. + download: http://purl.obolibrary.org/obo/fbbt.owl + homepage: http://purl.obolibrary.org/obo/fbbt + name: Drosophila Anatomy Ontology (DAO) + prefix: fbbt + version: 2022-04-13 + version.iri: http://purl.obolibrary.org/obo/fbbt/releases/2022-04-13/fbbt.owl + ontobee: + library: Library + name: Drosophila gross anatomy + prefix: FBBT + part_of: flybase + pattern: ^\d{8}$ + prefixcommons: + bioportal: '1015' + description: A structured controlled vocabulary of the anatomy of Drosophila melanogaster + example: FBbt_00005835 + homepage: http://www.flybase.org/ + keywords: + - obo + - anatomy + - fly + name: Drosophila gross anatomy + pattern: ^FBbt_\d{8}$ + prefix: fbbt + synonyms: + - FBbt + - FBbt_root + uri_format: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1 +fbcv: + biocontext: + is_identifiers: false + is_obo: true + prefix: FBcv + uri_format: http://purl.obolibrary.org/obo/FBcv_$1 + bioportal: + name: FlyBase Controlled Vocabulary + prefix: FB-CV + download_obo: https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo + example: '0000586' + fairsharing: + abbreviation: FBcv + description: A structured controlled vocabulary developed and used by FlyBase, including the Drosophila phenotype ontology. It is used in annotation and classification of data related to Drosophila, including phenotypes and expression. + id: '147' + name: FlyBase Controlled Vocabulary + prefix: FAIRsharing.6tgyxf + subjects: + - Life Science + mappings: + biocontext: FBcv + bioportal: FB-CV + fairsharing: FAIRsharing.6tgyxf + obofoundry: fbcv + ols: fbcv + ontobee: FBCV + prefixcommons: fbcv + obofoundry: + appears_in: + - ontoavida + contact: cp390@cam.ac.uk + contact.github: Clare72 + contact.label: Clare Pilgrim + contact.orcid: 0000-0002-1373-1705 + deprecated: false + description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. + download.json: http://purl.obolibrary.org/obo/fbcv.json + download.obo: http://purl.obolibrary.org/obo/fbcv.obo + download.owl: http://purl.obolibrary.org/obo/fbcv.owl + homepage: http://purl.obolibrary.org/obo/fbcv + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: FlyBase Controlled Vocabulary + preferredPrefix: FBcv + prefix: fbcv + repository: https://github.com/FlyBase/flybase-controlled-vocabulary + ols: + description: A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. + download: http://purl.obolibrary.org/obo/fbcv.owl + homepage: http://purl.obolibrary.org/obo/fbcv + name: FlyBase Controlled Vocabulary (FBcv) + prefix: fbcv + version: 2022-04-14 + version.iri: http://purl.obolibrary.org/obo/fbcv/releases/2022-04-14/fbcv.owl + ontobee: + library: Library + name: FlyBase Controlled Vocabulary + prefix: FBCV + part_of: flybase + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1017' + description: A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them. + example: FBcv_0000013 + homepage: http://www.flybase.org/ + keywords: + - obo + - descriptor + - fly + name: FlyBase Controlled Vocabulary + pattern: ^FBcv_\d{7}$ + prefix: fbcv + synonyms: + - FBcv +fbdv: + biocontext: + is_identifiers: false + is_obo: true + prefix: FBdv + uri_format: http://purl.obolibrary.org/obo/FBdv_$1 + bioportal: + name: Drosophila Development Ontology + prefix: FB-DV + example: '00000000' + fairsharing: + abbreviation: FBdv + description: An ontology of the developmental stages of Drosophila melanogaster. It provides a controlled vocabulary for use in annotation and classification of data related to Drosophila, such as gene expression, phenotypes and images. + id: '29' + name: Drosophila developmental ontology + prefix: FAIRsharing.p52pzj + subjects: + - Developmental Biology + - Life Science + mappings: + biocontext: FBdv + bioportal: FB-DV + fairsharing: FAIRsharing.p52pzj + obofoundry: fbdv + ols: fbdv + ontobee: FBdv + prefixcommons: fbdv + obofoundry: + contact: cp390@cam.ac.uk + contact.github: Clare72 + contact.label: Clare Pilgrim + contact.orcid: 0000-0002-1373-1705 + deprecated: false + description: A structured controlled vocabulary of the development of Drosophila melanogaster. + download.json: http://purl.obolibrary.org/obo/fbdv.json + download.obo: http://purl.obolibrary.org/obo/fbdv.obo + download.owl: http://purl.obolibrary.org/obo/fbdv.owl + homepage: http://purl.obolibrary.org/obo/fbdv + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Drosophila development + preferredPrefix: FBdv + prefix: fbdv + repository: https://github.com/FlyBase/drosophila-developmental-ontology + ols: + description: An ontology of Drosophila melanogaster developmental stages. + download: http://purl.obolibrary.org/obo/fbdv.owl + homepage: http://purl.obolibrary.org/obo/fbdv + name: FlyBase Developmental Ontology (FBdv) + prefix: fbdv + version: 2022-04-12 + version.iri: http://purl.obolibrary.org/obo/fbdv/releases/2022-04-12/fbdv.owl + ontobee: + library: Library + name: Drosophila development + prefix: FBdv + pattern: ^\d{8}$ + prefixcommons: + bioportal: '1016' + description: A structured controlled vocabulary of the development of Drosophila melanogaster. + example: FBdv_00005291 + homepage: http://www.flybase.org/ + keywords: + - obo + - development + - fly + name: Drosophila development + pattern: ^FBdv_\d{8}$ + prefix: fbdv + synonyms: + - FBdv +fbol: + biocontext: + is_identifiers: true + is_obo: false + prefix: FBOL + uri_format: http://identifiers.org/fbol/$1 + comment: Website down, checked on 2021-10-07 + deprecated: true + mappings: + biocontext: FBOL + miriam: fbol + n2t: fbol + ncbi: FBOL + miriam: + deprecated: false + description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. + homepage: http://www.fungalbarcoding.org/ + id: '00000410' + name: Fungal Barcode + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: fbol + sampleId: '2224' + uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T + n2t: + description: DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. + example: '2224' + homepage: http://www.fungalbarcoding.org/ + name: Fungal Barcode at Fungal Biodiversity Centre + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: fbol + uri_format: http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T + ncbi: + example: '2224' + homepage: http://www.fungalbarcoding.org/ + name: International Fungal Working Group Fungal Barcoding. + prefix: FBOL +fbql: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + example: '00005254' + name: FlyBase Qualifiers + pattern: ^\d+$ +fbrf: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: FlyBase internal citation identifiers + example: '0187632' + homepage: https://flybase.org + name: FlyBase Reference Report + part_of: flybase + pattern: ^\d{7}$ + uri_format: https://flybase.org/reports/FBrf$1 +fbsp: + biocontext: + is_identifiers: false + is_obo: true + prefix: FBSP + uri_format: http://purl.obolibrary.org/obo/FBSP_$1 + bioportal: + name: Fly Taxonomy + prefix: FB-SP + example: '00000000' + mappings: + biocontext: FBSP + bioportal: FB-SP + obofoundry: fbsp + obofoundry: + contact: cp390@cam.ac.uk + contact.github: Clare72 + contact.label: Clare Pilgrim + contact.orcid: 0000-0002-1373-1705 + deprecated: true + description: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. + download.owl: http://purl.obolibrary.org/obo/fbsp.owl + homepage: http://www.flybase.org/ + name: Fly taxonomy + prefix: fbsp + part_of: flybase + pattern: ^\d{8}$ +fbtc: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The cell line vocabulary inside FlyBase + example: '0000190' + homepage: https://flybase.org + name: Flybase Cell Line + part_of: flybase + pattern: ^\d{7}$ + uri_format: https://flybase.org/reports/FBtc$1 +fcb: + mappings: + miriam: fcb + miriam: + deprecated: false + description: >+ + Created by researchers and data managers professionals, the FAIR Cookbook + is an online resource for the Life Sciences with recipes that help you to + make and keep data Findable, Accessible, Interoperable, and Reusable + (FAIR). + + homepage: https://w3id.org + id: '00000891' + name: the FAIR Cookbook + namespaceEmbeddedInLui: false + pattern: ^FCB\d{3} + prefix: fcb + sampleId: FCB005 + uri_format: https://w3id.org/faircookbook/$1 +fcsfree: + cellosaurus: + category: Cell line databases/resources + homepage: https://fcs-free.org/ + name: Fetal Calf Serum-Free Database + prefix: FCS-free + uri_format: https://fcs-free.org/fcs-database?$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: 240-17-488-3-4-12 + homepage: https://fcs-free.org + mappings: + cellosaurus: FCS-free + name: Fetal Calf Serum-Free Database + uri_format: https://fcs-free.org/fcs-database?$1 +fideo: + bioportal: + name: Food Interactions with Drugs Evidence Ontology + prefix: FIDEO + example: '00000021' + mappings: + bioportal: FIDEO + obofoundry: fideo + ols: fideo + ontobee: FIDEO + obofoundry: + contact: georgeta.bordea@u-bordeaux.fr + contact.github: getbordea + contact.label: Georgeta Bordea + contact.orcid: 0000-0001-9921-8234 + deprecated: false + description: Food-Drug interactions automatically extracted from scientific literature + download.owl: http://purl.obolibrary.org/obo/fideo.owl + homepage: https://gitub.u-bordeaux.fr/erias/fideo + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Food Interactions with Drugs Evidence Ontology + preferredPrefix: FIDEO + prefix: fideo + repository: https://github.com/getbordea/fideo + ols: + description: The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there. + download: http://purl.obolibrary.org/obo/fideo.owl + homepage: https://gitub.u-bordeaux.fr/erias/fideo + name: Food Interactions with Drugs Evidence Ontology + prefix: fideo + ontobee: + library: Library + name: Food Interactions with Drugs Evidence Ontology + prefix: FIDEO + pattern: ^\d{8}$ +fishbase.species: + description: 'Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years.' + example: '6472' + homepage: http://fishbase.org + name: FishBase + pattern: ^\d+$ + synonyms: + - fishbase + wikidata: + database: Q837101 + prefix: P938 +fix: + biocontext: + is_identifiers: false + is_obo: true + prefix: FIX + uri_format: http://purl.obolibrary.org/obo/FIX_$1 + bioportal: + name: Physico-Chemical Methods and Properties + prefix: FIX + example: '0000390' + fairsharing: + abbreviation: FIX + description: 'FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties. While this ontology is available via BioPortal and the OBO Foundry, we cannot find a home page or a publication for the resource, and the resource itself is no longer maintained.' + id: '1241' + name: Physico-chemical methods and properties + prefix: FAIRsharing.wwy1ns + subjects: + - Chemistry + homepage: https://www.ebi.ac.uk/chebi/ + mappings: + biocontext: FIX + bioportal: FIX + fairsharing: FAIRsharing.wwy1ns + obofoundry: fix + ols: fix + ontobee: FIX + prefixcommons: fix + obofoundry: + contact.label: chEBI + deprecated: true + description: An ontology of physico-chemical methods and properties. + download.obo: http://purl.obolibrary.org/obo/fix.obo + download.owl: http://purl.obolibrary.org/obo/fix.owl + homepage: http://www.ebi.ac.uk/chebi + name: Physico-chemical methods and properties + prefix: fix + ols: + description: An ontology of physico-chemical methods and properties. + download: http://purl.obolibrary.org/obo/fix.owl + homepage: http://www.ebi.ac.uk/chebi + name: Physico-chemical methods and properties + prefix: fix + version: 2020-04-13 + version.iri: http://purl.obolibrary.org/obo/fix/releases/2020-04-13/fix.owl + ontobee: + library: Library + name: Physico-chemical methods and properties + prefix: FIX + part_of: chebi + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1014' + description: 'FIX consists of two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties.' + example: FIX_0000000 + keywords: + - obo + - property + - experiment + name: Physico-chemical methods and properties + pattern: ^FIX_\d{7}$ + prefix: fix +flopo: + biocontext: + is_identifiers: false + is_obo: true + prefix: FLOPO + uri_format: http://purl.obolibrary.org/obo/FLOPO_$1 + bioportal: + name: Flora Phenotype Ontology + prefix: FLOPO + example: '0005250' + fairsharing: + abbreviation: FLOPO + description: 'The Flora Phenotype Ontology is a domain ontology for the description of plant characters. FLOPO contains more than 25000 phenotype and traits classes, the creation of FLOPO is data-driven: For each trait/phenotype class exists a taxon annotation in the underlying Floras.' + id: '394' + name: Flora Phenotype Ontology + prefix: FAIRsharing.ny9vnm + subjects: + - Botany + - Biodiversity + - Plant Anatomy + mappings: + biocontext: FLOPO + bioportal: FLOPO + fairsharing: FAIRsharing.ny9vnm + obofoundry: flopo + ols: flopo + ontobee: FLOPO + obofoundry: + contact: robert.hoehndorf@kaust.edu.sa + contact.github: leechuck + contact.label: Robert Hoehndorf + contact.orcid: 0000-0001-8149-5890 + deprecated: false + description: Traits and phenotypes of flowering plants occurring in digitized Floras + download.owl: http://purl.obolibrary.org/obo/flopo.owl + homepage: https://github.com/flora-phenotype-ontology/flopoontology + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Flora Phenotype Ontology + preferredPrefix: FLOPO + prefix: flopo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/27842607 + title: 'The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants' + repository: https://github.com/flora-phenotype-ontology/flopoontology + ols: + description: Traits and phenotypes of flowering plants occurring in digitized Floras + download: http://purl.obolibrary.org/obo/flopo.owl + homepage: https://github.com/flora-phenotype-ontology/flopoontology + name: Flora Phenotype Ontology + prefix: flopo + version: 2019-09-09 + ontobee: + library: Library + name: Flora Phenotype Ontology + prefix: FLOPO + pattern: ^\d{7}$ +flowrepository: + fairsharing: + abbreviation: FlowRepository + description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. Data are generally associated with peer reviewed manuscripts. + id: '1727' + name: FlowRepository + prefix: FAIRsharing.veg2d6 + subjects: + - Life Science + - Cell Biology + - Biology + mappings: + fairsharing: FAIRsharing.veg2d6 + miriam: flowrepository + n2t: flowrepository + miriam: + deprecated: false + description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. + homepage: https://flowrepository.org/ + id: '00000672' + name: FlowRepository + namespaceEmbeddedInLui: false + pattern: ^FR\-FCM\-\w{4}$ + prefix: flowrepository + sampleId: FR-FCM-ZYGW + uri_format: https://flowrepository.org/id/$1 + n2t: + description: FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. + example: FR-FCM-ZYGW + homepage: https://flowrepository.org/ + name: FlowRepository + namespaceEmbeddedInLui: false + pattern: ^FR\-FCM\-\w{4}$ + prefix: flowrepository + uri_format: https://flowrepository.org/id/$1 +flu: + biocontext: + is_identifiers: false + is_obo: true + prefix: FLU + uri_format: http://purl.obolibrary.org/obo/FLU_$1 + bioportal: + name: Influenza Ontology + prefix: FLU + example: '0000404' + mappings: + biocontext: FLU + bioportal: FLU + obofoundry: flu + obofoundry: + contact: burkesquires@gmail.com + contact.label: Burke Squires + deprecated: true + download.owl: http://purl.obolibrary.org/obo/flu.owl + homepage: http://purl.obolibrary.org/obo/flu/ + name: Influenza Ontology + prefix: flu + pattern: ^\d{7}$ +flybase: + biocontext: + is_identifiers: false + is_obo: false + prefix: FlyBase + uri_format: http://flybase.org/reports/$1 + cellosaurus: + category: Organism-specific databases + homepage: https://flybase.org + name: Drosophila genome database + prefix: FlyBase + uri_format: https://flybase.org/reports/$1.html + fairsharing: + abbreviation: FlyBase + description: Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs. + id: '1582' + name: FlyBase + prefix: FAIRsharing.wrvze3 + subjects: + - Functional Genomics + - Anatomy + - Molecular biology + - Genomics + - Bioinformatics + - Genetics + - Life Science + - Molecular Genetics + - Comparative Genomics + go: + homepage: http://flybase.org/ + name: FlyBase + prefix: FB + synonyms: + - FlyBase + - FLYBASE + uri_format: http://flybase.org/reports/$1.html + mappings: + biocontext: FlyBase + cellosaurus: FlyBase + fairsharing: FAIRsharing.wrvze3 + go: FB + miriam: fb + n2t: fb + ncbi: FLYBASE + prefixcommons: flybase + uniprot: FlyBase + wikidata: P3852 + miriam: + deprecated: false + description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. + homepage: http://flybase.org/ + id: '00000030' + name: FlyBase + namespaceEmbeddedInLui: false + pattern: ^FB\w{2}\d{7}$ + prefix: fb + providers: + - code: bioentitylink + description: FlyBase through BioEntity Link + homepage: https://bioentity.link/ + name: FlyBase through BioEntity Link + uri_format: https://bioentity.link/#/lexicon/public/$1 + - code: agr + description: FlyBase through the Alliance of Genome Resources + homepage: https://www.alliancegenome.org + name: FlyBase through the Alliance of Genome Resources + uri_format: https://www.alliancegenome.org/gene/FB:$1 + sampleId: FBgn0011293 + uri_format: http://flybase.org/reports/$1.html + n2t: + description: FlyBase is the database of the Drosophila Genome Projects and of associated literature. + example: FBgn0011293 + homepage: https://www.alliancegenome.org + name: FlyBase through the Alliance of Genome Resources + namespaceEmbeddedInLui: false + pattern: ^FB\w{2}\d{7}$ + prefix: fb + uri_format: https://www.alliancegenome.org/gene/FB:$1 + name: FlyBase Gene + ncbi: + example: FBgn0000024 + homepage: http://www.flybase.org/ + name: Database of Genetic and molecular data of Drosophila. + prefix: FLYBASE + preferred_prefix: FlyBase + prefixcommons: + description: FlyBase is an integrated resource for genetic, molecular, and descriptive data concerning the Drosophilidae, including interactive genomic maps, gene product descriptions, mutant allele phenotypes, genetic interactions, expression patterns, transgenic constructs and their insertions, anatomy and images, and genetic stock collections. + example: FBgn0011293 + homepage: http://flybase.org/ + keywords: + - genome + - interaction + - anatomy + - DNA + name: Drosophila genome database + pattern: ^FB\w{2}\d{7}$ + prefix: flybase + uri_format: http://flybase.org/reports/$1.html + synonyms: + - FB + - FlyBase + uniprot: + category: Organism-specific databases + comment: Replacement for DMAP + identifier: '26' + link_is_explicit: 'true' + name: Drosophila genome database + prefix: FlyBase + uri_format: http://flybase.org/reports/$1.html + uri_format: https://flybase.org/reports/$1 + wikidata: + database: Q3074571 + database.homepage: https://flybase.org/ + database.label: FlyBase + homepage: http://flybase.org/ + name: FlyBase Gene ID + pattern: FBgn\d{7} + prefix: P3852 + uri_format: http://flybase.org/reports/$1 +flybrain.ndb: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A database of fly neurons and pathways with an associated 3D viewer. + example: '10531' + homepage: https://flybrain-ndb.virtualflybrain.org + name: FlyBrain Neuron Database + pattern: ^\d+$ + uri_format: https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html +fma: + biocontext: + is_identifiers: false + is_obo: true + prefix: FMA + uri_format: http://purl.obolibrary.org/obo/FMA_$1 + bioportal: + name: Foundational Model of Anatomy + prefix: FMA + example: '63189' + fairsharing: + abbreviation: FMA + description: The Foundational Model of Anatomy Ontology (FMA) is an evolving computer-based knowledge source for biomedical informatics; it is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. Its ontological framework can be applied and extended to all other species + id: '683' + name: Foundational Model of Anatomy + prefix: FAIRsharing.x56jsy + subjects: + - Anatomy + - Radiology + - Biomedical Science + go: + homepage: http://sig.biostr.washington.edu/projects/fm/index.html + name: Foundational Model of Anatomy + prefix: FMA + mappings: + biocontext: FMA + bioportal: FMA + fairsharing: FAIRsharing.x56jsy + go: FMA + miriam: fma + n2t: fma + obofoundry: fma + ols: fma + ontobee: FMA + prefixcommons: fma + miriam: + deprecated: false + description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. + homepage: https://www.ebi.ac.uk/ols/ontologies/fma/ + id: '00000067' + name: FMA + namespaceEmbeddedInLui: true + pattern: ^FMA:\d+$ + prefix: fma + sampleId: '67112' + uri_format: https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1 + n2t: + description: The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. + example: '67112' + homepage: http://bioportal.bioontology.org/ontologies/FMA + name: Foundational Model of Anatomy through BioPortal + namespaceEmbeddedInLui: true + pattern: ^FMA:\d+$ + prefix: fma + uri_format: http://purl.bioontology.org/ontology/FMA_subset/FMA:$1 + name: Foundational Model of Anatomy + obofoundry: + contact: mejino@u.washington.edu + contact.label: Onard Mejino + deprecated: true + description: This is currently a slimmed down version of FMA + download.owl: http://purl.obolibrary.org/obo/fma.owl + homepage: http://si.washington.edu/projects/fma + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Foundational Model of Anatomy Ontology (subset) + preferredPrefix: FMA + prefix: fma + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/18688289 + title: Translating the Foundational Model of Anatomy into OWL + - id: https://www.ncbi.nlm.nih.gov/pubmed/18360535 + title: 'The foundational model of anatomy in OWL: Experience and perspectives' + - id: https://www.ncbi.nlm.nih.gov/pubmed/16779026 + title: 'Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study' + repository: https://bitbucket.org/uwsig/fma + ols: + description: This is currently a slimmed down version of FMA + download: http://purl.obolibrary.org/obo/fma.owl + homepage: http://si.washington.edu/projects/fma + name: Foundational Model of Anatomy Ontology (subset) + prefix: fma + version: 2020-04-13 + version.iri: http://purl.obolibrary.org/obo/fma/releases/2020-04-13/fma.owl + ontobee: + library: Library + name: Foundational Model of Anatomy Ontology (subset) + prefix: FMA + pattern: ^\d+$ + prefixcommons: + bioportal: '1053' + description: FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. + example: FMA:67112 + homepage: http://sig.biostr.washington.edu/projects/fm/ + keywords: + - owl + - anatomy + - human + name: The Foundational Model of Anatomy Ontology + pattern: ^FMA:\d+$ + prefix: fma + pubmed_ids: + - '17271570' + synonyms: + - FMAID + - FMA_RETIRED +foaf: + biocontext: + is_identifiers: false + is_obo: false + prefix: foaf + uri_format: http://xmlns.com/foaf/0.1/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: foaf + uri_format: http://xmlns.com/foaf/0.1/$1 + bioportal: + name: Friend of a Friend Vocabulary + prefix: FOAF + description: "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world." + example: familyName + homepage: http://xmlns.com/foaf/spec/ + mappings: + biocontext: foaf + biolink: foaf + bioportal: FOAF + name: Friend of a Friend + uri_format: http://xmlns.com/foaf/0.1/$1 +fobi: + bioportal: + name: FOBI (Food-Biomarker Ontology) + prefix: FOBI + example: '030719' + homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology + mappings: + bioportal: FOBI + obofoundry: fobi + ols: fobi + ontobee: FOBI + name: Food-Biomarker Ontology + obofoundry: + contact: polcaes@gmail.com + contact.github: pcastellanoescuder + contact.label: Pol Castellano Escuder + contact.orcid: 0000-0001-6466-877X + depends_on: + - chebi + - foodon + deprecated: false + description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data + download.owl: http://purl.obolibrary.org/obo/fobi.owl + homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Food-Biomarker Ontology + preferredPrefix: FOBI + prefix: fobi + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/32556148 + title: 'FOBI: an ontology to represent food intake data and associate it with metabolomic data' + - id: https://www.ncbi.nlm.nih.gov/pubmed/34601570 + title: 'The fobitools framework: the first steps towards food enrichment analysis' + repository: https://github.com/pcastellanoescuder/FoodBiomarkerOntology + ols: + description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data + download: http://purl.obolibrary.org/obo/fobi.owl + homepage: https://github.com/pcastellanoescuder/FoodBiomarkerOntology + name: Food-Biomarker Ontology + prefix: fobi + version.iri: http://purl.obolibrary.org/obo/fobi/fobi.owl + ontobee: + library: Library + name: FOBI + prefix: FOBI + pattern: ^\d{6}$ +foodb.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: FOODB.COMPOUND + uri_format: http://identifiers.org/foodb.compound/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: foodb.compound + uri_format: http://foodb.ca/foods/$1 + homepage: https://foodb.ca/ + mappings: + biocontext: FOODB.COMPOUND + biolink: foodb.compound + miriam: foodb.compound + n2t: foodb.compound + miriam: + deprecated: false + description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. + homepage: http://foodb.ca/foods + id: '00000530' + name: FooDB Compound + namespaceEmbeddedInLui: false + pattern: ^FDB\d+$ + prefix: foodb.compound + sampleId: FDB002100 + uri_format: http://foodb.ca/compounds/$1 + n2t: + description: FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. + example: FDB002100 + homepage: http://foodb.ca/foods + name: FooDB database of food additives at University of Alberta + namespaceEmbeddedInLui: false + pattern: ^FDB\d+$ + prefix: foodb.compound + uri_format: http://foodb.ca/compounds/$1 + synonyms: + - foodb +foodon: + biocontext: + is_identifiers: false + is_obo: true + prefix: FOODON + uri_format: http://purl.obolibrary.org/obo/FOODON_$1 + bioportal: + name: The FoodOn Food Ontology + prefix: FOODON + fairsharing: + abbreviation: FOODON + description: The need to represent knowledge about food is central to many human activities including agriculture, medicine, food safety inspection, shopping patterns, and sustainable development. FoodOn is built to interoperate with the OBO Library and to represent entities which bear a food role. Initially the ontology will focus on the human-centric categorization and handling of food, but in the future it will also encompass materials in natural ecosystems and food webs. We aim to develop semantics for food safety, food security, the agricultural and animal husbandry practices linked to food production, culinary, nutritional and chemical ingredients and processes. + id: '638' + name: FoodOn + prefix: FAIRsharing.dzxae + subjects: + - Botany + - Environmental Science + - Medicine + - Agriculture + mappings: + biocontext: FOODON + bioportal: FOODON + fairsharing: FAIRsharing.dzxae + miriam: foodon + n2t: foodon + obofoundry: foodon + ols: foodon + ontobee: FOODON + miriam: + deprecated: false + description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. + homepage: https://foodon.org + id: '00000661' + name: FoodOn Food Ontology + namespaceEmbeddedInLui: true + pattern: ^FOODON:[0-9]{8}$ + prefix: foodon + sampleId: '03307879' + uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 + n2t: + description: FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. + example: '03307879' + homepage: https://foodon.org + name: FoodOn Food Ontology through OLS + namespaceEmbeddedInLui: true + pattern: ^FOODON:[0-9]{8}$ + prefix: foodon + uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 + name: The Food Ontology + obofoundry: + appears_in: + - agro + - envo + - fobi + - maxo + - one + - ons + contact: damion_dooley@sfu.ca + contact.github: ddooley + contact.label: Damion Dooley + contact.orcid: 0000-0002-8844-9165 + depends_on: + - bfo + - chebi + - envo + - eo + - ncbitaxon + - obi + - ro + - uberon + deprecated: false + description: A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research + download.owl: http://purl.obolibrary.org/obo/foodon.owl + homepage: https://foodon.org/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Food Ontology + preferredPrefix: FOODON + prefix: foodon + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/31304272 + title: 'FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration' + repository: https://github.com/FoodOntology/foodon + ols: + description: FoodOn (http://foodon.org) is a consortium-driven project to build a comprehensive and easily accessible global farm-to-fork ontology about food, that accurately and consistently describes foods commonly known in cultures from around the world. + download: http://purl.obolibrary.org/obo/foodon.owl + homepage: https://foodon.org/ + name: Food Ontology + prefix: foodon + version: 2022-02-01 + version.iri: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl + ontobee: + library: Library + name: FOODON + prefix: FOODON + pattern: ^[0-9]{8}$ +fovt: + bioportal: + name: FuTRES Ontology of Vertebrate Traits + prefix: FOVT + example: '0000009' + mappings: + bioportal: FOVT + obofoundry: fovt + ols: fovt + ontobee: FOVT + obofoundry: + contact: meghan.balk@gmail.com + contact.github: megbalk + contact.label: Meghan Balk + contact.orcid: 0000-0003-2699-3066 + depends_on: + - bco + - bfo + - bspo + - iao + - oba + - pato + - ro + - uberon + deprecated: false + description: FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA). + download.obo: http://purl.obolibrary.org/obo/fovt.obo + download.owl: http://purl.obolibrary.org/obo/fovt.owl + homepage: https://github.com/futres/fovt + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: FuTRES Ontology of Vertebrate Traits + preferredPrefix: FOVT + prefix: fovt + repository: https://github.com/futres/fovt + ols: + description: None + download: http://purl.obolibrary.org/obo/fovt.owl + homepage: https://github.com/futres/fovt + name: FuTRES Ontology of Vertebrate Traits + prefix: fovt + version: 2021-11-10 + version.iri: http://purl.obolibrary.org/obo/fovt/releases/2021-11-10/fovt.owl + ontobee: + library: Library + name: FuTRES Ontology of Vertebrate Traits + prefix: FOVT + pattern: ^\d{7}$ +fplx: + biocontext: + is_identifiers: true + is_obo: false + prefix: FPLX + uri_format: http://identifiers.org/fplx/$1 + bioportal: + name: FamPlex + prefix: FPLX + example: GPIb_IX_V + homepage: https://sorgerlab.github.io/famplex/ + mappings: + biocontext: FPLX + bioportal: FPLX + miriam: fplx + n2t: fplx + miriam: + deprecated: false + description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. + homepage: https://sorgerlab.github.io/famplex + id: '00000651' + name: FamPlex + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ + prefix: fplx + sampleId: RAS + uri_format: https://sorgerlab.github.io/famplex/$1 + n2t: + description: FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. + example: RAS + homepage: http://bioportal.bioontology.org/ontologies/FPLX/ + name: FPLX through BioPortal + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9][A-Za-z0-9_]+$ + prefix: fplx + uri_format: http://bioportal.bioontology.org/ontologies/FPLX/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFPLX%23_$1 + name: FamPlex + synonyms: + - famplex + uri_format: https://sorgerlab.github.io/famplex/$1 + wikidata: + paper: Q55505864 +fsnp: + biocontext: + is_identifiers: true + is_obo: false + prefix: FSNP + uri_format: http://identifiers.org/fsnp/$1 + mappings: + biocontext: FSNP + miriam: fsnp + n2t: fsnp + prefixcommons: fsnp + miriam: + deprecated: false + description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. + homepage: http://compbio.cs.queensu.ca/F-SNP/ + id: '00000496' + name: F-SNP + namespaceEmbeddedInLui: false + pattern: ^rs\d+$ + prefix: fsnp + sampleId: rs17852708 + uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1 + n2t: + description: The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. + example: rs17852708 + homepage: http://compbio.cs.queensu.ca/F-SNP/ + name: F-SNP at Queen's University (Canada) + namespaceEmbeddedInLui: false + pattern: ^rs\d+$ + prefix: fsnp + uri_format: http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1 + prefixcommons: + description: F-SNP database provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health. + example: rs36095613 + homepage: http://compbio.cs.queensu.ca/F-SNP/ + keywords: + - DNA + - protein + name: 'F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies' + pattern: ^rs\d+$ + prefix: fsnp +ftt: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific. + example: '273' + homepage: https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3 + name: Feature Type Thesaurus + pattern: ^\d+$ + references: + - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200 + - https://github.com/EnvironmentOntology/envo/issues/1130 + uri_format: https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1 +funcbase.fly: + biocontext: + is_identifiers: true + is_obo: false + prefix: FUNCBASE.FLY + uri_format: http://identifiers.org/funcbase.fly/$1 + mappings: + biocontext: FUNCBASE.FLY + miriam: funcbase.fly + n2t: funcbase.fly + miriam: + deprecated: false + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. + homepage: http://func.mshri.on.ca/fly + id: '00000461' + name: FuncBase Fly + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.fly + sampleId: '10194' + uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1 + n2t: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. + example: '10194' + homepage: http://func.mshri.on.ca/fly + name: FuncBase Fly at Harvard Medical School + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.fly + uri_format: http://func.mshri.on.ca/fly/genes/list_functional_scores/$1 +funcbase.human: + biocontext: + is_identifiers: true + is_obo: false + prefix: FUNCBASE.HUMAN + uri_format: http://identifiers.org/funcbase.human/$1 + mappings: + biocontext: FUNCBASE.HUMAN + miriam: funcbase.human + n2t: funcbase.human + miriam: + deprecated: false + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. + homepage: http://func.mshri.on.ca/human/ + id: '00000462' + name: FuncBase Human + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.human + sampleId: '119514' + uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1 + n2t: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. + example: '119514' + homepage: http://func.mshri.on.ca/human/ + name: FuncBase Human at Harvard Medical School + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.human + uri_format: http://func.mshri.on.ca/human/genes/list_functional_scores/$1 +funcbase.mouse: + biocontext: + is_identifiers: true + is_obo: false + prefix: FUNCBASE.MOUSE + uri_format: http://identifiers.org/funcbase.mouse/$1 + mappings: + biocontext: FUNCBASE.MOUSE + miriam: funcbase.mouse + n2t: funcbase.mouse + miriam: + deprecated: false + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. + homepage: http://func.mshri.on.ca/mouse/ + id: '00000463' + name: FuncBase Mouse + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.mouse + sampleId: '1351341' + uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 + n2t: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. + example: '1351341' + homepage: http://func.mshri.on.ca/mouse/ + name: FuncBase Mouse at Harvard Medical School + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.mouse + uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 +funcbase.yeast: + biocontext: + is_identifiers: true + is_obo: false + prefix: FUNCBASE.YEAST + uri_format: http://identifiers.org/funcbase.yeast/$1 + mappings: + biocontext: FUNCBASE.YEAST + miriam: funcbase.yeast + n2t: funcbase.yeast + miriam: + deprecated: false + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. + homepage: http://func.mshri.on.ca/yeast + id: '00000464' + name: FuncBase Yeast + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.yeast + sampleId: '2701' + uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 + n2t: + description: Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. + example: '2701' + homepage: http://func.mshri.on.ca/yeast + name: FuncBase Yeast at Harvard Medical School + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: funcbase.yeast + uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 +funderregistry: + mappings: + miriam: funderregistry + miriam: + deprecated: false + description: The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world. + homepage: https://www.crossref.org/ + id: '00000847' + name: FunderRegistry + namespaceEmbeddedInLui: false + pattern: ^\d{9,9}$ + prefix: funderregistry + sampleId: '100000001' + uri_format: http://data.crossref.org/fundingdata/funder/10.13039/$1 +fungidb: + biocontext: + is_identifiers: true + is_obo: false + prefix: FUNGIDB + uri_format: http://identifiers.org/fungidb/$1 + fairsharing: + abbreviation: FungiDB + description: FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining. + id: '1585' + name: Fungal and Oomycete genomics resource + prefix: FAIRsharing.xf30yc + subjects: + - Genomics + mappings: + biocontext: FUNGIDB + fairsharing: FAIRsharing.xf30yc + miriam: fungidb + n2t: fungidb + miriam: + deprecated: false + description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. + homepage: https://fungidb.org/fungidb + id: '00000365' + name: FungiDB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: fungidb + sampleId: CNBG_0001 + uri_format: https://fungidb.org/fungidb/app/record/gene/$1 + n2t: + description: FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. + example: CNBG_0001 + homepage: https://fungidb.org/fungidb + name: FungiDB at University of California + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+$ + prefix: fungidb + uri_format: https://fungidb.org/fungidb/app/record/gene/$1 +fyeco: + biolink: + is_identifiers: false + is_obo: false + prefix: FYECO + uri_format: https://www.pombase.org/term/$1 + comment: Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future. + contact: + email: vw253@cam.ac.uk + github: ValWood + name: Val Wood + orcid: 0000-0001-6330-7526 + contributor: + email: vw253@cam.ac.uk + github: ValWood + name: Val Wood + orcid: 0000-0001-6330-7526 + description: PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase. + example: '0000003' + homepage: https://github.com/pombase/fypo + mappings: + biolink: FYECO + name: Fission Yeast Experimental Conditions Ontology + pattern: ^\d{7}$ + preferred_prefix: FYECO + repository: https://github.com/pombase/fypo + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 +fyler: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'A hierarchical classification of congenital heart disease ' + example: '4447' + homepage: https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906 + name: Fyler + pattern: ^\d+$ + references: + - https://github.com/obophenotype/human-phenotype-ontology/issues/2568 + - https://github.com/obophenotype/human-phenotype-ontology/issues/2511 +fypo: + biocontext: + is_identifiers: false + is_obo: true + prefix: FYPO + uri_format: http://purl.obolibrary.org/obo/FYPO_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: FYPO + uri_format: http://purl.obolibrary.org/obo/FYPO_$1 + bioportal: + name: Fission Yeast Phenotype Ontology + prefix: FYPO + download_obo: http://purl.obolibrary.org/obo/fypo.obo + example: '0001707' + fairsharing: + abbreviation: FYPO + description: FYPO is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource (www.pombase.org). Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions. + id: '314' + name: Fission Yeast Phenotype Ontology + prefix: FAIRsharing.4vr0ys + subjects: + - Genetics + - Phylogenetics + - Life Science + go: + homepage: http://www.pombase.org/ + name: Fission Yeast Phenotype Ontology + prefix: FYPO + mappings: + biocontext: FYPO + biolink: FYPO + bioportal: FYPO + fairsharing: FAIRsharing.4vr0ys + go: FYPO + obofoundry: fypo + ols: fypo + ontobee: FYPO + name: Fission Yeast Phenotype Ontology + obofoundry: + contact: vw253@cam.ac.uk + contact.github: ValWood + contact.label: Val Wood + contact.orcid: 0000-0001-6330-7526 + deprecated: false + description: FYPO is a formal ontology of phenotypes observed in fission yeast. + download.obo: http://purl.obolibrary.org/obo/fypo.obo + download.owl: http://purl.obolibrary.org/obo/fypo.owl + homepage: https://github.com/pombase/fypo + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Fission Yeast Phenotype Ontology + preferredPrefix: FYPO + prefix: fypo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/23658422 + title: 'FYPO: The Fission Yeast Phenotype Ontology.' + repository: https://github.com/pombase/fypo + ols: + description: A formal ontology of phenotypes observed in fission yeast. + download: http://purl.obolibrary.org/obo/fypo.owl + homepage: https://github.com/pombase/fypo + name: Fission Yeast Phenotype Ontology (FYPO) + prefix: fypo + version: 2022-04-28 + version.iri: http://purl.obolibrary.org/obo/fypo/releases/2022-04-28/fypo.owl + ontobee: + library: Library + name: Fission Yeast Phenotype Ontology + prefix: FYPO + pattern: ^\d{7}$ +ga4ghdos: + biocontext: + is_identifiers: true + is_obo: false + prefix: GA4GHDOS + uri_format: http://identifiers.org/ga4ghdos/$1 + mappings: + biocontext: GA4GHDOS + miriam: ga4ghdos + n2t: ga4ghdos + miriam: + deprecated: false + description: Assists in resolving data across cloud resources. + homepage: http://github.com/ga4gh/data-object-service-schemas + id: '00000671' + name: Data Object Service + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9\-:#/\.]+$ + prefix: ga4ghdos + sampleId: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d + uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 + n2t: + description: Assists in resolving data across cloud resources. + example: dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d + homepage: http://github.com/ga4gh/data-object-service-schemas + name: Data Object Service + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9\-:#/\.]+$ + prefix: ga4ghdos + uri_format: https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 +gabi: + biocontext: + is_identifiers: true + is_obo: false + prefix: GABI + uri_format: http://identifiers.org/gabi/$1 + mappings: + biocontext: GABI + miriam: gabi + n2t: gabi + ncbi: GABI + prefixcommons: gabi + miriam: + deprecated: false + description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. + homepage: http://www.gabipd.org/ + id: '00000164' + name: GABI + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gabi + sampleId: '2679240' + uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject + n2t: + description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. + example: '2679240' + homepage: http://www.gabipd.org/ + name: GABI at Max Planck + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gabi + uri_format: http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject + ncbi: + example: HA05J18 + homepage: http://www.gabipd.org/information/about.shtml + name: Network of Different Plant Genomic Research Projects + prefix: GABI + prefixcommons: + description: GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. + example: '2679240' + homepage: http://www.gabi.de/ + keywords: + - gene + - genome + - plant + name: Network of Different Plant Genomic Research Projects + pattern: ^\w+$ + prefix: gabi + pubmed_ids: + - '18812395' + uri_format: http://gabi.rzpd.de/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject +galen: + bioportal: + name: Galen Ontology + prefix: GALEN + comment: I really tried, but could not figure out what GALEN stands for + deprecated: true + example: MagnitudeValueType + homepage: https://www.opengalen.org + mappings: + bioportal: GALEN + name: GALEN +gard: + description: Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. + example: '6038' + homepage: https://rarediseases.info.nih.gov/diseases + name: Genetic and Rare Diseases Information Center + pattern: ^\d+$ + synonyms: + - GARD + - Genetic and Rare Diseases Information Center + wikidata: + prefix: P4317 +gateway: + mappings: + miriam: gateway + miriam: + deprecated: false + description: The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access. + homepage: https://www.hdruk.ac.uk + id: '00000796' + name: gateway + namespaceEmbeddedInLui: false + pattern: ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ + prefix: gateway + sampleId: fd8d0743-344a-4758-bb97-f8ad84a37357 + uri_format: https://web.www.healthdatagateway.org/dataset/$1 + name: Health Data Research Innovation Gateway +gaz: + biocontext: + is_identifiers: false + is_obo: true + prefix: GAZ + uri_format: http://purl.obolibrary.org/obo/GAZ_$1 + bioportal: + name: Gazetteer + prefix: GAZ + download_obo: http://purl.obolibrary.org/obo/gaz.obo + example: '00620027' + fairsharing: + abbreviation: GAZ + description: A controlled vocabulary following ontological rules that describes named geographical locations. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles, that describes places and place names and the relations between them. + id: '384' + name: Gazetteer + prefix: FAIRsharing.wkdjpb + subjects: + - Environmental Science + mappings: + biocontext: GAZ + bioportal: GAZ + fairsharing: FAIRsharing.wkdjpb + obofoundry: gaz + ols: gaz + ontobee: GAZ + obofoundry: + appears_in: + - scdo + contact: lschriml@som.umaryland.edu + contact.github: lschriml + contact.label: Lynn Schriml + contact.orcid: 0000-0001-8910-9851 + deprecated: true + description: A gazetteer constructed on ontological principles + download.obo: http://purl.obolibrary.org/obo/gaz.obo + download.owl: http://purl.obolibrary.org/obo/gaz.owl + homepage: http://environmentontology.github.io/gaz/ + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Gazetteer + prefix: gaz + repository: https://github.com/EnvironmentOntology/gaz + ols: + download: http://purl.obolibrary.org/obo/gaz.obo + name: gaz + prefix: gaz + ontobee: + library: Library + name: Gazetteer + prefix: GAZ + pattern: ^\d{8}$ + wikidata: + prefix: P6778 +gbif: + description: >- + Database of living organisms, taxonomic. + The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth. + example: '4238' + fairsharing: + abbreviation: GBIF.org + description: >- + GBIF—the Global Biodiversity Information Facility—is an international + network and data infrastructure funded by the world's governments and + aimed at providing anyone, anywhere, open access to data about all types + of life on Earth. + + + Strictly speaking, GBIF is not a data repository. Rather, GBIF indexes thousands of datasets through a distributed infrastructure involving more than 100 formal participants that supports hundreds of data-publishing institutions worldwide. GBIF.org makes the FAIR and open data discoverable and citable, assigning each download a DOI and storing it for an extended period of time. More than three peer-reviewed research articles make use of data from the GBIF network every day, in studies spanning the impacts of climate change, the spread of pests and diseases, priority areas for conservation and food security. + + + To share data with GBIF, follow this quick guide: http://www.gbif.org/publishing-data/quick-guide. To deposit or host data, we suggest using one of the trusted data hosting centres (DHC) listed in FAIRsharing.org that uses GBIF's IPT (Integrated Publishing Toolkit) software. The DHC provides data publishers with a hosted IPT account enabling them to manage and publish datasets through GBIF.org. + id: '2163' + name: GBIF.org + prefix: FAIRsharing.zv11j3 + subjects: + - Metagenomics + - Bioinformatics + - Taxonomy + - Marine Biology + - Biodiversity + - Natural Science + - Natural History + homepage: https://www.gbif.org/species + mappings: + fairsharing: FAIRsharing.zv11j3 + name: Global Biodiversity Information Facility + pattern: ^\d+$ + uri_format: https://www.gbif.org/species/$1 + wikidata: + prefix: P846 +gc: + comment: 'see comment here: https://github.com/obophenotype/ncbitaxon/issues/47' + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries. + example: '11' + homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html + name: Genetic Code + pattern: ^\d+$ + references: + - https://github.com/obophenotype/ncbitaxon/issues/47 + synonyms: + - gc_id + uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1 +gcst: + mappings: + miriam: gcst + n2t: gcst + miriam: + deprecated: false + description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. + homepage: https://www.ebi.ac.uk + id: '00000715' + name: GWAS Catalog + namespaceEmbeddedInLui: false + pattern: ^GCST\d{6}\d*$ + prefix: gcst + sampleId: GCST000035 + uri_format: https://www.ebi.ac.uk/gwas/studies/$1 + n2t: + description: The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. + example: GCST000035 + homepage: https://www.ebi.ac.uk/gwas/studies + name: GWAS Catalog + namespaceEmbeddedInLui: false + pattern: ^GCST\d{6}$ + prefix: gcst + uri_format: https://www.ebi.ac.uk/gwas/studies/$1 +gdc: + biocontext: + is_identifiers: true + is_obo: false + prefix: GDC + uri_format: http://identifiers.org/gdc/$1 + mappings: + biocontext: GDC + miriam: gdc + n2t: gdc + miriam: + deprecated: false + description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. + homepage: https://gdc.cancer.gov + id: '00000604' + name: Genomic Data Commons Data Portal + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ + prefix: gdc + sampleId: ae8c77fe-e6c8-44d5-8265-4a38c637bbef + uri_format: https://portal.gdc.cancer.gov/cases/$1 + n2t: + description: The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. + example: ae8c77fe-e6c8-44d5-8265-4a38c637bbef + homepage: https://gdc.cancer.gov + name: Genomic Data Commons + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ + prefix: gdc + uri_format: https://portal.gdc.cancer.gov/cases/$1 +gdsc: + cellosaurus: + category: Chemistry resources + homepage: https://www.cancerrxgene.org + name: Genomics of Drug Sensitivity in Cancer Project + prefix: GDSC + uri_format: https://www.cancerrxgene.org/translation/CellLine/$1 + mappings: + cellosaurus: GDSC + miriam: gdsc + n2t: gdsc + miriam: + deprecated: false + description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. + homepage: https://www.cancerrxgene.org + id: '00000678' + name: Genomics of Drug Sensitivity in Cancer + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: gdsc + sampleId: '1242' + uri_format: https://www.cancerrxgene.org/translation/Drug/$1 + n2t: + description: The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. + example: '1242' + homepage: https://www.cancerrxgene.org + name: Genomics of Drug Sensitivity in Cancer + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: gdsc + uri_format: https://www.cancerrxgene.org/translation/Drug/$1 +gecko: + bioportal: + name: Genomics Cohorts Knowledge Ontology + prefix: GECKO + example: '0000044' + fairsharing: + abbreviation: GECKO + description: GECKO is an ontology to represent genomics cohort attributes. The GECKO is maintained by the CINECA project, and standardises attributes commonly used for genomics cohort description as well as individual-level data items. + id: '3626' + name: Genomics Cohorts Knowledge Ontology + prefix: FAIRsharing.3da56b + subjects: + - Genomics + - Statistics + - Life Science + mappings: + bioportal: GECKO + fairsharing: FAIRsharing.3da56b + obofoundry: gecko + ols: gecko + ontobee: GECKO + obofoundry: + contact: rbca.jackson@gmail.com + contact.github: beckyjackson + contact.label: Rebecca Jackson + contact.orcid: 0000-0003-4871-5569 + deprecated: false + description: An ontology to represent genomics cohort attributes + download.owl: http://purl.obolibrary.org/obo/gecko.owl + homepage: https://github.com/IHCC-cohorts/GECKO + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Genomics Cohorts Knowledge Ontology + preferredPrefix: GECKO + prefix: gecko + repository: https://github.com/IHCC-cohorts/GECKO + ols: + description: An ontology to represent genomics cohort attributes. + download: http://purl.obolibrary.org/obo/gecko.owl + homepage: https://github.com/IHCC-cohorts/GECKO + name: Genomics Cohorts Knowledge Ontology + prefix: gecko + version: 2021-01-18 + version.iri: http://purl.obolibrary.org/obo/gecko/releases/2021-01-18/gecko.owl + ontobee: + library: Library + name: Genomics Cohorts Knowledge Ontology + prefix: GECKO + pattern: ^\d{7}$ +gemet: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts. + example: '627' + homepage: https://www.eionet.europa.eu/gemet/en/themes/ + name: General Multilingual Environmental Thesaurus + pattern: ^\d+$ + uri_format: https://www.eionet.europa.eu/gemet/en/concept/$1 +genatlas: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENATLAS + uri_format: http://identifiers.org/genatlas/$1 + fairsharing: + abbreviation: GenAtlas + description: GenAtlas is a database containing information on human genes, markers and phenotypes. + id: '1912' + name: GenAtlas + prefix: FAIRsharing.pmg2vd + subjects: + - Life Science + mappings: + biocontext: GENATLAS + fairsharing: FAIRsharing.pmg2vd + miriam: genatlas + n2t: genatlas + prefixcommons: genatlas + uniprot: GenAtlas + miriam: + deprecated: false + description: GenAtlas is a database containing information on human genes, markers and phenotypes. + homepage: http://genatlas.medecine.univ-paris5.fr/ + id: '00000208' + name: Genatlas + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: genatlas + sampleId: HBB + uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 + n2t: + description: GenAtlas is a database containing information on human genes, markers and phenotypes. + example: HBB + homepage: http://genatlas.medecine.univ-paris5.fr/ + name: Genatlas at Paris Descartes University + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: genatlas + uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 + prefixcommons: + description: GenAtlas is a database containing information on human genes, markers and phenotypes. + example: HBB + homepage: http://www.genatlas.org/ + keywords: + - disorder + - gene + - human + name: 'GenAtlas: human gene database' + pattern: ^\w+$ + prefix: genatlas + pubmed_ids: + - '9835018' + uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 + uniprot: + category: Organism-specific databases + identifier: '27' + name: 'GenAtlas: human gene database' + prefix: GenAtlas + uri_format: http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 +genbank: + biocontext: + is_identifiers: false + is_obo: false + prefix: GenBank + uri_format: http://www.ncbi.nlm.nih.gov/nuccore/$1 + cheminf: + description: [] + name: GenBank Nucleotide Identifier + obsolete: false + prefix: '000304' + description: GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). + example: U49845 + fairsharing: + abbreviation: GenBank + description: GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release. GenBank is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis. + id: '1547' + name: GenBank + prefix: FAIRsharing.9kahy4 + subjects: + - Functional Genomics + - Metagenomics + - Genomics + - Bioinformatics + - Data Management + - Virology + - Transcriptomics + - Epidemiology + go: + description: The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. + homepage: http://www.ncbi.nlm.nih.gov/Genbank/ + name: GenBank + prefix: GenBank + synonyms: + - GB + homepage: https://www.ncbi.nlm.nih.gov/genbank/ + mappings: + biocontext: GenBank + cheminf: '000304' + fairsharing: FAIRsharing.9kahy4 + go: GenBank + prefixcommons: genbank + uniprot: GenBank + name: GenBank + prefixcommons: + description: GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. + example: AP008229 + homepage: http://www.ncbi.nlm.nih.gov/genbank/ + keywords: + - DNA + name: GenBank + pattern: ^\w+$ + prefix: genbank + uri_format: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1 + uniprot: + category: Sequence databases + identifier: '28' + name: GenBank nucleotide sequence database + prefix: GenBank + uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 + uri_format: https://www.ncbi.nlm.nih.gov/nucleotide/$1 +genecards: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENECARDS + uri_format: http://identifiers.org/genecards/$1 + fairsharing: + abbreviation: GeneCards + description: GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes. + id: '2123' + name: Human Gene Database + prefix: FAIRsharing.g7jbvn + subjects: + - Genetics + - Life Science + - Transcriptomics + mappings: + biocontext: GENECARDS + fairsharing: FAIRsharing.g7jbvn + miriam: genecards + n2t: genecards + prefixcommons: genecards + uniprot: GeneCards + miriam: + deprecated: false + description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. + homepage: http://www.genecards.org/ + id: '00000323' + name: GeneCards + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+(\@)?$ + prefix: genecards + sampleId: ABL1 + uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 + n2t: + description: The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. + example: ABL1 + homepage: http://www.genecards.org/ + name: GeneCards at Weizmann Institute + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+(\@)?$ + prefix: genecards + uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 + prefixcommons: + description: GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes. + example: ABL1 + homepage: http://bioinfo.weizmann.ac.il/genecards/ + keywords: + - genome + name: 'GeneCards: human genes, protein and diseases' + pattern: ^\w+$ + prefix: genecards + pubmed_ids: + - '20689021' + uri_format: http://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 + uniprot: + category: Organism-specific databases + identifier: '30' + link_is_explicit: 'true' + name: 'GeneCards: human genes, protein and diseases' + prefix: GeneCards + uri_format: https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 +genedb: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENEDB + uri_format: http://identifiers.org/genedb/$1 + deprecated: true + fairsharing: + abbreviation: GeneDB + description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. + id: '1589' + name: GeneDB + prefix: FAIRsharing.j7esqq + subjects: + - Life Science + go: + homepage: http://www.genedb.org/gene/ + name: GeneDB + prefix: GeneDB + uri_format: http://www.genedb.org/gene/$1 + mappings: + biocontext: GENEDB + fairsharing: FAIRsharing.j7esqq + go: GeneDB + miriam: genedb + n2t: genedb + ncbi: GeneDB + prefixcommons: genedb + uniprot: GeneDB + wikidata: P3382 + miriam: + deprecated: false + description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. + homepage: https://www.genedb.org/ + id: '00000106' + name: GeneDB + namespaceEmbeddedInLui: false + pattern: ^[\w\d\.-]*$ + prefix: genedb + sampleId: LinJ.20.0070 + uri_format: https://www.genedb.org/gene/$1 + n2t: + description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. + example: LinJ.20.0070 + homepage: https://www.genedb.org/ + name: GeneDB at Sanger Institute + namespaceEmbeddedInLui: false + pattern: ^[\w\d\.-]*$ + prefix: genedb + uri_format: https://www.genedb.org/gene/$1 + name: GeneDB + ncbi: + example: SPCC285.16c + homepage: http://www.genedb.org/ + name: Curated gene database for Leishmania major and Trypanosoma brucei + prefix: GeneDB + prefixcommons: + description: GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. + example: Cj1536c + homepage: http://www.genedb.org/ + keywords: + - genome + - sequence + name: GeneDB + pattern: ^[\w\d\.-]*$ + prefix: genedb + pubmed_ids: + - '14681429' + uri_format: http://www.genedb.org/gene/$1 + uniprot: + category: Genome annotation databases + identifier: '199' + link_is_explicit: 'true' + name: GeneDB pathogen genome database from Sanger Institute + prefix: GeneDB + uri_format: https://www.genedb.org/gene/$1 + wikidata: + database: Q5531047 + database.homepage: http://www.genedb.org/ + database.label: GeneDB + homepage: http://www.genedb.org/ + name: GeneDB ID + prefix: P3382 + uri_format: https://www.genedb.org/gene/$1 +genefarm: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENEFARM + uri_format: http://identifiers.org/genefarm/$1 + fairsharing: + abbreviation: GeneFarm + description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. + id: '2116' + name: Structural and functional annotation of Arabidopsis thaliana gene and protein families + prefix: FAIRsharing.2mayq0 + subjects: + - Life Science + mappings: + biocontext: GENEFARM + fairsharing: FAIRsharing.2mayq0 + miriam: genefarm + n2t: genefarm + prefixcommons: genefarm + miriam: + deprecated: false + description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. + homepage: http://urgi.versailles.inra.fr/Genefarm/ + id: '00000211' + name: GeneFarm + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: genefarm + sampleId: '4892' + uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 + n2t: + description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. + example: '4892' + homepage: http://urgi.versailles.inra.fr/Genefarm/ + name: GeneFarm at Unité de Recherche en Génomique Végétale + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: genefarm + uri_format: https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 + prefixcommons: + description: GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. + example: '4892' + homepage: http://urgi.versailles.inra.fr/Genefarm/index.htpl + keywords: + - expression + - genome + - nucleotide + - sequence + name: Structural and functional annotation of Arabidopsis thaliana gene and protein families. + pattern: ^\d+$ + prefix: genefarm + pubmed_ids: + - '15608279' + uri_format: http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 +genepio: + biocontext: + is_identifiers: false + is_obo: true + prefix: GENEPIO + uri_format: http://purl.obolibrary.org/obo/GENEPIO_$1 + example: '0001885' + fairsharing: + abbreviation: GenEpiO + description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research food-borne pathogens, infectious disease surveillance and outbreak investigations. This includes descriptions of the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for food-borne infectious disease surveillance and outbreak investigations. + id: '279' + name: Genomic Epidemiology Ontology + prefix: FAIRsharing.y1mmbv + subjects: + - Genomics + - Epidemiology + mappings: + biocontext: GENEPIO + fairsharing: FAIRsharing.y1mmbv + obofoundry: genepio + ols: genepio + ontobee: GENEPIO + obofoundry: + contact: damion_dooley@sfu.ca + contact.github: ddooley + contact.label: Damion Dooley + contact.orcid: 0000-0002-8844-9165 + depends_on: + - chebi + - ncbitaxon + - po + - ro + - uberon + deprecated: false + description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. + download.owl: http://purl.obolibrary.org/obo/genepio.owl + homepage: http://genepio.org/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Genomic Epidemiology Ontology + preferredPrefix: GENEPIO + prefix: genepio + repository: https://github.com/GenEpiO/genepio + ols: + description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. + download: http://purl.obolibrary.org/obo/genepio.owl + homepage: http://genepio.org/ + name: Genomic Epidemiology Ontology + prefix: genepio + version: 2022-02-06 + version.iri: http://purl.obolibrary.org/obo/genepio/releases/2022-02-06/genepio.owl + ontobee: + library: Library + name: Genomic Epidemiology Ontology + prefix: GENEPIO + pattern: ^\d{7}$ +genetree: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENETREE + uri_format: http://identifiers.org/genetree/$1 + mappings: + biocontext: GENETREE + miriam: genetree + n2t: genetree + prefixcommons: genetree + uniprot: GeneTree + miriam: + deprecated: false + description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. + homepage: http://www.ensembl.org/ + id: '00000214' + name: GeneTree + namespaceEmbeddedInLui: false + pattern: ^ENSGT\d+$ + prefix: genetree + sampleId: ENSGT00550000074763 + uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 + n2t: + description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. + example: ENSGT00550000074763 + homepage: http://www.ensembl.org/ + name: GeneTree at Ensembl + namespaceEmbeddedInLui: false + pattern: ^ENSGT\d+$ + prefix: genetree + uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 + prefixcommons: + description: Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. + example: ENSGT00550000074763 + keywords: + - classification + - gene + - protein + name: Ensembl GeneTree + pattern: ^ENSGT\d+$ + prefix: genetree + pubmed_ids: + - '16381931' + uri_format: http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 + uniprot: + category: Phylogenomic databases + identifier: '162' + link_is_explicit: 'true' + name: Ensembl GeneTree + prefix: GeneTree + uri_format: http://www.ensemblgenomes.org/id-genetree/$1 +genewiki: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENEWIKI + uri_format: http://identifiers.org/genewiki/$1 + fairsharing: + abbreviation: Gene Wiki + description: 'The goal of the Gene Wiki is to apply community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated with the Molecular and Cellular Biology Wikiproject. Our specific aims are summarized as follows: To provide a well written and informative Wikipedia article for every notable human gene; To invite participation by interested lay editors, students, professionals, and academics from around the world; To integrate Gene Wiki articles with existing Wikipedia content through the use of internal wiki links increasing the value of both.' + id: '1677' + name: Gene Wiki + prefix: FAIRsharing.t3snf + subjects: + - Genetics + - Life Science + mappings: + biocontext: GENEWIKI + fairsharing: FAIRsharing.t3snf + miriam: genewiki + n2t: genewiki + uniprot: GeneWiki + miriam: + deprecated: false + description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. + homepage: http://en.wikipedia.org/wiki/Gene_Wiki + id: '00000487' + name: Gene Wiki + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: genewiki + sampleId: '1017' + uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 + n2t: + description: The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. + example: '1017' + homepage: http://en.wikipedia.org/wiki/Gene_Wiki + name: Gene Wiki through BioGPS + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: genewiki + uri_format: http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 + uniprot: + category: Miscellaneous databases + identifier: '180' + link_is_explicit: 'true' + name: The Gene Wiki collection of pages on human genes and proteins + prefix: GeneWiki + uri_format: https://en.wikipedia.org/wiki/$1 +geno: + biocontext: + is_identifiers: false + is_obo: true + prefix: GENO + uri_format: http://purl.obolibrary.org/obo/GENO_$1 + bioportal: + name: Genotype Ontology + prefix: GENO + download_obo: https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo + example: '0000632' + fairsharing: + abbreviation: GENO + description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. + id: '688' + name: Genotype Ontology + prefix: FAIRsharing.kpbna7 + subjects: [] + mappings: + biocontext: GENO + bioportal: GENO + fairsharing: FAIRsharing.kpbna7 + obofoundry: geno + ols: geno + ontobee: GENO + obofoundry: + contact: mhb120@gmail.com + contact.github: mbrush + contact.label: Matthew Brush + contact.orcid: 0000-0002-1048-5019 + deprecated: false + description: An integrated ontology for representing the genetic variations described in genotypes, and their causal relationships to phenotype and diseases. + download.owl: http://purl.obolibrary.org/obo/geno.owl + homepage: https://github.com/monarch-initiative/GENO-ontology/ + license: CC BY-SA 2.0 + license.url: https://creativecommons.org/licenses/by-sa/2.0/ + name: Genotype Ontology + preferredPrefix: GENO + prefix: geno + repository: https://github.com/monarch-initiative/GENO-ontology + ols: + description: >- + GENO is an OWL model of genotypes, their more fundamental sequence + components, and links to related biological and experimental entities. At + present many parts of the model are exploratory and set to undergo + refactoring. In addition, many classes and properties have GENO URIs but + are place holders for classes that will be imported from an external + ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will + implement a model of genotype-to-phenotype associations. This will support + description of asserted and inferred relationships between a genotypes, + phenotypes, and environments, and the evidence/provenance behind these + associations. + + + Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013 + download: http://purl.obolibrary.org/obo/geno.owl + homepage: https://github.com/monarch-initiative/GENO-ontology/ + name: GENO ontology + prefix: geno + version: 2022-03-05 + version.iri: http://purl.obolibrary.org/obo/geno/releases/2022-03-05/geno.owl + ontobee: + library: Library + name: Genotype Ontology + prefix: GENO + pattern: ^\d{7}$ +genpept: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENPEPT + uri_format: http://identifiers.org/genpept/$1 + mappings: + biocontext: GENPEPT + miriam: genpept + n2t: genpept + miriam: + deprecated: false + description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. + homepage: https://www.ncbi.nlm.nih.gov/protein + id: '00000345' + name: GenPept + namespaceEmbeddedInLui: false + pattern: ^\w{3}\d{5}(\.\d+)?$ + prefix: genpept + sampleId: CAA71118.1 + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept + n2t: + description: The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. + example: CAA71118.1 + homepage: https://www.ncbi.nlm.nih.gov/protein + name: GenPept at NCBI + namespaceEmbeddedInLui: false + pattern: ^\w{3}\d{5}(\.\d+)?$ + prefix: genpept + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept +genprop: + biocontext: + is_identifiers: true + is_obo: false + prefix: GENPROP + uri_format: http://identifiers.org/genprop/$1 + mappings: + biocontext: GENPROP + miriam: genprop + n2t: genprop + miriam: + deprecated: false + description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. + homepage: https://www.ebi.ac.uk/interpro/genomeproperties/ + id: '00000443' + name: Genome Properties + namespaceEmbeddedInLui: false + pattern: ^GenProp\d+$ + prefix: genprop + sampleId: GenProp0699 + uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1 + n2t: + description: Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. + example: GenProp0699 + homepage: https://www.ebi.ac.uk/interpro/genomeproperties/ + name: Genome Properties + namespaceEmbeddedInLui: false + pattern: ^GenProp\d+$ + prefix: genprop + uri_format: https://www.ebi.ac.uk/interpro/genomeproperties/#$1 +geo: + biocontext: + formatter: http://purl.obolibrary.org/obo/GEO_$1 + is_identifiers: false + is_obo: true + prefix: GEO + cellosaurus: + category: Gene expression databases + homepage: https://www.ncbi.nlm.nih.gov/geo/ + name: Gene Expression Omnibus + prefix: GEO + uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 + fairsharing: + abbreviation: GEO + description: The Geographical Entity Ontology (GEO) is an ontology of geographical entities (such as sovereign states and their administrative subdivisions) as well as various geographical regions (including but not limited to the specific ones over which the governments have jurisdiction). + id: '823' + name: Geographical Entity Ontology + prefix: FAIRsharing.27rndz + subjects: + - Human Geography + - Physical Geography + go: + homepage: http://www.ncbi.nlm.nih.gov/geo/ + name: NCBI Gene Expression Omnibus + prefix: GEO + uri_format: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$1 + mappings: + biocontext: GEO + cellosaurus: GEO + fairsharing: FAIRsharing.27rndz + go: GEO + miriam: geo + n2t: geo + prefixcommons: geo + miriam: + deprecated: false + description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. + homepage: https://www.ncbi.nlm.nih.gov/geo/ + id: '00000054' + name: GEO + namespaceEmbeddedInLui: false + pattern: ^G(PL|SM|SE|DS)\d+$ + prefix: geo + sampleId: GDS1234 + uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 + n2t: + description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. + example: GDS1234 + homepage: https://www.ncbi.nlm.nih.gov/geo/ + name: Gene Expression Omnibus at NCBI + namespaceEmbeddedInLui: false + pattern: ^G(PL|SM|SE|DS)\d+$ + prefix: geo + uri_format: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 + prefixcommons: + description: The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. + example: GDS1234 + homepage: http://www.ncbi.nlm.nih.gov/geo/ + keywords: + - gene expression + - genome + name: Gene Expression Omnibus + pattern: ^GDS\d+$ + prefix: geo + pubmed_ids: + - '11752295' + uri_format: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$1 +geogeo: + biocontext: + is_identifiers: false + is_obo: true + prefix: GEO + uri_format: http://purl.obolibrary.org/obo/GEO_$1 + bioportal: + name: Geographical Entity Ontology + prefix: GEO + example: '000000021' + mappings: + biocontext: GEO + bioportal: GEO + miriam: geogeo + obofoundry: geo + ols: geo + ontobee: GEO + miriam: + deprecated: false + description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in "The US declared war on Germany" vs. the US in "The plane entered US airspace". + homepage: https://github.com/ufbmi + id: '00000824' + name: Geographical Entity Ontology + namespaceEmbeddedInLui: false + pattern: ^GEO_[0-9]{9}$ + prefix: geogeo + sampleId: GEO_000000021 + uri_format: http://purl.obolibrary.org/obo/$1 + obofoundry: + contact: hoganwr@gmail.com + contact.label: Bill Hogan + deprecated: false + description: An ontology of geographical entities + download.owl: http://purl.obolibrary.org/obo/geo.owl + homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki + license: CC-BY 4.0 + name: Geographical Entity Ontology + prefix: geo + ols: + description: An ontology of geographical entities + download: http://purl.obolibrary.org/obo/geo.owl + homepage: https://github.com/ufbmi/geographical-entity-ontology/wiki + name: Geographical Entity Ontology + prefix: geo + version: 2016-03-26 + ontobee: + library: Library + name: Geographical Entity Ontology + prefix: GEO + pattern: ^\d{9}$ + preferred_prefix: GEOGEO + repository: https://github.com/ufbmi/geographical-entity-ontology + uri_format: http://purl.obolibrary.org/obo/GEO_$1 +geonames: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. + example: '3532759' + fairsharing: + abbreviation: GeoNames + description: GeoNames integrates geographical data such as names of places in various languages, elevation, population and others from various sources. Users may manually edit, correct and add new names using a user friendly wiki interface. + id: '2880' + name: GeoNames + prefix: FAIRsharing.56a0Uj + subjects: + - Demographics + - Geography + homepage: https://www.geonames.org + mappings: + fairsharing: FAIRsharing.56a0Uj + name: GeoNames + pattern: ^\d+$ + synonyms: + - Geomames + - Geonamaes + uri_format: https://www.geonames.org/$1 +geonames.feature: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. + example: ADM1 + homepage: https://www.geonames.org/export/codes.html + name: GeoNames Feature Code + uri_format: https://www.geonames.org/recent-changes/featurecode/$1/ +gexo: + bioportal: + name: Gene Expression Ontology + prefix: GEXO + download_obo: https://www.bio.ntnu.no/ontology/GeXO/gexo.obo + download_owl: https://www.bio.ntnu.no/ontology/GeXO/gexo.owl + fairsharing: + abbreviation: GeXO + description: An application ontology for the domain of gene expression. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO. + id: '1230' + name: Gene Expression Ontology + prefix: FAIRsharing.3e0sn4 + subjects: + - Life Science + mappings: + bioportal: GEXO + fairsharing: FAIRsharing.3e0sn4 + ols: gexo + no_own_terms: true + ols: + contact: vladimir.n.mironov@gmail.com + description: Gene Expression Ontology + download: http://www.bio.ntnu.no/ontology/GeXO/gexo.rdf + homepage: http://www.semantic-systems-biology.org/apo + name: Gene Expression Ontology + prefix: gexo + version: 2019-09-18 +ghr: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA). + example: saddan + homepage: https://medlineplus.gov/genetics/condition + name: Genetics Home Reference + uri_format: https://medlineplus.gov/genetics/condition/$1 +giardiadb: + biocontext: + is_identifiers: true + is_obo: false + prefix: GIARDIADB + uri_format: http://identifiers.org/giardiadb/$1 + fairsharing: + abbreviation: GiardiaDB + description: A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence. + id: '1880' + name: GiardiaDB + prefix: FAIRsharing.e7skwg + subjects: + - Life Science + mappings: + biocontext: GIARDIADB + fairsharing: FAIRsharing.e7skwg + miriam: giardiadb + n2t: giardiadb + prefixcommons: giardiadb + miriam: + deprecated: false + description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: https://giardiadb.org/giardiadb/ + id: '00000151' + name: GiardiaDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: giardiadb + sampleId: GL50803_102438 + uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1 + n2t: + description: GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: GL50803_102438 + homepage: https://giardiadb.org/giardiadb/ + name: GiardiaDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: giardiadb + uri_format: https://giardiadb.org/giardiadb/app/record/gene/$1 + prefixcommons: + description: A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence. + example: GL50803_102438 + homepage: http://giardiadb.org + keywords: + - eukaryotic + - genome + name: GiardiaDB + pattern: ^GL\d+_\d+$ + prefix: giardiadb + pubmed_ids: + - '18824479' + uri_format: http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=$1 +github: + example: biopragmatics/bioregistry + example_extras: + - biopragmatics + - cthoyt + fairsharing: + abbreviation: GitHub + description: GitHub Inc. is a Git-based software repository that provides version control. It offers all of the distributed version control and source code management (SCM) functionality of Git as well as adding its own features. It provides access control and several collaboration features such as bug tracking, feature requests, task management, and wikis for each project. It provides a number of different access levels, from free through to paid services. + id: '2667' + name: GitHub + prefix: FAIRsharing.c55d5e + subjects: + - Knowledge and Information Systems + - Subject Agnostic + - Software Engineering + mappings: + fairsharing: FAIRsharing.c55d5e + miriam: github + miriam: + deprecated: false + description: GitHub is an online host of Git source code repositories. + homepage: https://github.com/ + id: '00000853' + name: github + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$ + prefix: github + sampleId: identifiers-org/registry + uri_format: https://github.com/$1 + pattern: ^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ +gitlab: + fairsharing: + abbreviation: GitLab + description: GitLab is a Git-based source code repository with wiki and issue tracker functionality. It provides a number of different access levels, from free through to a number of paid services. + id: '3277' + name: GitLab + prefix: FAIRsharing.530e61 + subjects: + - Knowledge and Information Systems + - Subject Agnostic + - Software Engineering + mappings: + fairsharing: FAIRsharing.530e61 + miriam: gitlab + miriam: + deprecated: false + description: GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability. + homepage: https://gitlab.com/ + id: '00000901' + name: GitLab + namespaceEmbeddedInLui: false + pattern: ^[0-9A-Za-z_][0-9A-Za-z-_()\. ]*/[0-9A-Za-z_][0-9A-Za-z-_\. ]*$ + prefix: gitlab + sampleId: morpheus.lab/morpheus + uri_format: https://gitlab.com/$1 + pattern: ^.*/.*$ +glida.gpcr: + biocontext: + is_identifiers: true + is_obo: false + prefix: GLIDA.GPCR + uri_format: http://identifiers.org/glida.gpcr/$1 + mappings: + biocontext: GLIDA.GPCR + miriam: glida.gpcr + n2t: glida.gpcr + miriam: + deprecated: false + description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. + homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ + id: '00000493' + name: GLIDA GPCR + namespaceEmbeddedInLui: false + pattern: ^[A-Z-_0-9]+$ + prefix: glida.gpcr + sampleId: ACM1_HUMAN + uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1 + n2t: + description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. + example: ACM1_HUMAN + homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ + name: GLIDA GPCR at Kyoto University + namespaceEmbeddedInLui: false + pattern: ^[A-Z-_0-9]+$ + prefix: glida.gpcr + uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1 +glida.ligand: + biocontext: + is_identifiers: true + is_obo: false + prefix: GLIDA.LIGAND + uri_format: http://identifiers.org/glida.ligand/$1 + mappings: + biocontext: GLIDA.LIGAND + miriam: glida.ligand + n2t: glida.ligand + miriam: + deprecated: false + description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. + homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ + id: '00000494' + name: GLIDA Ligand + namespaceEmbeddedInLui: false + pattern: ^L\d+$ + prefix: glida.ligand + sampleId: L000001 + uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1 + n2t: + description: The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. + example: L000001 + homepage: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ + name: GLIDA Ligand at Kyoto University + namespaceEmbeddedInLui: false + pattern: ^L\d+$ + prefix: glida.ligand + uri_format: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1 +glycoepitope: + biocontext: + is_identifiers: true + is_obo: false + prefix: GLYCOEPITOPE + uri_format: http://identifiers.org/glycoepitope/$1 + mappings: + biocontext: GLYCOEPITOPE + miriam: glycoepitope + n2t: glycoepitope + miriam: + deprecated: false + description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. + homepage: https://www.glycoepitope.jp/epitopes/ + id: '00000478' + name: GlycoEpitope + namespaceEmbeddedInLui: false + pattern: ^EP\d{4}$ + prefix: glycoepitope + sampleId: EP0311 + uri_format: https://www.glycoepitope.jp/epitopes/$1 + n2t: + description: GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. + example: EP0311 + homepage: https://www.glycoepitope.jp/epitopes/ + name: GlycoEpitope at Ritsumeikan University + namespaceEmbeddedInLui: false + pattern: ^EP\d{4}$ + prefix: glycoepitope + uri_format: https://www.glycoepitope.jp/epitopes/$1 +glycomedb: + biocontext: + is_identifiers: true + is_obo: false + prefix: GLYCOMEDB + uri_format: http://identifiers.org/glycomedb/$1 + comment: this is exactly the same as glytoucan. Idk why there are two different ones + fairsharing: + abbreviation: GlycomeDB + description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. + id: '1888' + name: GlycomeDB + prefix: FAIRsharing.k5k0yh + subjects: + - Life Science + has_canonical: glytoucan + mappings: + biocontext: GLYCOMEDB + fairsharing: FAIRsharing.k5k0yh + miriam: glycomedb + n2t: glycomedb + prefixcommons: glycomedb + miriam: + deprecated: false + description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. + homepage: https://glytoucan.org/ + id: '00000114' + name: GlycomeDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: glycomedb + sampleId: G77500AY + uri_format: https://glytoucan.org/Structures/Glycans/$1 + n2t: + description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. + example: G77500AY + homepage: https://glytoucan.org/ + name: GlycomeDB carbohydrate structure database + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: glycomedb + uri_format: https://glytoucan.org/Structures/Glycans/$1 + prefixcommons: + description: GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. + example: '1' + homepage: http://www.glycome-db.org/showMenu.action?major=database + keywords: + - molecules + - small molecules + - structure + name: GlycomeDB Carbohydrate Structure Database + pattern: ^\d+$ + prefix: glycomedb + pubmed_ids: + - '19759275' + uri_format: http://www.glycome-db.org/database/showStructure.action?glycomeId=$1 +glyconavi: + example_extras: + - GN_GlyTouCan_G03681DA + fairsharing: + abbreviation: GlycoNAVI + description: GlycoNAVI is a repository of data relevant to carbohydrate research. It contains a free suite of carbohydrate research tools organized by domain, including glycans, proteins, lipids, genes, diseases and samples. + id: '1548' + name: GlycoNAVI + prefix: FAIRsharing.wvp1t7 + subjects: + - Organic Chemistry + - Chemistry + - Life Science + - Glycomics + mappings: + fairsharing: FAIRsharing.wvp1t7 + miriam: glyconavi + miriam: + deprecated: false + description: GlycoNAVI is a website for carbohydrate research. It consists of the "GlycoNAVI Database" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the "GlycoNAVI tools" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools. + homepage: https://www.noguchi.or.jp/ + id: '00000830' + name: GlycoNAVI + namespaceEmbeddedInLui: false + pattern: ^GN_[A-Za-z0-9]+$ + prefix: glyconavi + sampleId: GN_G03681DA + uri_format: https://glyconavi.org/hub/?id=$1 + pattern: ^GN_[A-Za-z0-9_:]+$ +glycopost: + fairsharing: + abbreviation: GlycoPOST + description: GlycoPOST is a mass spectrometry data repository for glycomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines. + id: '3185' + name: GlycoPOST + prefix: FAIRsharing.2y1KMt + subjects: + - Life Science + - Glycomics + mappings: + fairsharing: FAIRsharing.2y1KMt + miriam: glycopost + miriam: + deprecated: false + description: GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines. + homepage: https://glycopost.glycosmos.org + id: '00000721' + name: GlycoPOST + namespaceEmbeddedInLui: false + pattern: ^GPST[0-9]{6}$ + prefix: glycopost + sampleId: GPST000024 + uri_format: https://glycopost.glycosmos.org/entry/$1 +glygen: + description: GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. + example: G24361QY + fairsharing: + abbreviation: GlyGen + description: GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone. + id: '2874' + name: 'GlyGen: Computational and Informatics Resources for Glycoscience' + prefix: FAIRsharing.aI1J5W + subjects: + - Life Science + - Glycomics + homepage: https://glygen.org/glycan/ + mappings: + fairsharing: FAIRsharing.aI1J5W + uniprot: GlyGen + name: Computational and Informatics Resources for Glycoscience + uniprot: + category: PTM databases + identifier: '254' + link_is_explicit: 'true' + name: 'GlyGen: Computational and Informatics Resources for Glycoscience' + prefix: GlyGen + uri_format: https://glygen.org/protein/$1#glycosylation + uri_format: https://glygen.org/glycan/$1 +glytoucan: + biocontext: + is_identifiers: true + is_obo: false + prefix: GLYTOUCAN + uri_format: http://identifiers.org/glytoucan/$1 + mappings: + biocontext: GLYTOUCAN + miriam: glytoucan + n2t: glytoucan + miriam: + deprecated: false + description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. + homepage: https://glytoucan.org + id: '00000608' + name: GlyTouCan + namespaceEmbeddedInLui: false + pattern: ^G[0-9]{5}[A-Z]{2}$ + prefix: glytoucan + sampleId: G00054MO + uri_format: https://glytoucan.org/Structures/Glycans/$1 + n2t: + description: GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. + example: G00054MO + homepage: https://glytoucan.org + name: The Glycan Repository + namespaceEmbeddedInLui: false + pattern: ^G[0-9]{5}[A-Z]{2}$ + prefix: glytoucan + uri_format: https://glytoucan.org/Structures/Glycans/$1 +gmd: + biocontext: + is_identifiers: true + is_obo: false + prefix: GMD + uri_format: http://identifiers.org/gmd/$1 + fairsharing: + abbreviation: GMD + description: The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers. + id: '1729' + name: Golm Metabolome Database + prefix: FAIRsharing.jykmkw + subjects: + - Life Science + - Metabolomics + mappings: + biocontext: GMD + fairsharing: FAIRsharing.jykmkw + miriam: gmd + n2t: gmd + miriam: + deprecated: false + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. + homepage: http://gmd.mpimp-golm.mpg.de/ + id: '00000274' + name: Golm Metabolome Database + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd + sampleId: 68513255-fc44-4041-bc4b-4fd2fae7541d + uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx + n2t: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. + example: 68513255-fc44-4041-bc4b-4fd2fae7541d + homepage: http://gmd.mpimp-golm.mpg.de/ + name: Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd + uri_format: http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx +gmd.analyte: + biocontext: + is_identifiers: true + is_obo: false + prefix: GMD.ANALYTE + uri_format: http://identifiers.org/gmd.analyte/$1 + mappings: + biocontext: GMD.ANALYTE + miriam: gmd.analyte + n2t: gmd.analyte + miriam: + deprecated: false + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. + homepage: http://gmd.mpimp-golm.mpg.de/ + id: '00000426' + name: Golm Metabolome Database Analyte + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.analyte + sampleId: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 + uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1 + n2t: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. + example: 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 + homepage: http://gmd.mpimp-golm.mpg.de/ + name: Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.analyte + uri_format: http://gmd.mpimp-golm.mpg.de/Analytes/$1 +gmd.gcms: + biocontext: + is_identifiers: true + is_obo: false + prefix: GMD.GCMS + uri_format: http://identifiers.org/gmd.gcms/$1 + mappings: + biocontext: GMD.GCMS + miriam: gmd.gcms + n2t: gmd.gcms + miriam: + deprecated: false + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. + homepage: http://gmd.mpimp-golm.mpg.de/ + id: '00000424' + name: Golm Metabolome Database GC-MS spectra + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.gcms + sampleId: 53d583d8-40c6-40e1-9296-23f821cd77a5 + uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1 + n2t: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. + example: 53d583d8-40c6-40e1-9296-23f821cd77a5 + homepage: http://gmd.mpimp-golm.mpg.de/ + name: Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.gcms + uri_format: http://gmd.mpimp-golm.mpg.de/Spectrums/$1 +gmd.profile: + biocontext: + is_identifiers: true + is_obo: false + prefix: GMD.PROFILE + uri_format: http://identifiers.org/gmd.profile/$1 + mappings: + biocontext: GMD.PROFILE + miriam: gmd.profile + n2t: gmd.profile + miriam: + deprecated: false + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. + homepage: http://gmd.mpimp-golm.mpg.de/ + id: '00000423' + name: Golm Metabolome Database Profile + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.profile + sampleId: 10b38aaf-b977-4950-85b8-f4775f66658d + uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 + n2t: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. + example: 10b38aaf-b977-4950-85b8-f4775f66658d + homepage: http://gmd.mpimp-golm.mpg.de/ + name: Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.profile + uri_format: http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 +gmd.ref: + biocontext: + is_identifiers: true + is_obo: false + prefix: GMD.REF + uri_format: http://identifiers.org/gmd.ref/$1 + mappings: + biocontext: GMD.REF + miriam: gmd.ref + n2t: gmd.ref + miriam: + deprecated: false + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. + homepage: http://gmd.mpimp-golm.mpg.de/ + id: '00000425' + name: Golm Metabolome Database Reference Substance + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.ref + sampleId: 8cf84adb-b4db-4807-ac98-0004247c35df + uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 + n2t: + description: Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. + example: 8cf84adb-b4db-4807-ac98-0004247c35df + homepage: http://gmd.mpimp-golm.mpg.de/ + name: Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology + namespaceEmbeddedInLui: false + pattern: ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ + prefix: gmd.ref + uri_format: http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 +gmelin: + description: The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. + example: '1466' + homepage: https://link.springer.com/bookseries/562 + name: Gmelins Handbuch der anorganischen Chemie + pattern: ^[1-9][0-9]{3,6}$ + references: + - https://en.wikipedia.org/wiki/Gmelin_database + wikidata: + prefix: P1578 +gno: + bioportal: + name: Glycan Naming Ontology + prefix: GNO + example: '10004892' + mappings: + bioportal: GNO + obofoundry: gno + ols: gno + ontobee: GNO + name: Glycan Naming and Subsumption Ontology + obofoundry: + contact: nje5@georgetown.edu + contact.github: edwardsnj + contact.label: Nathan Edwards + contact.orcid: 0000-0001-5168-3196 + deprecated: false + description: GlyTouCan provides stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations). GNOme organizes these stable accessions for interative browsing, for text-based searching, and for automated reasoning with well-defined characterization levels. + download.json: http://purl.obolibrary.org/obo/gno.json + download.obo: http://purl.obolibrary.org/obo/gno.obo + download.owl: http://purl.obolibrary.org/obo/gno.owl + homepage: https://gnome.glyomics.org/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Glycan Naming and Subsumption Ontology (GNOme) + preferredPrefix: GNO + prefix: gno + repository: https://github.com/glygen-glycan-data/GNOme + ols: + description: An ontology for glycans based on GlyTouCan, but organized by subsumption. + download: http://purl.obolibrary.org/obo/gno.owl + homepage: https://gnome.glyomics.org/ + name: Glycan Naming Ontology + prefix: gno + version: 1.10.0 + version.iri: http://purl.obolibrary.org/obo/gno/2022-02-23/gno.owl + ontobee: + library: Library + name: Glycan Naming and Subsumption Ontology (GNOme) + prefix: GNO + pattern: ^\d{8}$ +gnpis: + biocontext: + is_identifiers: true + is_obo: false + prefix: GNPIS + uri_format: http://identifiers.org/gnpis/$1 + fairsharing: + abbreviation: GnpIS + description: GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools. + id: '2263' + name: Genetic and Genomic Information System + prefix: FAIRsharing.dw22y3 + subjects: + - Life Science + mappings: + biocontext: GNPIS + fairsharing: FAIRsharing.dw22y3 + miriam: gnpis + n2t: gnpis + miriam: + deprecated: false + description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. + homepage: https://urgi.versailles.inra.fr/gnpis/ + id: '00000627' + name: GnpIS + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: gnpis + sampleId: AY109603 + uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1 + n2t: + description: GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. + example: AY109603 + homepage: https://urgi.versailles.inra.fr/gnpis/ + name: GnpIS + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: gnpis + uri_format: https://urgi.versailles.inra.fr/gnpis/#result/term=$1 +go: + biocontext: + is_identifiers: false + is_obo: true + prefix: GO + uri_format: http://purl.obolibrary.org/obo/GO_$1 + bioportal: + name: Gene Ontology + prefix: GO + example: '0032571' + fairsharing: + abbreviation: GO + description: The Gene Ontology (GO) is a structured vocabulary for use by the research community for the annotation of genes, gene products and sequences. The GO defines concepts/classes used to describe gene function and relationships between these concepts. + id: '1417' + name: Gene Ontology + prefix: FAIRsharing.6xq0ee + subjects: + - Life Science + go: + homepage: http://amigo.geneontology.org/ + name: Gene Ontology Database + prefix: GO + mappings: + biocontext: GO + bioportal: GO + fairsharing: FAIRsharing.6xq0ee + go: GO + miriam: go + n2t: go + ncbi: GO + obofoundry: go + ols: go + ontobee: GO + prefixcommons: go + uniprot: GO + miriam: + deprecated: false + description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. + homepage: http://amigo.geneontology.org/ + id: '00000022' + name: Gene Ontology + namespaceEmbeddedInLui: true + pattern: ^GO:\d{7}$ + prefix: go + providers: + - code: quickgo + description: QuickGO (Gene Ontology browser) + homepage: https://www.ebi.ac.uk/QuickGO/ + name: QuickGO (Gene Ontology browser) + uri_format: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1 + - code: CURATOR_REVIEW + description: GO Browser + homepage: http://www.informatics.jax.org/searches/GO_form.shtml + name: GO Browser + uri_format: http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1 + - code: CURATOR_REVIEW + description: GO through PANTHER + homepage: http://www.pantherdb.org/ + name: GO through PANTHER + uri_format: http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1 + sampleId: '0006915' + uri_format: http://amigo.geneontology.org/amigo/term/GO:$1 + n2t: + description: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. + example: '0006915' + homepage: http://amigo.geneontology.org/ + name: AmiGO 2 + namespaceEmbeddedInLui: true + pattern: ^GO:\d{7}$ + prefix: go + uri_format: http://amigo.geneontology.org/amigo/term/GO:$1 + ncbi: + example: '123' + homepage: http://amigo.geneontology.org/ + name: Gene Ontology Database identifier + prefix: GO + obofoundry: + appears_in: + - agro + - chiro + - cl + - ecocore + - ecto + - envo + - maxo + - pcl + - pco + - planp + - uberon + - xpo + - zp + contact: suzia@stanford.edu + contact.github: suzialeksander + contact.label: Suzi Aleksander + contact.orcid: 0000-0001-6787-2901 + depends_on: + - cl + - ncbitaxon + - ro + - uberon + deprecated: false + description: An ontology for describing the function of genes and gene products + download.json: http://purl.obolibrary.org/obo/go.json + download.obo: http://purl.obolibrary.org/obo/go.obo + download.owl: http://purl.obolibrary.org/obo/go.owl + homepage: http://geneontology.org/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Gene Ontology + preferredPrefix: GO + prefix: go + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/10802651 + title: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium' + - id: https://www.ncbi.nlm.nih.gov/pubmed/33290552 + title: 'The Gene Ontology resource: enriching a GOld mine' + repository: https://github.com/geneontology/go-ontology + twitter: news4go + ols: + description: The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. + download: http://purl.obolibrary.org/obo/go.owl + name: Gene Ontology + prefix: go + version: 2022-03-10 + version.iri: http://purl.obolibrary.org/obo/go/releases/2022-03-10/go.owl + ontobee: + library: Foundry + name: Gene Ontology + prefix: GO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1070' + description: 'The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains: cellular component, molecular function, and biological process.' + example: '0006915' + homepage: http://www.geneontology.org/ + keywords: + - obo + - gene + - ontology + name: The Gene Ontology + pattern: ^\d{7}$ + prefix: go + pubmed_ids: + - '14681407' + - '10802651' + uri_format: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:$1 + synonyms: + - gobp + - gobpid + - gocc + - goccid + - gomf + - gomfid + uniprot: + category: Ontologies + identifier: '37' + link_is_explicit: 'true' + name: Gene Ontology + prefix: GO + uri_format: https://www.ebi.ac.uk/QuickGO/term/$1 + wikidata: + prefix: P686 +go.model: + description: GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform. + example: 5fce9b7300001250 + go: + homepage: http://www.geneontology.org/gocam + name: Gene Ontology Causal Activity Model Database + prefix: gomodel + uri_format: http://www.geneontology.org/gocam/$1 + mappings: + go: gomodel + name: Gene Ontology Causal Assembly Model + uri_format: noctua.geneontology.org/editor/graph/gomodel:$1 +go.ref: + banana: GO_REF + biocontext: + is_identifiers: false + is_obo: false + prefix: GO_REF + uri_format: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:$1 + go: + homepage: http://current.geneontology.org/metadata/gorefs/index.html + name: Gene Ontology Database references + prefix: GO_REF + mappings: + biocontext: GO_REF + go: GO_REF + miriam: go_ref + n2t: go.ref + miriam: + deprecated: false + description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. + homepage: http://www.geneontology.org/cgi-bin/references.cgi + id: '00000450' + name: Gene Ontology Reference + namespaceEmbeddedInLui: true + pattern: ^GO_REF:\d{7}$ + prefix: go_ref + sampleId: '0000041' + uri_format: https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md + n2t: + description: The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. + example: GO_REF:0000041 + homepage: http://www.geneontology.org/cgi-bin/references.cgi + name: Gene Ontology Reference at The Gene Ontology Consortium + namespaceEmbeddedInLui: false + pattern: ^GO_REF:\d{7}$ + prefix: go.ref + uri_format: http://www.geneontology.org/cgi-bin/references.cgi#$1 + pattern: ^\d{7}$ +go.resource: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A database-specific registry supporting curation in the Gene Ontology + example: CHEBI + homepage: http://geneontology.org/ + name: Gene Ontology Registry + uri_format: https://bioregistry.io/metaregistry/go/$1 +goa: + biocontext: + is_identifiers: true + is_obo: false + prefix: GOA + uri_format: http://identifiers.org/goa/$1 + fairsharing: + abbreviation: GOA + description: The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotation supplied by members of the Gene Onotology Consortium and computationally assigned GO terms describing gene products. Annotation type is clearly indicated by associated evidence codes and there are links to the source data. + id: '1852' + name: Gene Ontology Annotation Database + prefix: FAIRsharing.7zffgc + subjects: + - Life Science + - Biology + mappings: + biocontext: GOA + fairsharing: FAIRsharing.7zffgc + miriam: goa + n2t: goa + ncbi: GOA + prefixcommons: goa + miriam: + deprecated: false + description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. + homepage: https://www.ebi.ac.uk/GOA/ + id: '00000196' + name: GOA + namespaceEmbeddedInLui: false + pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ + prefix: goa + sampleId: P12345 + uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1 + n2t: + description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. + example: P12345 + homepage: https://www.ebi.ac.uk/GOA/ + name: GOA through QuickGO + namespaceEmbeddedInLui: false + pattern: ^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$ + prefix: goa + uri_format: https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1 + name: Gene Ontology Annotation Database + ncbi: + example: P01100 + homepage: http://www.ebi.ac.uk/GOA/ + name: Gene Ontology Annotation Database Identifier + prefix: GOA + prefixcommons: + description: The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. + example: go:0006915 + homepage: http://www.ebi.ac.uk/GOA + keywords: + - gene + - ontology + - protein + name: Gene Ontology Annotation + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: goa + pubmed_ids: + - '18957448' + uri_format: http://www.ebi.ac.uk/QuickGO/GTerm?id=$1 + provides: uniprot +goche: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Represent chemical entities having particular CHEBI roles + download_owl: https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl + example: '25512' + homepage: https://github.com/geneontology/go-ontology + name: GO Chemicals + pattern: ^\d+$ + preferred_prefix: GOCHE + references: + - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400 + - https://github.com/geneontology/go-ontology/issues/19535 + repository: https://github.com/geneontology/go-ontology + synonyms: + - go.chebi + - go.chemical + - go.chemicals +goeco: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported. + example: IPI + homepage: http://geneontology.org/docs/guide-go-evidence-codes/ + name: GO Evidence Code +gold: + fairsharing: + abbreviation: GOLD + description: 'The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.' + id: '1661' + name: Genomes OnLine Database + prefix: FAIRsharing.5q1p14 + subjects: + - Metagenomics + - Genomics + - Phylogenetics + - Metabolomics + mappings: + fairsharing: FAIRsharing.5q1p14 + miriam: gold + prefixcommons: gold + miriam: + deprecated: false + description: 'The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.' + homepage: https://gold.jgi.doe.gov/ + id: '00000733' + name: Genomes OnLine Database (GOLD) + namespaceEmbeddedInLui: false + pattern: ^[A-Z][a-z][0-9]+$ + prefix: gold + sampleId: Gs0000008 + uri_format: https://gold.jgi.doe.gov/resolver?id=$1 + name: Genomes Online Database + prefixcommons: + description: 'GOLD: Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects, as well as metagenomes and metadata, around the world.' + example: Gc01070 + homepage: http://www.genomesonline.org/ + keywords: + - genome + name: Genomes Online Database + pattern: ^G[a-z]\d+$ + prefix: gold + uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 +gold.genome: + biocontext: + is_identifiers: true + is_obo: false + prefix: GOLD.GENOME + uri_format: http://identifiers.org/gold.genome/$1 + mappings: + biocontext: GOLD.GENOME + miriam: gold.genome + n2t: gold.genome + miriam: + deprecated: false + description: >- + - DEPRECATION NOTE - + + Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. + + + The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes. + homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi + id: '00000401' + name: GOLD genome + namespaceEmbeddedInLui: false + pattern: ^(Gi|Gc)\d+$ + prefix: gold.genome + sampleId: Gi07796 + uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1 + n2t: + description: The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes. + example: Gi07796 + homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi + name: GOLD genome at Department of Energy Joint Genome Institute + namespaceEmbeddedInLui: false + pattern: ^[Gi|Gc]\d+$ + prefix: gold.genome + uri_format: http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1 +gold.meta: + biocontext: + is_identifiers: true + is_obo: false + prefix: GOLD.META + uri_format: http://identifiers.org/gold.meta/$1 + mappings: + biocontext: GOLD.META + miriam: gold.meta + n2t: gold.meta + miriam: + deprecated: false + description: >- + - DEPRECATION NOTE - + + Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. + + + The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples. + homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi + id: '00000402' + name: GOLD metadata + namespaceEmbeddedInLui: false + pattern: ^Gm\d+$ + prefix: gold.meta + sampleId: Gm00047 + uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 + n2t: + description: The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples. + example: Gm00047 + homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi + name: GOLD metadata at Department of Energy Joint Genome Institute + namespaceEmbeddedInLui: false + pattern: ^Gm\d+$ + prefix: gold.meta + uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 +google.patent: + biocontext: + is_identifiers: true + is_obo: false + prefix: GOOGLE.PATENT + uri_format: http://identifiers.org/google.patent/$1 + cellosaurus: + category: Reference resources + homepage: https://patents.google.com + name: Google Patents + prefix: Patent + uri_format: https://patents.google.com/patent/$1 + mappings: + biocontext: GOOGLE.PATENT + cellosaurus: Patent + miriam: google.patent + n2t: google.patent + miriam: + deprecated: false + description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. + homepage: https://www.google.com/patents/ + id: '00000537' + name: Google Patents + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}\d+([A-Z])?$ + prefix: google.patent + sampleId: US4145692 + uri_format: https://www.google.com/patents/$1 + n2t: + description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. + example: US4145692 + homepage: https://www.google.com/patents/ + name: Google Patents at Google + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}\d+([A-Z])?$ + prefix: google.patent + uri_format: https://www.google.com/patents/$1 + synonyms: + - patent +google.scholar: + biolink: + is_identifiers: false + is_obo: false + prefix: GSID + uri_format: https://scholar.google.com/citations?user=$1 + description: 'Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.' + example: PjrpzUIAAAAJ + homepage: https://scholar.google.com/ + mappings: + biolink: GSID + name: Google Scholar Researcher +gorel: + biolink: + is_identifiers: false + is_obo: true + prefix: GOREL + uri_format: http://purl.obolibrary.org/obo/GOREL_$1 + description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. + download_owl: ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl + example: '0002005' + go: + description: Additional relations pending addition into RO + name: GO Extensions to OBO Relation Ontology Ontology + prefix: GOREL + homepage: http://geneontology.org/docs/ontology-relations/ + mappings: + biolink: GOREL + go: GOREL + name: GO Relations + pattern: ^\d{7}$ +gpcrdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: GPCRDB + uri_format: http://identifiers.org/gpcrdb/$1 + fairsharing: + abbreviation: GPCRdb + description: The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models. + id: '1832' + name: Information system for G protein-coupled receptors + prefix: FAIRsharing.e4n3an + subjects: + - Life Science + mappings: + biocontext: GPCRDB + fairsharing: FAIRsharing.e4n3an + miriam: gpcrdb + n2t: gpcrdb + prefixcommons: gpcrdb + uniprot: GPCRDB + miriam: + deprecated: false + description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. + homepage: http://www.gpcrdb.org/ + id: '00000212' + name: GPCRDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gpcrdb + sampleId: RL3R1_HUMAN + uri_format: http://www.gpcrdb.org/protein/$1/ + n2t: + description: The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. + example: RL3R1_HUMAN + homepage: http://www.gpcrdb.org/ + name: GPCRDB at Radboud University + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gpcrdb + uri_format: http://www.gpcrdb.org/protein/$1/ + name: G protein-coupled receptor database + prefixcommons: + description: The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, many different types of computationally derived data are stored such as multiple sequence alignments and homology models. + example: RL3R1_HUMAN + homepage: http://www.gpcr.org/7tm/ + keywords: + - small molecule + - protein + name: Information system for G protein-coupled receptors (GPCRs) + pattern: ^\w+$ + prefix: gpcrdb + pubmed_ids: + - '21045054' + uri_format: http://www.gpcr.org/7tm/proteins/$1 + uniprot: + category: Protein family/group databases + identifier: '38' + name: Information system for G protein-coupled receptors (GPCRs) + prefix: GPCRDB + uri_format: https://gpcrdb.org/protein/$1/ + uri_format: https://gpcrdb.org/protein/$1 +gpmdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: GPMDB + uri_format: http://identifiers.org/gpmdb/$1 + fairsharing: + abbreviation: gpmDB + description: 'The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.' + id: '1949' + name: The Global Proteome Machine Database + prefix: FAIRsharing.fhcmwq + subjects: + - Bioinformatics + - Proteomics + mappings: + biocontext: GPMDB + fairsharing: FAIRsharing.fhcmwq + miriam: gpmdb + n2t: gpmdb + miriam: + deprecated: false + description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. + homepage: http://gpmdb.thegpm.org/ + id: '00000649' + name: GPMDB + namespaceEmbeddedInLui: false + pattern: ^GPM\d+$ + prefix: gpmdb + providers: + - code: omicsdi + description: GPMDB through OmicsDI + homepage: https://www.omicsdi.org/ + name: GPMDB through OmicsDI + uri_format: https://www.omicsdi.org/dataset/gpmdb/$1 + sampleId: GPM32310002988 + uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1 + n2t: + description: The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. + example: GPM32310002988 + homepage: http://gpmdb.thegpm.org/ + name: GPMDB + namespaceEmbeddedInLui: false + pattern: ^GPM\d+$ + prefix: gpmdb + uri_format: http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1 + name: Global Proteome Machine Database +graingenes.reference: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A database for Triticeae and Avena references. + example: WGS-95-1333 + homepage: http://wheat.pw.usda.gov + name: GrainGenes + uri_format: https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1 +graingenes.symbol: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A database for Triticeae and Avena gene symbols. + example: 1-FEH+w3 + homepage: http://wheat.pw.usda.gov + name: GrainGenes + uri_format: http://wheat.pw.usda.gov/report?class=gene;name=$1 +gramene.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: GRAMENE.GENE + uri_format: http://identifiers.org/gramene.gene/$1 + go: + homepage: http://www.gramene.org/ + name: Gramene + prefix: GR_GENE + synonyms: + - GR_gene + uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 + mappings: + biocontext: GRAMENE.GENE + go: GR_GENE + miriam: gramene.gene + n2t: gramene.gene + miriam: + deprecated: false + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. + homepage: http://www.gramene.org/ + id: '00000182' + name: Gramene genes + namespaceEmbeddedInLui: false + pattern: ^GR\:\d+$ + prefix: gramene.gene + sampleId: GR:0080039 + uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 + n2t: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. + example: GR:0080039 + homepage: http://www.gramene.org/ + name: Gramene Genes at Cold Spring Harbor + namespaceEmbeddedInLui: false + pattern: ^GR\:\d+$ + prefix: gramene.gene + uri_format: http://www.gramene.org/db/genes/search_gene?acc=$1 + name: Gramene Gene + synonyms: + - GR_GENE +gramene.growthstage: + banana: gramene.growthstage:GRO\ + biocontext: + is_identifiers: true + is_obo: false + prefix: GRAMENE.GROWTHSTAGE + uri_format: http://identifiers.org/gramene.growthstage/$1 + mappings: + biocontext: GRAMENE.GROWTHSTAGE + miriam: gramene.growthstage + n2t: gramene.growthstage + miriam: + deprecated: false + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. + homepage: http://www.gramene.org/ + id: '00000508' + name: Gramene Growth Stage Ontology + namespaceEmbeddedInLui: true + pattern: ^GRO\:\d+$ + prefix: gramene.growthstage + sampleId: '0007133' + uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 + n2t: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. + example: '0007133' + homepage: http://www.gramene.org/ + name: Gramene Growth Stage Ontology at Cold Spring Harbor + namespaceEmbeddedInLui: true + pattern: ^GRO\:\d+$ + prefix: gramene.growthstage + uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 + name: Gramene Growth Stage Ontology + namespace_in_lui: false + pattern: ^\d{7}$ + uri_format: http://www.gramene.org/db/ontology/search?id=GRO:$1 +gramene.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: GRAMENE.PROTEIN + uri_format: http://identifiers.org/gramene.protein/$1 + go: + homepage: http://www.gramene.org/ + name: Gramene + prefix: GR_PROTEIN + synonyms: + - GR_protein + uri_format: http://www.gramene.org/db/protein/protein_search?acc=$1 + mappings: + biocontext: GRAMENE.PROTEIN + go: GR_PROTEIN + miriam: gramene.protein + n2t: gramene.protein + miriam: + deprecated: false + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. + homepage: http://www.gramene.org/ + id: '00000181' + name: Gramene protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: gramene.protein + sampleId: '78073' + uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1 + n2t: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. + example: '78073' + homepage: http://www.gramene.org/ + name: Gramene Protein at Cold Spring Harbor + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: gramene.protein + uri_format: http://www.gramene.org/db/protein/protein_search?protein_id=$1 + name: Gramene protein + synonyms: + - GR_PROTEIN +gramene.qtl: + biocontext: + is_identifiers: true + is_obo: false + prefix: GRAMENE.QTL + uri_format: http://identifiers.org/gramene.qtl/$1 + go: + homepage: http://www.gramene.org/ + name: Gramene + prefix: GR_QTL + uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 + mappings: + biocontext: GRAMENE.QTL + go: GR_QTL + miriam: gramene.qtl + n2t: gramene.qtl + miriam: + deprecated: false + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. + homepage: http://www.gramene.org/ + id: '00000184' + name: Gramene QTL + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gramene.qtl + sampleId: CQG5 + uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 + n2t: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. + example: CQG5 + homepage: http://www.gramene.org/ + name: Gramene Quantitative Trait Loci at Cold Spring Harbor + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gramene.qtl + uri_format: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1 + name: Gramene QTL + synonyms: + - GR_QTL +gramene.reference: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Literature references in Gramene + example: '6200' + homepage: http://www.gramene.org + name: Gramene Reference + pattern: ^\d+$ + synonyms: + - gramene.ref + uri_format: http://www.gramene.org/db/literature/pub_search?ref_id=$1 +gramene.taxonomy: + biocontext: + is_identifiers: true + is_obo: false + prefix: GRAMENE.TAXONOMY + uri_format: http://identifiers.org/gramene.taxonomy/$1 + mappings: + biocontext: GRAMENE.TAXONOMY + miriam: gramene.taxonomy + n2t: gramene.taxonomy + miriam: + deprecated: false + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. + homepage: http://www.gramene.org/ + id: '00000183' + name: Gramene Taxonomy + namespaceEmbeddedInLui: false + pattern: ^GR\_tax\:\d+$ + prefix: gramene.taxonomy + sampleId: GR_tax:013681 + uri_format: http://www.gramene.org/db/ontology/search?id=$1 + n2t: + description: Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. + example: GR_tax:013681 + homepage: http://www.gramene.org/ + name: Gramene Taxonomy at Cold Spring Harbor + namespaceEmbeddedInLui: false + pattern: ^GR\_tax\:\d+$ + prefix: gramene.taxonomy + uri_format: http://www.gramene.org/db/ontology/search?id=$1 +grassbase: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species. + example: imp10873 + homepage: https://www.kew.org/data/grasses-syn/index.htm + name: GrassBase + pattern: ^(imp|gen)\d{5}$ + uri_format: https://www.kew.org/data/grasses-db/www/$1 +greengenes: + biocontext: + is_identifiers: true + is_obo: false + prefix: GREENGENES + uri_format: http://identifiers.org/greengenes/$1 + fairsharing: + abbreviation: Greengenes + description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. + id: '1947' + name: Greengenes + prefix: FAIRsharing.bpxgb6 + subjects: + - Genetics + - Life Science + mappings: + biocontext: GREENGENES + fairsharing: FAIRsharing.bpxgb6 + miriam: greengenes + n2t: greengenes + ncbi: Greengenes + prefixcommons: greengenes + miriam: + deprecated: false + description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. + homepage: http://greengenes.lbl.gov/ + id: '00000165' + name: GreenGenes + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: greengenes + sampleId: '100000' + uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 + n2t: + description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. + example: '100000' + homepage: http://greengenes.lbl.gov/ + name: GreenGenes at Lawrence Berkeley + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: greengenes + uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 + ncbi: + example: '269185' + homepage: http://greengenes.lbl.gov/ + name: 16S rRNA gene database + prefix: Greengenes + prefixcommons: + description: A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. + example: '100000' + homepage: http://greengenes.lbl.gov + keywords: + - RNA + name: Greengenes:16S rRNA gene database + pattern: ^\d+$ + prefix: greengenes + pubmed_ids: + - '16820507' + uri_format: http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1 +grid: + biocontext: + is_identifiers: true + is_obo: false + prefix: GRID + uri_format: http://identifiers.org/grid/$1 + fairsharing: + abbreviation: GRID + description: Global Research Identifier Database (GRID) stores information on research-related organisations worldwide. GRID record contains a unique GRID ID, relevant metadata, and relationships between associated institutions. + id: '3040' + name: Global Research Identifier Database + prefix: FAIRsharing.0pUMYW + subjects: + - Data Management + mappings: + biocontext: GRID + fairsharing: FAIRsharing.0pUMYW + miriam: grid + n2t: grid + miriam: + deprecated: false + description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. + homepage: https://www.grid.ac/ + id: '00000593' + name: GRID + namespaceEmbeddedInLui: false + pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ + prefix: grid + sampleId: grid.225360.0 + uri_format: https://www.grid.ac/institutes/$1 + n2t: + description: International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. + example: grid.225360.0 + homepage: https://www.grid.ac/ + name: GRID at Digital Science & Research Ltd. + namespaceEmbeddedInLui: false + pattern: ^grid\.[0-9]+\.[a-f0-9]{1,2}$ + prefix: grid + uri_format: https://www.grid.ac/institutes/$1 + name: Global Research Identifier Database +grin.taxonomy: + biocontext: + is_identifiers: true + is_obo: false + prefix: GRIN.TAXONOMY + uri_format: http://identifiers.org/grin.taxonomy/$1 + go: + homepage: https://www.ars-grin.gov/ + name: Germplasm Resources Information Network + prefix: GRIN + synonyms: + - grin + uri_format: https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=$1 + mappings: + biocontext: GRIN.TAXONOMY + go: GRIN + miriam: grin.taxonomy + n2t: grin.taxonomy + ncbi: GRIN + miriam: + deprecated: false + description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. + homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en + id: '00000166' + name: GRIN Plant Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: grin.taxonomy + sampleId: '19333' + uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1 + n2t: + description: GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. + example: '19333' + homepage: http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en + name: GRIN at Maryland + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: grin.taxonomy + uri_format: http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1 + ncbi: + example: '1005973' + homepage: http://www.ars-grin.gov/ + name: Germplasm Resources Information Network + prefix: GRIN +gro: + bioportal: + name: Gene Regulation Ontology + prefix: GRO + deprecated: true + mappings: + bioportal: GRO +grsdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: GRSDB + uri_format: http://identifiers.org/grsdb/$1 + mappings: + biocontext: GRSDB + miriam: grsdb + n2t: grsdb + prefixcommons: grsdb + miriam: + deprecated: false + description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. + homepage: http://bioinformatics.ramapo.edu/GRSDB2/ + id: '00000495' + name: GRSDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: grsdb + sampleId: '10142' + uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 + n2t: + description: GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. + example: '10142' + homepage: http://bioinformatics.ramapo.edu/GRSDB2/ + name: GRSDB v2 at Ramapo College of New Jersey + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: grsdb + uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 + name: G-Rich Sequences Database + prefixcommons: + description: GRSDB2 is a second generation database of G-quadruplexes. Like its first version, GRSDB, it contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). + example: '3191' + homepage: http://bioinformatics.ramapo.edu/GRSDB2/ + keywords: + - DNA + - RNA + name: GRSDB + pattern: ^\d+$ + prefix: grsdb + uri_format: http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 +gsfa: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The "Codex General Standard for Food Additives" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database. + example: '174' + homepage: http://www.fao.org/gsfaonline + name: General Standard for Food Additives Online Database + pattern: ^\d+$ + synonyms: + - FAO/WHO_standards + uri_format: http://www.fao.org/gsfaonline/additives/details.html?id=$1 +gsso: + bioportal: + name: Gender, Sex, and Sexual Orientation Ontology + prefix: GSSO + mappings: + bioportal: GSSO + miriam: gsso + obofoundry: gsso + ols: gsso + ontobee: GSSO + miriam: + deprecated: false + description: The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. + homepage: https://bioportal.bioontology.org/ + id: '00000712' + name: Gender, Sex, and Sexual Orientation (GSSO) Ontology + namespaceEmbeddedInLui: true + pattern: ^GSSO:\d{6}$ + prefix: gsso + sampleId: '002368' + uri_format: http://purl.obolibrary.org/obo/GSSO_$1 + name: Gender, Sex, and Sexual Orientation Ontology + obofoundry: + appears_in: + - ontoavida + - scdo + contact: kronkcj@mail.uc.edu + contact.github: Superraptor + contact.label: Clair Kronk + contact.orcid: 0000-0001-8397-8810 + deprecated: false + description: The Gender, Sex, and Sexual Orientation (GSSO) ontology has terms for annotating interdisciplinary information concerning gender, sex, and sexual orientation for primary usage in the biomedical and adjacent sciences. + download.json: http://purl.obolibrary.org/obo/gsso.json + download.obo: http://purl.obolibrary.org/obo/gsso.obo + download.owl: http://purl.obolibrary.org/obo/gsso.owl + homepage: https://gsso.research.cchmc.org/ + license: Apache 2.0 License + license.url: http://www.apache.org/licenses/LICENSE-2.0 + name: Gender, Sex, and Sexual Orientation (GSSO) ontology + preferredPrefix: GSSO + prefix: gsso + repository: https://github.com/Superraptor/GSSO + ols: + description: GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior. + download: http://purl.obolibrary.org/obo/gsso.owl + homepage: https://gsso.research.cchmc.org/ + name: GSSO - the Gender, Sex, and Sexual Orientation ontology + prefix: gsso + version: 2.0.5 + version.iri: http://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl + ontobee: + library: Library + name: Gender, Sex, and Sexual Orientation (GSSO) ontology + prefix: GSSO + pattern: ^\d{6}$ +gtex: + biocontext: + is_identifiers: true + is_obo: false + prefix: GTEX + uri_format: http://identifiers.org/gtex/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: GTEx + uri_format: https://www.gtexportal.org/home/gene/$1 + mappings: + biocontext: GTEX + biolink: GTEx + miriam: gtex + n2t: gtex + miriam: + deprecated: false + description: The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. + homepage: https://www.gtexportal.org + id: '00000663' + name: GTEx + namespaceEmbeddedInLui: false + pattern: ^\w.+$ + prefix: gtex + sampleId: BRIP1 + uri_format: https://www.gtexportal.org/home/gene/$1 + n2t: + description: 'The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. ' + example: BRIP1 + homepage: https://www.gtexportal.org + name: The GTEx Project + namespaceEmbeddedInLui: false + pattern: ^\w.+$ + prefix: gtex + uri_format: https://www.gtexportal.org/home/gene/$1 + name: Genotype-Tissue Expression +gtr: + appears_in: + - mondo + comment: Identifiers appearing in MONDO don't match any of the resources apparent endpoints + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease + example: AN0097748 + homepage: https://www.ncbi.nlm.nih.gov/gtr/ + name: Genetic Testing Registry + synonyms: + - medgen.gtr + uri_format: https://www.ncbi.nlm.nih.gov/gtr/conditions/$1 +gudmap: + biocontext: + is_identifiers: true + is_obo: false + prefix: GUDMAP + uri_format: http://identifiers.org/gudmap/$1 + fairsharing: + abbreviation: GUDMAP + description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) provides data and tools to facilitate research on the GenitoUrinary (GU) tract for the scientific and medical community. In addition to current GUDMAP data, this resource incorporates data generated by previous phases of GUDMAP and by the (Re)Building a Kidney (RBK) consortium. + id: '3324' + name: GenitoUrinary Development Molecular Anatomy Project + prefix: FAIRsharing.910c39 + subjects: + - Molecular biology + - Genomics + - Developmental Biology + - Cell Biology + mappings: + biocontext: GUDMAP + fairsharing: FAIRsharing.910c39 + miriam: gudmap + n2t: gudmap + miriam: + deprecated: false + description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. + homepage: http://www.gudmap.org/ + id: '00000643' + name: GUDMAP + namespaceEmbeddedInLui: false + pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ + prefix: gudmap + sampleId: Q-2958 + uri_format: https://gudmap.org/id/$1 + n2t: + description: The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. + example: Q-2958 + homepage: http://www.gudmap.org/ + name: GUDMAP + namespaceEmbeddedInLui: false + pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ + prefix: gudmap + uri_format: https://gudmap.org/id/$1 + name: Genitourinary Development Molecular Anatomy Project +gwascentral.marker: + biocontext: + is_identifiers: true + is_obo: false + prefix: GWASCENTRAL.MARKER + uri_format: http://identifiers.org/gwascentral.marker/$1 + homepage: https://www.gwascentral.org/markers + mappings: + biocontext: GWASCENTRAL.MARKER + miriam: gwascentral.marker + n2t: gwascentral.marker + miriam: + deprecated: false + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. + homepage: https://www.gwascentral.org/markers/ + id: '00000542' + name: GWAS Central Marker + namespaceEmbeddedInLui: false + pattern: ^HGVM\d+$ + prefix: gwascentral.marker + sampleId: HGVM15354 + uri_format: https://www.gwascentral.org/marker/$1 + n2t: + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. + example: HGVM15354 + homepage: https://www.gwascentral.org/markers/ + name: GWAS Central Marker at University of Leicester + namespaceEmbeddedInLui: false + pattern: ^HGVM\d+$ + prefix: gwascentral.marker + uri_format: https://www.gwascentral.org/marker/$1 +gwascentral.phenotype: + biocontext: + is_identifiers: true + is_obo: false + prefix: GWASCENTRAL.PHENOTYPE + uri_format: http://identifiers.org/gwascentral.phenotype/$1 + homepage: https://www.gwascentral.org/phenotypes + mappings: + biocontext: GWASCENTRAL.PHENOTYPE + miriam: gwascentral.phenotype + n2t: gwascentral.phenotype + miriam: + deprecated: false + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. + homepage: https://www.gwascentral.org/phenotypes + id: '00000543' + name: GWAS Central Phenotype + namespaceEmbeddedInLui: false + pattern: ^HGVPM\d+$ + prefix: gwascentral.phenotype + sampleId: HGVPM623 + uri_format: https://www.gwascentral.org/phenotype/$1 + n2t: + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. + example: HGVPM623 + homepage: https://www.gwascentral.org/phenotypes + name: GWAS Central Phenotype at University of Leicester + namespaceEmbeddedInLui: false + pattern: ^HGVP\d+$ + prefix: gwascentral.phenotype + uri_format: https://www.gwascentral.org/phenotype/$1 + pattern: ^HGVPM\d+$ +gwascentral.study: + biocontext: + is_identifiers: true + is_obo: false + prefix: GWASCENTRAL.STUDY + uri_format: http://identifiers.org/gwascentral.study/$1 + homepage: https://www.gwascentral.org/studies + mappings: + biocontext: GWASCENTRAL.STUDY + miriam: gwascentral.study + n2t: gwascentral.study + miriam: + deprecated: false + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. + homepage: https://www.gwascentral.org/studies + id: '00000540' + name: GWAS Central Study + namespaceEmbeddedInLui: false + pattern: ^HGVST\d+$ + prefix: gwascentral.study + sampleId: HGVST1828 + uri_format: https://www.gwascentral.org/study/$1 + n2t: + description: GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. + example: HGVST1828 + homepage: https://www.gwascentral.org/studies + name: GWAS Central Study at University of Leicester + namespaceEmbeddedInLui: false + pattern: ^HGVST\d+$ + prefix: gwascentral.study + uri_format: https://www.gwascentral.org/study/$1 +gxa.expt: + biocontext: + is_identifiers: true + is_obo: false + prefix: GXA.EXPT + uri_format: http://identifiers.org/gxa.expt/$1 + mappings: + biocontext: GXA.EXPT + miriam: gxa.expt + n2t: gxa.expt + miriam: + deprecated: false + description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. + homepage: https://www.ebi.ac.uk/gxa/ + id: '00000379' + name: GXA Expt + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: gxa.expt + providers: + - code: omicsdi + description: GXA Expt through OmicsDI + homepage: https://www.omicsdi.org/ + name: GXA Expt through OmicsDI + uri_format: https://www.omicsdi.org/dataset/atlas-experiments/$1 + sampleId: E-MTAB-2037 + uri_format: https://www.ebi.ac.uk/gxa/experiments/$1 + n2t: + description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. + example: E-MTAB-2037 + homepage: https://www.ebi.ac.uk/gxa/ + name: GXA Expt at EBI + namespaceEmbeddedInLui: false + pattern: ^[AEP]-\w{4}-\d+$ + prefix: gxa.expt + uri_format: https://www.ebi.ac.uk/gxa/experiments/$1 +gxa.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: GXA.GENE + uri_format: http://identifiers.org/gxa.gene/$1 + mappings: + biocontext: GXA.GENE + miriam: gxa.gene + n2t: gxa.gene + miriam: + deprecated: false + description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. + homepage: https://www.ebi.ac.uk/gxa/ + id: '00000378' + name: GXA Gene + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gxa.gene + sampleId: AT4G01080 + uri_format: https://www.ebi.ac.uk/gxa/genes/$1 + n2t: + description: The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. + example: AT4G01080 + homepage: https://www.ebi.ac.uk/gxa/ + name: GXA Gene at EBI + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: gxa.gene + uri_format: https://www.ebi.ac.uk/gxa/genes/$1 +habronattus: + biocontext: + is_identifiers: false + is_obo: true + prefix: HABRONATTUS + uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1 + mappings: + biocontext: HABRONATTUS + obofoundry: habronattus + obofoundry: + contact: peteremidford@yahoo.com + contact.label: Peter Midford + contact.orcid: 0000-0001-6512-3296 + deprecated: true + homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html + name: Habronattus courtship + prefix: habronattus +hamap: + biocontext: + is_identifiers: true + is_obo: false + prefix: HAMAP + uri_format: http://identifiers.org/hamap/$1 + fairsharing: + abbreviation: HAMAP + description: 'HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.' + id: '2059' + name: HAMAP database of microbial protein families + prefix: FAIRsharing.63m4ss + subjects: + - Life Science + go: + homepage: http://hamap.expasy.org/ + name: High-quality Automated and Manual Annotation of microbial Proteomes + prefix: HAMAP + uri_format: http://hamap.expasy.org/unirule/$1 + mappings: + biocontext: HAMAP + fairsharing: FAIRsharing.63m4ss + go: HAMAP + miriam: hamap + n2t: hamap + prefixcommons: hamap + uniprot: HAMAP + miriam: + deprecated: false + description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. + homepage: https://hamap.expasy.org/ + id: '00000292' + name: HAMAP + namespaceEmbeddedInLui: false + pattern: ^MF_\d+$ + prefix: hamap + sampleId: MF_01400 + uri_format: https://hamap.expasy.org/unirule/$1 + n2t: + description: HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. + example: MF_01400 + homepage: https://hamap.expasy.org/ + name: HAPMAP at Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^MF_\d+$ + prefix: hamap + uri_format: https://hamap.expasy.org/unirule/$1 + prefixcommons: + description: 'HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.' + example: MF_00323 + homepage: http://us.expasy.org/sprot/hamap/ + keywords: + - protein + name: HAMAP database of microbial protein families + pattern: ^MF_\d+$ + prefix: hamap + uri_format: http://us.expasy.org/unirule/$1 + uniprot: + category: Family and domain databases + identifier: '41' + link_is_explicit: 'true' + name: HAMAP database of protein families + prefix: HAMAP + uri_format: https://hamap.expasy.org/signature/$1 +hancestro: + biolink: + is_identifiers: false + is_obo: false + prefix: HANCESTRO + uri_format: http://www.ebi.ac.uk/ancestro/ancestro_$1 + bioportal: + name: Human Ancestry Ontology + prefix: HANCESTRO + example: '0290' + fairsharing: + abbreviation: HANCESTRO + description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. + id: '681' + name: Human Ancestry Ontology + prefix: FAIRsharing.rja8qp + subjects: + - Demographics + - Human Genetics + - Population Genetics + mappings: + biolink: HANCESTRO + bioportal: HANCESTRO + fairsharing: FAIRsharing.rja8qp + obofoundry: hancestro + ols: hancestro + ontobee: HANCESTRO + obofoundry: + contact: danielle.welter@uni.lu + contact.github: daniwelter + contact.label: Danielle Welter + contact.orcid: 0000-0003-1058-2668 + deprecated: false + description: The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies. + download.owl: http://purl.obolibrary.org/obo/hancestro.owl + homepage: https://github.com/EBISPOT/ancestro + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Human Ancestry Ontology + preferredPrefix: HANCESTRO + prefix: hancestro + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/29448949 + title: A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog + repository: https://github.com/EBISPOT/ancestro + ols: + description: Human ancestry ontology for the NHGRI GWAS Catalog + download: http://purl.obolibrary.org/obo/hancestro.owl + homepage: https://github.com/EBISPOT/ancestro + name: Human Ancestry Ontology + prefix: hancestro + version: '2.5' + version.iri: http://purl.obolibrary.org/obo/hancestro/releases/2020-12-18/hancestro.owl + ontobee: + library: Library + name: Human Ancestry Ontology + prefix: HANCESTRO + pattern: ^\d{4}$ +hao: + biocontext: + is_identifiers: false + is_obo: true + prefix: HAO + uri_format: http://purl.obolibrary.org/obo/HAO_$1 + bioportal: + name: Hymenoptera Anatomy Ontology + prefix: HAO + example: '0000187' + fairsharing: + abbreviation: HAO + description: The Hymenoptera Anatomy Ontology is a structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) + id: '219' + name: Hymenoptera Anatomy Ontology + prefix: FAIRsharing.kj3m5n + subjects: + - Anatomy + - Life Science + mappings: + biocontext: HAO + bioportal: HAO + fairsharing: FAIRsharing.kj3m5n + obofoundry: hao + ols: hao + ontobee: HAO + obofoundry: + contact: diapriid@gmail.com + contact.github: mjy + contact.label: Matt Yoder + contact.orcid: 0000-0002-5640-5491 + deprecated: false + description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) + download.obo: http://purl.obolibrary.org/obo/hao.obo + download.owl: http://purl.obolibrary.org/obo/hao.owl + homepage: http://hymao.org + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Hymenoptera Anatomy Ontology + preferredPrefix: HAO + prefix: hao + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/21209921 + title: A gross anatomy ontology for hymenoptera + repository: https://github.com/hymao/hao + ols: + description: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) + download: http://purl.obolibrary.org/obo/hao.owl + homepage: http://hymao.org + name: Hymenoptera Anatomy Ontology + prefix: hao + version: 2021-03-05 + version.iri: http://purl.obolibrary.org/obo/hao/2021-03-05/hao.owl + ontobee: + library: Library + name: Hymenoptera Anatomy Ontology + prefix: HAO + pattern: ^\d{7}$ +hba: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A controlled vocabulary to support the study of transcription in the human brain + download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo + example: '4005' + example_extras: + - '265504410' + homepage: https://human.brain-map.org + name: Human Brain Atlas + pattern: ^\d+$ + preferred_prefix: HBA +hcao: + homepage: https://www.humancellatlas.org + mappings: + ols: hcao + no_own_terms: true + ols: + description: Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. + download: https://raw.githubusercontent.com/ebi-ait/ontology/master/hcao.owl + name: Human Cell Atlas Ontology + prefix: hcao + version: 2022-04-19 + version.iri: http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2022-04-19/hcao.owl +hcpcs: + biolink: + is_identifiers: false + is_obo: false + prefix: HCPCS + uri_format: http://purl.bioontology.org/ontology/HCPCS/$1 + bioportal: + name: Healthcare Common Procedure Coding System + prefix: HCPCS + description: HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers. + example: G8944 + fairsharing: + abbreviation: HCPCS + description: Each year, in the United States, health care insurers process over 5 billion claims for payment. For Medicare and other health insurance programs to ensure that these claims are processed in an orderly and consistent manner, standardized coding systems are essential. The HCPCS is divided into two principal subsystems, referred to as level I and level II of the HCPCS. Level I of the HCPCS is comprised of CPT (Current Procedural Terminology), a numeric coding system maintained by the American Medical Association (AMA). Level II of the HCPCS is a standardized coding system that is used primarily to identify products, supplies, and services not included in the CPT codes, such as ambulance services and durable medical equipment, prosthetics, orthotics, and supplies (DMEPOS) when used outside a physician's office. + id: '1006' + name: Healthcare Common Procedure Coding System + prefix: FAIRsharing.x81wz8 + subjects: + - Business Administration + - Biomedical Science + homepage: https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo + mappings: + biolink: HCPCS + bioportal: HCPCS + fairsharing: FAIRsharing.x81wz8 + name: Healthcare Common Procedure Coding System +hcvdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: HCVDB + uri_format: http://identifiers.org/hcvdb/$1 + homepage: http://euhcvdb.ibcp.fr + mappings: + biocontext: HCVDB + miriam: hcvdb + n2t: hcvdb + miriam: + deprecated: false + description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. + homepage: http://euhcvdb.ibcp.fr/euHCVdb/ + id: '00000207' + name: HCVDB + namespaceEmbeddedInLui: false + pattern: ^M\d{5}$ + prefix: hcvdb + sampleId: M58335 + uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 + n2t: + description: the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. + example: M58335 + homepage: http://euhcvdb.ibcp.fr/euHCVdb/ + name: HCVDB at CNRS + namespaceEmbeddedInLui: false + pattern: ^M\d{5}$ + prefix: hcvdb + uri_format: https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1 + name: Hepatitis C Virus Database +hdr: + biocontext: + is_identifiers: true + is_obo: false + prefix: HDR + uri_format: http://identifiers.org/hdr/$1 + mappings: + biocontext: HDR + miriam: hdr + n2t: hdr + prefixcommons: hdr + miriam: + deprecated: false + description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. + homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/ + id: '00000497' + name: Homeodomain Research + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hdr + sampleId: '63' + uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 + n2t: + description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. + example: '63' + homepage: http://research.nhgri.nih.gov/apps/homeodomain/web/ + name: Homeodomain Research at National Human Genome Research Institute (NIH) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hdr + uri_format: http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1 + prefixcommons: + description: The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic, and functional information on the homeodomain family. A description of each of the major sections of the database can be found below, and users can navigate through the site using the links found in the menu that appears on the left-hand side of every page within the site. + example: '5978' + homepage: http://research.nhgri.nih.gov/homeodomain/ + keywords: + - genome + name: Homeodomain Resource Database + pattern: ^\d+$ + prefix: hdr + uri_format: http://research.nhgri.nih.gov/homeodomain/?mode=view&view=proteins&id=$1 +hgmd: + biocontext: + is_identifiers: false + is_obo: false + prefix: HGMD + uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 + mappings: + biocontext: HGMD + miriam: hgmd + n2t: hgmd + miriam: + deprecated: false + description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. + homepage: http://www.hgmd.cf.ac.uk/ac/index.php + id: '00000392' + name: HGMD + namespaceEmbeddedInLui: false + pattern: ^[A-Z_0-9]+$ + prefix: hgmd + sampleId: CALM1 + uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 + n2t: + description: The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. + example: CALM1 + homepage: http://www.hgmd.cf.ac.uk/ac/index.php + name: HGMD at Cardiff University + namespaceEmbeddedInLui: false + pattern: ^[A-Z_0-9]+$ + prefix: hgmd + uri_format: http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1 + name: Human Gene Mutation Database +hgnc: + biocontext: + is_identifiers: false + is_obo: false + prefix: HGNC + uri_format: http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$1 + bioportal: + name: HUGO Gene Nomenclature + prefix: HGNC + cellosaurus: + category: Organism-specific databases + homepage: https://www.genenames.org + name: Human Gene Nomenclature Committee Database + prefix: HGNC + uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1 + example: '16793' + fairsharing: + abbreviation: HGNC + description: The HGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications. + id: '741' + name: HGNC Gene Symbols, Gene Names and IDs + prefix: FAIRsharing.amcv1e + subjects: + - Life Science + go: + homepage: http://www.genenames.org/ + name: HUGO Gene Nomenclature Committee + prefix: HGNC + uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$1 + homepage: http://www.genenames.org + mappings: + biocontext: HGNC + bioportal: HGNC + cellosaurus: HGNC + fairsharing: FAIRsharing.amcv1e + go: HGNC + miriam: hgnc + n2t: hgnc + ncbi: HGNC + prefixcommons: hgnc + uniprot: HGNC + miriam: + deprecated: false + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. + homepage: https://www.genenames.org + id: '00000080' + name: HGNC + namespaceEmbeddedInLui: false + pattern: ^((HGNC|hgnc):)?\d{1,5}$ + prefix: hgnc + sampleId: '2674' + uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 + n2t: + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. + example: '2674' + homepage: https://www.genenames.org + name: HUGO Genome Nomenclature Committee + namespaceEmbeddedInLui: false + pattern: ^((HGNC|hgnc):)?\d{1,5}$ + prefix: hgnc + uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 + name: HUGO Gene Nomenclature Committee + ncbi: + example: HGNC:2041 + homepage: http://www.genenames.org/cgi-bin/search + name: Human Gene Nomenclature Database + prefix: HGNC + prefixcommons: + bioportal: '1528' + description: The HGNC gives unique and meaningful names to every human gene. For each known human gene we approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database. + example: '7' + homepage: http://www.genenames.org/ + keywords: + - classification + - gene + name: HUGO Gene Nomenclature Committee + pattern: ^\d+$ + prefix: hgnc + uri_format: http://www.genenames.org/data/hgnc_data.php?hgnc_id=$1 + providers: + - code: indra + description: A large scale database of biomedical statements. + homepage: https://db.indra.bio + name: INDRA Database + uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC + - code: gencc + description: The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s Health, Mass General Brigham Laboratory for Molecular Medicine). + homepage: https://thegencc.org + name: The Gene Curation Coalition + uri_format: https://search.thegencc.org/genes/HGNC:$1 + uniprot: + category: Organism-specific databases + comment: Replacement for Genew + identifier: '42' + link_is_explicit: 'true' + name: Human Gene Nomenclature Database + prefix: HGNC + uri_format: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1 + wikidata: + prefix: P354 +hgnc.genefamily: + biocontext: + is_identifiers: true + is_obo: false + prefix: HGNC.GENEFAMILY + uri_format: http://identifiers.org/hgnc.genefamily/$1 + example: '2029' + has_canonical: hgnc.genegroup + homepage: http://www.genenames.org + mappings: + biocontext: HGNC.GENEFAMILY + miriam: hgnc.family + n2t: hgnc.genefamily + miriam: + deprecated: true + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol. + id: '00000520' + name: HGNC Family + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9-]+(#[A-Z0-9-]+)?$ + prefix: hgnc.family + sampleId: PADI + n2t: + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. + example: '141' + homepage: https://www.genenames.org/ + name: HGNC gene family at HUGO Genome Nomenclature Committee + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hgnc.genefamily + uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1 + synonyms: + - GFAM + - HGNC_GROUP + - hgnc.family +hgnc.genegroup: + mappings: + miriam: hgnc.genegroup + miriam: + deprecated: false + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. + homepage: https://www.genenames.org + id: '00000709' + name: HGNC Gene Group + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hgnc.genegroup + sampleId: '141' + uri_format: https://www.genenames.org/cgi-bin/genefamilies/set/$1 +hgnc.symbol: + biocontext: + is_identifiers: true + is_obo: false + prefix: HGNC.SYMBOL + uri_format: http://identifiers.org/hgnc.symbol/$1 + mappings: + biocontext: HGNC.SYMBOL + miriam: hgnc.symbol + n2t: hgnc.symbol + miriam: + deprecated: false + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. + homepage: https://www.genenames.org/ + id: '00000362' + name: HGNC Symbol + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+(\@)?$ + prefix: hgnc.symbol + sampleId: DAPK1 + uri_format: https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1 + n2t: + description: The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. + example: DAPK1 + homepage: https://www.genenames.org/ + name: HGNC Symbol at HUGO Genome Nomenclature Committee + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+(\@)?$ + prefix: hgnc.symbol + uri_format: https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1 + providers: + - code: depmap + description: DepMap summary of the given gene + homepage: https://depmap.org + name: DepMap Gene Summary + uri_format: https://depmap.org/portal/gene/$1 + - code: pathwaycommons + description: Interactions between a given gene and other molecular entities + homepage: https://www.pathwaycommons.org/ + name: Pathway Commons Gene Interations + uri_format: https://apps.pathwaycommons.org/interactions?source=$1 + - code: oncomx + description: Mutation profiles for a gene + homepage: https://oncomx.org + name: OncoMX + uri_format: https://oncomx.org/searchview/?gene=$1 +hinv.locus: + biocontext: + is_identifiers: true + is_obo: false + prefix: HINV.LOCUS + uri_format: http://identifiers.org/hinv.locus/$1 + mappings: + biocontext: HINV.LOCUS + miriam: hinv.locus + n2t: hinv.locus + miriam: + deprecated: false + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. + homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp + id: '00000167' + name: H-InvDb Locus + namespaceEmbeddedInLui: false + pattern: ^HIX\d{7}(\.\d+)?$ + prefix: hinv.locus + sampleId: HIX0004394 + uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1 + n2t: + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. + example: HIX0004394 + homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp + name: H-Invitational Locus View at BIRC + namespaceEmbeddedInLui: false + pattern: ^HIX\d{7}(\.\d+)?$ + prefix: hinv.locus + uri_format: http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1 +hinv.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: HINV.PROTEIN + uri_format: http://identifiers.org/hinv.protein/$1 + mappings: + biocontext: HINV.PROTEIN + miriam: hinv.protein + n2t: hinv.protein + miriam: + deprecated: false + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. + homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp + id: '00000169' + name: H-InvDb Protein + namespaceEmbeddedInLui: false + pattern: ^HIP\d{9}(\.\d+)?$ + prefix: hinv.protein + sampleId: HIP000030660 + uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1 + n2t: + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. + example: HIP000030660 + homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp + name: H-Invitational Protein View at BIRC + namespaceEmbeddedInLui: false + pattern: ^HIP\d{9}(\.\d+)?$ + prefix: hinv.protein + uri_format: http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1 +hinv.transcript: + biocontext: + is_identifiers: true + is_obo: false + prefix: HINV.TRANSCRIPT + uri_format: http://identifiers.org/hinv.transcript/$1 + mappings: + biocontext: HINV.TRANSCRIPT + miriam: hinv.transcript + n2t: hinv.transcript + miriam: + deprecated: false + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. + homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp + id: '00000168' + name: H-InvDb Transcript + namespaceEmbeddedInLui: false + pattern: ^HIT\d{9}(\.\d+)?$ + prefix: hinv.transcript + sampleId: HIT000195363 + uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1 + n2t: + description: H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. + example: HIT000195363 + homepage: http://h-invitational.jp/hinv/ahg-db/index.jsp + name: H-Invitational Transcript View at BIRC + namespaceEmbeddedInLui: false + pattern: ^HIT\d{9}(\.\d+)?$ + prefix: hinv.transcript + uri_format: http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1 +hipsci: + cellosaurus: + category: Cell line databases/resources + homepage: http://www.hipsci.org + name: Human Induced Pluripotent Stem Cells Initiative + prefix: HipSci + uri_format: http://www.hipsci.org/lines/#/lines/$1 + example: HPSI0114i-bezi_1 + mappings: + cellosaurus: HipSci +hivreagentprogram: + cellosaurus: + category: Cell line collections + homepage: https://www.hivreagentprogram.org/Home.aspx + name: NIH HIV Reagent Program + prefix: HIVReagentProgram + uri_format: https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx + example: ARP-1513 + mappings: + cellosaurus: HIVReagentProgram +hmdb: + biocontext: + is_identifiers: false + is_obo: false + prefix: HMDB + uri_format: http://www.hmdb.ca/metabolites/$1 + cheminf: + description: Database identifier used by Human Metabolome Database. + name: HMDB + obsolete: false + prefix: '000408' + fairsharing: + abbreviation: HMDB + description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. + id: '2084' + name: The Human Metabolome Database + prefix: FAIRsharing.sye5js + subjects: + - Molecular biology + - Biochemistry + - Life Science + - Metabolomics + mappings: + biocontext: HMDB + cheminf: '000408' + fairsharing: FAIRsharing.sye5js + miriam: hmdb + n2t: hmdb + prefixcommons: hmdb + wikidata: P2057 + miriam: + deprecated: false + description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. + homepage: http://www.hmdb.ca/ + id: '00000051' + name: HMDB + namespaceEmbeddedInLui: false + pattern: ^HMDB\d+$ + prefix: hmdb + sampleId: HMDB00001 + uri_format: http://www.hmdb.ca/metabolites/$1 + n2t: + description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. + example: HMDB00001 + homepage: http://www.hmdb.ca/ + name: The Human Metabolome Database + namespaceEmbeddedInLui: false + pattern: ^HMDB\d+$ + prefix: hmdb + uri_format: http://www.hmdb.ca/metabolites/$1 + name: Human Metabolome Database + prefixcommons: + description: The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. + example: HMDB00001 + homepage: http://www.hmdb.ca + keywords: + - chemical + - human + - metabolite + name: The Human Metabolome Database + pattern: ^HMDB\d{5}$ + prefix: hmdb + pubmed_ids: + - '17202168' + uri_format: http://www.hmdb.ca/metabolites/$1 + synonyms: + - HMDB + wikidata: + database: Q5937262 + database.homepage: https://hmdb.ca + database.label: Human Metabolome Database + name: Human Metabolome Database ID + pattern: HMDB\d+ + prefix: P2057 + uri_format: https://www.hmdb.ca/metabolites/$1 +hms.lincs.compound: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. + example: 10001-101 + homepage: https://lincs.hms.harvard.edu/db/sm/ + name: HMS LINCS Compound + synonyms: + - HMS-LINCS + - hmsl_id + uri_format: https://lincs.hms.harvard.edu/db/sm/$1 +hog: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc. + download_obo: ftp://ftp.bgee.org/general/ontologies/HOG.obo + example: '0000255' + homepage: https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships + name: Homologous Organ Groups + pattern: ^\d{7}$ +hogenom: + biocontext: + is_identifiers: true + is_obo: false + prefix: HOGENOM + uri_format: http://identifiers.org/hogenom/$1 + fairsharing: + abbreviation: HOGENOM + description: HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms. + id: '2033' + name: HOGENOM + prefix: FAIRsharing.qe8tz8 + subjects: + - Phylogeny + - Phylogenetics + - Life Science + mappings: + biocontext: HOGENOM + fairsharing: FAIRsharing.qe8tz8 + miriam: hogenom + n2t: hogenom + prefixcommons: hogenom + uniprot: HOGENOM + miriam: + deprecated: false + description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. + homepage: http://pbil.univ-lyon1.fr/databases/hogenom/ + id: '00000213' + name: HOGENOM + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: hogenom + sampleId: HBG284870 + uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 + n2t: + description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. + example: HBG284870 + homepage: http://pbil.univ-lyon1.fr/databases/hogenom/ + name: HOGENOM at CNRS + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: hogenom + uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 + name: Database of Complete Genome Homologous Genes Families + prefixcommons: + description: HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. + example: HBG284870 + homepage: http://pbil.univ-lyon1.fr/databases/hogenom.php + keywords: + - classification + - sequence + name: The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms + pattern: ^\w+$ + prefix: hogenom + pubmed_ids: + - '19534752' + uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 + uniprot: + category: Phylogenomic databases + identifier: '44' + link_is_explicit: 'true' + name: The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms + prefix: HOGENOM + uri_format: http://hogenom.univ-lyon1.fr/query_sequence?seq=$1 +hom: + biocontext: + is_identifiers: false + is_obo: true + prefix: HOM + uri_format: http://purl.obolibrary.org/obo/HOM_$1 + bioportal: + name: Ontology of Homology and Related Concepts in Biology + prefix: HOM + example: '0000049' + fairsharing: + abbreviation: HOM + description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. + id: '48' + name: HOMology + prefix: FAIRsharing.efv7gw + subjects: + - Anatomy + - Life Science + mappings: + biocontext: HOM + bioportal: HOM + fairsharing: FAIRsharing.efv7gw + obofoundry: hom + ols: hom + ontobee: HOM + obofoundry: + contact: bgee@sib.swiss + contact.github: fbastian + contact.label: Frederic Bastian + contact.orcid: 0000-0002-9415-5104 + deprecated: false + description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. + download.owl: http://purl.obolibrary.org/obo/hom.owl + homepage: https://github.com/BgeeDB/homology-ontology + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Homology Ontology + preferredPrefix: HOM + prefix: hom + repository: https://github.com/BgeeDB/homology-ontology + ols: + description: This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. + download: http://purl.obolibrary.org/obo/hom.owl + homepage: https://github.com/BgeeDB/homology-ontology + name: Homology Ontology + prefix: hom + version: 2015-01-07 + version.iri: http://purl.obolibrary.org/obo/hom/releases/2015-01-07/hom.owl + ontobee: + library: Library + name: Homology Ontology + prefix: HOM + pattern: ^\d{7}$ +homd.seq: + biocontext: + is_identifiers: true + is_obo: false + prefix: HOMD.SEQ + uri_format: http://identifiers.org/homd.seq/$1 + mappings: + biocontext: HOMD.SEQ + miriam: homd.seq + n2t: homd.seq + prefixcommons: homd.seq + miriam: + deprecated: false + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. + homepage: http://www.homd.org/index.php + id: '00000170' + name: HOMD Sequence Metainformation + namespaceEmbeddedInLui: false + pattern: ^SEQF\d+$ + prefix: homd.seq + sampleId: SEQF1003 + uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 + n2t: + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. + example: SEQF1003 + homepage: http://www.homd.org/index.php + name: HOMD sequence metainformation at The Forsyth Institute + namespaceEmbeddedInLui: false + pattern: ^SEQF\d+$ + prefix: homd.seq + uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 + prefixcommons: + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. + example: SEQF1003 + keywords: + - genome + - microbial + name: HOMD Sequence Metainformation + pattern: ^SEQF\d+$ + prefix: homd.seq + pubmed_ids: + - '20624719' + uri_format: http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 +homd.taxon: + biocontext: + is_identifiers: true + is_obo: false + prefix: HOMD.TAXON + uri_format: http://identifiers.org/homd.taxon/$1 + mappings: + biocontext: HOMD.TAXON + miriam: homd.taxon + n2t: homd.taxon + prefixcommons: homd.taxon + miriam: + deprecated: false + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. + homepage: http://www.homd.org/index.php + id: '00000171' + name: HOMD Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: homd.taxon + sampleId: '811' + uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic + n2t: + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. + example: '811' + homepage: http://www.homd.org/index.php + name: HOMD taxon information at The Forsyth Institute + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: homd.taxon + uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic + prefixcommons: + description: The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. + example: '811' + keywords: + - microbial + - taxonomy + name: HOMD Taxonomy + pattern: ^\d+$ + prefix: homd.taxon + pubmed_ids: + - '20624719' + uri_format: http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$1&view=dynamic + uri_format: www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1 +homologene: + biocontext: + is_identifiers: false + is_obo: false + prefix: HOMOLOGENE + uri_format: http://www.ncbi.nlm.nih.gov/homologene/$1 + fairsharing: + abbreviation: HomoloGene + description: HomoloGene is an automated system for the detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. HomoloGene takes protein sequences from differing species and compares them to one another (using blastp) and matches are placed into groups, using a tree built from sequence similarity to guide the process, where closer related organisms are matched up first, and then further organisms are added as the tree is traversed toward the root. The protein alignments are mapped back to their corresponding DNA sequences, where distance metrics can be calculated (e.g. molecular distance, Ka/Ks ratio). Sequences are matched using synteny when applicable. Remaining sequences are matched up by using an algorithm for maximizing the score globally, rather than locally, in a bipartite matching. Cutoffs on bits per position and Ks values are set to prevent unlikely "orthologs" from being grouped together. These cutoffs are calculated based on the respective score distribution for the given groups of organisms. Paralogs are identified by finding sequences that are closer within species than other species. + id: '1977' + name: NCBI HomoloGene Database + prefix: FAIRsharing.mzc066 + subjects: + - Life Science + mappings: + biocontext: HOMOLOGENE + fairsharing: FAIRsharing.mzc066 + miriam: homologene + n2t: homologene + prefixcommons: homologene + wikidata: P593 + miriam: + deprecated: false + description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. + homepage: https://www.ncbi.nlm.nih.gov/homologene/ + id: '00000275' + name: HomoloGene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: homologene + providers: + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: http://homologene.bio2rdf.org/fct + name: Bio2RDF + uri_format: http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1 + sampleId: '1000' + uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1 + n2t: + description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. + example: '1000' + homepage: https://www.ncbi.nlm.nih.gov/homologene/ + name: Homologene at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: homologene + uri_format: https://www.ncbi.nlm.nih.gov/homologene/$1 + name: HomoloGene + prefixcommons: + description: HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. + example: '1000' + homepage: http://wwww.ncbi.nlm.nih.gov/homologene + keywords: + - gene + - genome + name: NCBI Homologene + pattern: ^\d+$ + prefix: homologene + pubmed_ids: + - '21097890' + uri_format: http://www.ncbi.nlm.nih.gov/homologene/[?id] + wikidata: + database: Q468215 + database.homepage: http://www.ncbi.nlm.nih.gov/homologene + database.label: HomoloGene + homepage: http://www.ncbi.nlm.nih.gov/homologene + name: HomoloGene ID + pattern: '[1-9]\d{0,5}' + prefix: P593 + uri_format: https://www.ncbi.nlm.nih.gov/homologene?term=$1 +horizon_discovery: + cellosaurus: + category: Cell line collections + homepage: https://horizondiscovery.com/ + name: Horizon Discovery cell line collection + prefix: Horizon_Discovery + uri_format: https://horizondiscovery.com/en/search?searchterm=$1 + example: HD+118-001 + mappings: + cellosaurus: Horizon_Discovery +hovergen: + biocontext: + is_identifiers: true + is_obo: false + prefix: HOVERGEN + uri_format: http://identifiers.org/hovergen/$1 + fairsharing: + abbreviation: HOVERGEN + description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. + id: '2034' + name: Homologous Vertebrate Genes Database + prefix: FAIRsharing.dg1f0e + subjects: + - Life Science + homepage: https://pbil.univ-lyon1.fr/databases/hovergen.php + mappings: + biocontext: HOVERGEN + fairsharing: FAIRsharing.dg1f0e + miriam: hovergen + n2t: hovergen + prefixcommons: hovergen + miriam: + deprecated: false + description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. + homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php + id: '00000074' + name: HOVERGEN + namespaceEmbeddedInLui: false + pattern: ^HBG\d+$ + prefix: hovergen + sampleId: HBG004341 + uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN + n2t: + description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. + example: HBG004341 + homepage: http://pbil.univ-lyon1.fr/databases/hovergen.php + name: Hovergen + namespaceEmbeddedInLui: false + pattern: ^HBG\d+$ + prefix: hovergen + uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN + name: Homologous Vertebrate Genes Database + prefixcommons: + description: HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. + example: HBG004341 + homepage: http://pbil.univ-lyon1.fr/databases/hovergen.html + keywords: + - gene + - DNA + - protein + name: 'HOVERGEN: Homologous Vertebrate Genes Database' + pattern: ^HBG\d+$ + prefix: hovergen + pubmed_ids: + - '15713731' + uri_format: http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN +hp: + biocontext: + is_identifiers: false + is_obo: false + prefix: HPO + uri_format: http://human-phenotype-ontology.org/$1 + bioportal: + name: Human Phenotype Ontology + prefix: HP + download_obo: http://purl.obolibrary.org/obo/hp.obo + example: '0011140' + fairsharing: + abbreviation: HP + description: The Human Phenotype Ontology has been developed to provide a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. The goal is to provide resource for the computational analysis of the human phenome, with a focus on monogenic diseases listed in the Online Mendelian Inheritance in Man (OMIM) and Orphanet databases, for which annotations are also provided. + id: '757' + name: Human Phenotype Ontology + prefix: FAIRsharing.kbtt7f + subjects: + - Genetics + - Phenomics + - Biomedical Science + - Preclinical Studies + mappings: + biocontext: HPO + bioportal: HP + fairsharing: FAIRsharing.kbtt7f + miriam: hp + n2t: hp + obofoundry: hp + ols: hp + ontobee: HP + wikidata: P3841 + miriam: + deprecated: false + description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. + homepage: http://human-phenotype-ontology.github.io/ + id: '00000571' + name: Human Phenotype Ontology + namespaceEmbeddedInLui: true + pattern: ^HP:\d{7}$ + prefix: hp + sampleId: '0000118' + uri_format: https://hpo.jax.org/app/browse/term/HP:$1 + n2t: + description: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. + example: '0000118' + homepage: http://human-phenotype-ontology.github.io/ + name: Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics + namespaceEmbeddedInLui: true + pattern: ^HP:\d{7}$ + prefix: hp + uri_format: http://compbio.charite.de/hpoweb/showterm?id=HP:$1 + obofoundry: + appears_in: + - chiro + - scdo + contact: dr.sebastian.koehler@gmail.com + contact.github: drseb + contact.label: Sebastian Koehler + contact.orcid: 0000-0002-5316-1399 + deprecated: false + description: A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease. + download.obo: http://purl.obolibrary.org/obo/hp.obo + download.owl: http://purl.obolibrary.org/obo/hp.owl + homepage: http://www.human-phenotype-ontology.org/ + license: hpo + license.url: https://hpo.jax.org/app/license + name: Human Phenotype Ontology + preferredPrefix: HP + prefix: hp + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/18950739 + title: 'The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.' + - id: https://www.ncbi.nlm.nih.gov/pubmed/26119816 + title: 'The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.' + - id: https://www.ncbi.nlm.nih.gov/pubmed/24217912 + title: 'The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.' + - id: https://www.ncbi.nlm.nih.gov/pubmed/30476213 + title: Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. + repository: https://github.com/obophenotype/human-phenotype-ontology + twitter: hp_ontology + ols: + description: The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease. + download: http://purl.obolibrary.org/obo/hp.owl + homepage: http://www.human-phenotype-ontology.org/ + name: Human Phenotype Ontology + prefix: hp + version: 2022-04-14 + version.iri: http://purl.obolibrary.org/obo/hp/releases/2022-04-14/hp.owl + ontobee: + library: Library + name: Human Phenotype Ontology + prefix: HP + pattern: ^\d{7}$ + synonyms: + - hpo + wikidata: + database: Q17027854 + database.homepage: http://www.human-phenotype-ontology.org/ + database.label: Human Phenotype Ontology + homepage: http://human-phenotype-ontology.github.io/about.html + name: Human Phenotype Ontology ID + pattern: HP:[0-9]{7} + prefix: P3841 + uri_format: https://hpo.jax.org/app/browse/term/$1 +hpa: + biocontext: + is_identifiers: true + is_obo: false + prefix: HPA + uri_format: http://identifiers.org/hpa/$1 + fairsharing: + abbreviation: HPA + description: 'The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in a number of different wild-type tissues, cancer types and human cell lines. The goal of the HPA is to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas, the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.' + id: '1945' + name: Human Protein Atlas + prefix: FAIRsharing.j0t0pe + subjects: + - Proteomics + - Transcriptomics + - Biomedical Science + - Systems Biology + go: + homepage: http://www.proteinatlas.org/ + name: Human Protein Atlas tissue profile information + prefix: HPA + uri_format: http://www.proteinatlas.org/tissue_profile.php?antibody_id=$1 + mappings: + biocontext: HPA + fairsharing: FAIRsharing.j0t0pe + go: HPA + miriam: hpa + n2t: hpa + prefixcommons: hpa + uniprot: HPA + miriam: + deprecated: false + description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. + homepage: http://www.proteinatlas.org/ + id: '00000336' + name: HPA + namespaceEmbeddedInLui: false + pattern: ^ENSG\d{11}$ + prefix: hpa + sampleId: ENSG00000026508 + uri_format: http://www.proteinatlas.org/$1 + n2t: + description: The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. + example: ENSG00000026508 + homepage: http://www.proteinatlas.org/ + name: Human Protein Atlas at AlbaNova University + namespaceEmbeddedInLui: false + pattern: ^ENSG\d{11}$ + prefix: hpa + uri_format: http://www.proteinatlas.org/$1 + prefixcommons: + description: The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in 48 different normal tissues and 20 different cancer types as well as 47 different human cell lines. + example: ENSG00000026508 + homepage: http://www.proteinatlas.org/ + keywords: + - protein + - structure + name: Human Protein Atlas + pattern: ^ENSG\d{11}$ + prefix: hpa + pubmed_ids: + - '18669619' + uri_format: http://www.proteinatlas.org/gene_info.php?ensembl_gene_id=$1 + uniprot: + category: Organism-specific databases + identifier: '46' + link_is_explicit: 'true' + name: Human Protein Atlas + prefix: HPA + uri_format: https://www.proteinatlas.org/$1 +hpath: + example: '2000191' + mappings: + ols: hpath + ols: + description: An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. + download: https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo + homepage: https://github.com/Novartis/hpath + name: Histopathology Ontology + prefix: hpath + version: 2019-07-05 + pattern: ^\d+$ + repository: https://github.com/Novartis/hpath + synonyms: + - MC +hpm.peptide: + biocontext: + is_identifiers: true + is_obo: false + prefix: HPM.PEPTIDE + uri_format: http://identifiers.org/hpm.peptide/$1 + mappings: + biocontext: HPM.PEPTIDE + miriam: hpm.peptide + n2t: hpm.peptide + miriam: + deprecated: false + description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. + homepage: http://www.humanproteomemap.org/index.php + id: '00000527' + name: Human Proteome Map Peptide + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hpm.peptide + sampleId: '9606117' + uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1 + n2t: + description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. + example: '9606117' + homepage: http://www.humanproteomemap.org/index.php + name: Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hpm.peptide + uri_format: http://www.humanproteomemap.org/spectrum.php?pep_id=$1 +hpm.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: HPM.PROTEIN + uri_format: http://identifiers.org/hpm.protein/$1 + mappings: + biocontext: HPM.PROTEIN + miriam: hpm.protein + n2t: hpm.protein + miriam: + deprecated: false + description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. + homepage: http://www.humanproteomemap.org/index.php + id: '00000526' + name: Human Proteome Map Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hpm.protein + sampleId: '1968' + uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1 + n2t: + description: The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. + example: '1968' + homepage: http://www.humanproteomemap.org/index.php + name: Human Proteome Map Protein at Institute of Bioinformatics (Bangalore) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hpm.protein + uri_format: http://www.humanproteomemap.org/protein.php?hpm_id=$1 +hprd: + biocontext: + is_identifiers: false + is_obo: false + prefix: HPRD + uri_format: http://www.hprd.org/protein/$1 + fairsharing: + abbreviation: HPRD + description: The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. + id: '1930' + name: Human Protein Reference Database + prefix: FAIRsharing.y2qws7 + subjects: [] + mappings: + biocontext: HPRD + fairsharing: FAIRsharing.y2qws7 + miriam: hprd + n2t: hprd + prefixcommons: hprd + miriam: + deprecated: false + description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. + homepage: http://www.hprd.org/ + id: '00000377' + name: HPRD + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hprd + sampleId: '00001' + uri_format: http://www.hprd.org/protein/$1 + n2t: + description: The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. + example: '00001' + homepage: http://www.hprd.org/ + name: Human Protein Reference Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: hprd + uri_format: http://www.hprd.org/protein/$1 + name: Human Protein Reference Database + prefixcommons: + description: The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. + example: '00001' + homepage: http://www.hprd.org/ + keywords: + - protein + - structure + name: Human Protein Reference Database + pattern: ^\d+$ + prefix: hprd + pubmed_ids: + - '18988627' +hpscreg: + cellosaurus: + category: Cell line databases/resources + homepage: https://hpscreg.eu + name: Human Pluripotent Stem Cell Registry + prefix: hPSCreg + uri_format: https://hpscreg.eu/cell-line/$1 + fairsharing: + abbreviation: hPSCreg + description: The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application. + id: '2664' + name: Human Pluripotent Stem Cell Registry + prefix: FAIRsharing.7C0aVE + subjects: + - Life Science + - Biomedical Science + mappings: + cellosaurus: hPSCreg + fairsharing: FAIRsharing.7C0aVE + miriam: hpscreg + n2t: hpscreg + miriam: + deprecated: false + description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). + homepage: https://hpscreg.eu/ + id: '00000674' + name: Human Pluripotent Stem Cell Registry + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ + prefix: hpscreg + sampleId: BCRTi001-A + uri_format: https://hpscreg.eu/cell-line/$1 + n2t: + description: hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). + example: BCRTi001-A + homepage: https://hpscreg.eu/ + name: Human Pluripotent Stem Cell Registry + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ + prefix: hpscreg + uri_format: https://hpscreg.eu/cell-line/$1 +hsapdv: + biocontext: + is_identifiers: false + is_obo: true + prefix: HSAPDV + uri_format: http://purl.obolibrary.org/obo/HSAPDV_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: HsapDv + uri_format: http://purl.obolibrary.org/obo/HsapDv_$1 + bioportal: + name: Human Developmental Stages Ontology + prefix: HSAPDV + example: '0000194' + fairsharing: + abbreviation: HSAPDV + description: Life cycle stages for Human. HsapDv was developed by the Bgee group with assistance from the core Uberon developers and the Human developmental anatomy ontology (EHDAA2) developers. Currently it includes both embryonic (Carnegie) stages and adult stages. + id: '804' + name: Human Developmental Stages Ontology + prefix: FAIRsharing.c6vhm3 + subjects: [] + mappings: + biocontext: HSAPDV + biolink: HsapDv + bioportal: HSAPDV + fairsharing: FAIRsharing.c6vhm3 + obofoundry: hsapdv + ols: hsapdv + ontobee: HSAPDV + obofoundry: + appears_in: + - scdo + contact: frederic.bastian@unil.ch + contact.github: fbastian + contact.label: Frédéric Bastian + contact.orcid: 0000-0002-9415-5104 + deprecated: false + description: Life cycle stages for Human + download.obo: http://purl.obolibrary.org/obo/hsapdv.obo + download.owl: http://purl.obolibrary.org/obo/hsapdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Human Developmental Stages + preferredPrefix: HsapDv + prefix: hsapdv + repository: https://github.com/obophenotype/developmental-stage-ontologies + ols: + description: Life cycle stages for Human + download: http://purl.obolibrary.org/obo/hsapdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv + name: Human Developmental Stages + prefix: hsapdv + version: 2020-03-10 + version.iri: http://purl.obolibrary.org/obo/hsapdv/releases/2020-03-10/hsapdv.owl + ontobee: + library: Library + name: Human Developmental Stages + prefix: HSAPDV + pattern: ^\d{7}$ + synonyms: + - HsapDv +hsdb: + description: The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. + example: '5621' + homepage: https://pubchem.ncbi.nlm.nih.gov/source/hsdb + name: Hazardous Substances Data Bank + pattern: ^\d+$ + uri_format: https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1 + wikidata: + prefix: P2062 +hso: + bioportal: + name: Health Surveillance Ontology + prefix: HSO + example: '0000062' + mappings: + bioportal: HSO + obofoundry: hso + ols: hso + ontobee: HSO + obofoundry: + contact: fernanda.dorea@sva.se + contact.github: nandadorea + contact.label: Fernanda Dorea + contact.orcid: 0000-0001-8638-8525 + depends_on: + - bfo + - ncbitaxon + - obi + - ro + - uberon + deprecated: false + description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. + download.owl: http://purl.obolibrary.org/obo/hso.owl + homepage: https://w3id.org/hso + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Health Surveillance Ontology + preferredPrefix: HSO + prefix: hso + repository: https://github.com/SVA-SE/HSO + ols: + description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance. + download: http://purl.obolibrary.org/obo/hso.owl + homepage: https://w3id.org/hso + name: Health Surveillance Ontology + prefix: hso + version: 2021-12-13 + version.iri: http://purl.obolibrary.org/obo/hso/2021-12-13/hso.owl + ontobee: + library: Library + name: Health Surveillance Ontology + prefix: HSO + pattern: ^\d{7}$ +hssp: + biocontext: + is_identifiers: true + is_obo: false + prefix: HSSP + uri_format: http://identifiers.org/hssp/$1 + mappings: + biocontext: HSSP + miriam: hssp + n2t: hssp + ncbi: HSSP + prefixcommons: hssp + miriam: + deprecated: false + description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. + homepage: http://swift.cmbi.kun.nl/swift/hssp/ + id: '00000215' + name: HSSP + namespaceEmbeddedInLui: false + pattern: ^\w{4}$ + prefix: hssp + providers: + - code: CURATOR_REVIEW + description: HSSP at CMBI + homepage: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/ + name: HSSP at CMBI + uri_format: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2 + sampleId: 102l + uri_format: ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2 + n2t: + description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. + example: 102l + homepage: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/ + name: HSSP at CMBI + namespaceEmbeddedInLui: false + pattern: ^\w{4}$ + prefix: hssp + uri_format: ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2 + ncbi: + example: 12GS + name: Database of homology-derived secondary structure of proteins + prefix: HSSP + prefixcommons: + description: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. + example: 102l + homepage: http://www.cmbi.kun.nl/gv/hssp/ + keywords: + - clustering + - protein + - sequence + name: Homology-derived secondary structure of proteins database + pattern: ^\w{4}$ + prefix: hssp + pubmed_ids: + - '7937066' + - '8594579' +htn: + bioportal: + name: Hypertension Ontology + prefix: HTN + example: '00000014' + mappings: + bioportal: HTN + obofoundry: htn + ols: htn + ontobee: HTN + obofoundry: + contact: aellenhicks@gmail.com + contact.github: aellenhicks + contact.label: Amanda Hicks + contact.orcid: 0000-0002-1795-5570 + deprecated: false + description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines + download.owl: http://purl.obolibrary.org/obo/htn.owl + homepage: https://github.com/aellenhicks/htn_owl + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Hypertension Ontology + preferredPrefix: HTN + prefix: htn + repository: https://github.com/aellenhicks/htn_owl + ols: + description: An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines + download: http://purl.obolibrary.org/obo/htn.owl + homepage: https://github.com/aellenhicks/htn_owl + name: Hypertension Ontology For Clinical Data + prefix: htn + version: 2019-06-10 + ontobee: + library: Library + name: Hypertension Ontology + prefix: HTN + pattern: ^\d{8}$ +huge: + biocontext: + is_identifiers: true + is_obo: false + prefix: HUGE + uri_format: http://identifiers.org/huge/$1 + fairsharing: + abbreviation: HUGE + description: HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb). + id: '1941' + name: Human Unidentified Gene-Encoded large proteins database + prefix: FAIRsharing.zx2ztd + subjects: + - Computational Biology + - Life Science + mappings: + biocontext: HUGE + fairsharing: FAIRsharing.zx2ztd + miriam: huge + n2t: huge + prefixcommons: huge + uniprot: HUGE + miriam: + deprecated: false + description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. + homepage: http://www.kazusa.or.jp/huge/ + id: '00000263' + name: HUGE + namespaceEmbeddedInLui: false + pattern: ^KIAA\d{4}$ + prefix: huge + sampleId: KIAA0001 + uri_format: http://www.kazusa.or.jp/huge/gfpage/$1/ + n2t: + description: The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. + example: KIAA0001 + homepage: http://www.kazusa.or.jp/huge/ + name: HUGE at Kazusa DNA Research Institute + namespaceEmbeddedInLui: false + pattern: ^KIAA\d{4}$ + prefix: huge + uri_format: http://www.kazusa.or.jp/huge/gfpage/$1/ + name: Human Unidentified Gene-Encoded + prefixcommons: + description: HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb). + example: KIAA0001 + homepage: http://www.kazusa.or.jp/huge/ + keywords: + - protein + - DNA + - structure + name: Human Unidentified Gene-Encoded large proteins database + pattern: ^KIAA\d{4}$ + prefix: huge + pubmed_ids: + - '14681467' + uri_format: http://www.kazusa.or.jp/huge/cgi/view_direct.cgi?id=$1 + uniprot: + category: Organism-specific databases + identifier: '49' + name: Human Unidentified Gene-Encoded large proteins database + prefix: HUGE + uri_format: http://www.kazusa.or.jp/huge/gfpage/$1 + uri_format: https://www.kazusa.or.jp/huge/gfpage/$1 +iao: + biocontext: + is_identifiers: false + is_obo: true + prefix: IAO + uri_format: http://purl.obolibrary.org/obo/IAO_$1 + bioportal: + name: Information Artifact Ontology + prefix: IAO + fairsharing: + abbreviation: IAO + description: The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. + id: '58' + name: Information Artifact Ontology + prefix: FAIRsharing.gq1xtx + subjects: + - Knowledge and Information Systems + - Data Management + - Subject Agnostic + - Biomedical Science + go: + description: Ontology of information entities, including ontology metadata relations. + name: Information Artifact Ontology + prefix: IAO + mappings: + biocontext: IAO + bioportal: IAO + fairsharing: FAIRsharing.gq1xtx + go: IAO + miriam: iao + n2t: iao + obofoundry: iao + ols: iao + ontobee: IAO + miriam: + deprecated: false + description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. + homepage: http://www.ontobee.org/ontology/IAO + id: '00000603' + name: Information Artifact Ontology + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: iao + sampleId: '0000030' + uri_format: http://purl.obolibrary.org/obo/IAO_$1 + n2t: + description: An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. + example: '0000030' + homepage: http://www.ontobee.org/ontology/IAO + name: IAO through Ontobee + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: iao + uri_format: http://purl.obolibrary.org/obo/IAO_$1 + obofoundry: + appears_in: + - agro + - clyh + - duo + - ecocore + - ecto + - fovt + - labo + - maxo + - pco + - psdo + - xpo + contact: jiezheng@pennmedicine.upenn.edu + contact.github: zhengj2007 + contact.label: Jie Zheng + contact.orcid: 0000-0002-2999-0103 + deprecated: false + description: An ontology of information entities. + download.owl: http://purl.obolibrary.org/obo/iao.owl + homepage: https://github.com/information-artifact-ontology/IAO/ + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Information Artifact Ontology + preferredPrefix: IAO + prefix: iao + repository: https://github.com/information-artifact-ontology/IAO + ols: + description: The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. + download: http://purl.obolibrary.org/obo/iao.owl + homepage: https://github.com/information-artifact-ontology/IAO/ + name: Information Artifact Ontology (IAO) + prefix: iao + version: 2020-12-09 + version.iri: http://purl.obolibrary.org/obo/iao/2020-12-09/iao.owl + ontobee: + library: Library + name: Information Artifact Ontology + prefix: IAO +icd10: + biocontext: + is_identifiers: true + is_obo: false + prefix: ICD + uri_format: http://identifiers.org/icd/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: ICD10 + uri_format: https://icd.codes/icd9cm/$1 + bioportal: + name: International Classification of Diseases, Version 10 + prefix: ICD10 + fairsharing: + abbreviation: ICD-10 + description: The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization (WHO). It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. + id: '1315' + name: International Classification of Diseases Version 10 + prefix: FAIRsharing.nj16g + subjects: + - Health Science + - Global Health + - Biomedical Science + - Epidemiology + homepage: https://icd.who.int/browse10 + mappings: + biocontext: ICD + biolink: ICD10 + bioportal: ICD10 + fairsharing: FAIRsharing.nj16g + miriam: icd + n2t: icd + prefixcommons: icd + miriam: + deprecated: false + description: The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. + homepage: http://www.who.int/classifications/icd/en/ + id: '00000009' + name: ICD + namespaceEmbeddedInLui: false + pattern: ^[A-Z]\d+(\.[-\d+])?$ + prefix: icd + sampleId: C34 + uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1 + n2t: + description: The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. + example: C34 + homepage: http://www.who.int/classifications/icd/en/ + name: International Statistical Classification of Diseases and Related Health Problems + namespaceEmbeddedInLui: false + pattern: ^[A-Z]\d+(\.[-\d+])?$ + prefix: icd + uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1 + name: International Classification of Diseases, 10th Revision + prefixcommons: + description: The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. + example: C34 + homepage: http://www.who.int/classifications/icd/en/ + keywords: + - disease + - taxonomy + - classification + name: International Classification of Diseases + pattern: ^[A-Z]\d+(\.[-\d+])?$ + prefix: icd + uri_format: http://apps.who.int/classifications/icd10/browse/2010/en#/$1 + references: + - https://icdcodelookup.com/icd-10/codes/A01.1 + synonyms: + - ICD + - ICD-10 + - ICD10 + wikidata: + prefix: P494 +icd10cm: + bioportal: + name: International Classification of Diseases, Version 10 - Clinical Modification + prefix: ICD10CM + description: ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. + example: F4521 + fairsharing: + abbreviation: ICD-10-CM + description: The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) is a morbidity classification for classifying diagnoses and reason for visits in all American health care settings. The ICD-10-CM is based on the ICD-10, the statistical classification of disease published by the World Health Organization (WHO) which replaces ICD-9. ICD-10-CM replaced ICD-9-CM Volumes 1 and 2 from October 2015 onwards. + id: '1523' + name: International Classification of Diseases, Tenth Revision, Clinical Modification + prefix: FAIRsharing.hpvbxb + subjects: + - Medicine + - Health Science + - Biomedical Science + homepage: https://www.icd10data.com/ICD10CM + mappings: + bioportal: ICD10CM + fairsharing: FAIRsharing.hpvbxb + name: International Classification of Diseases, 10th Revision, Clinical Modification + synonyms: + - ICD10CM + uri_format: https://icd.codes/icd10cm/$1 + wikidata: + prefix: P4229 +icd10pcs: + bioportal: + name: International Classification of Diseases, Version 10 - Procedure Coding System + prefix: ICD10PCS + description: >- + ICD-10-PCS is being developed as the successor to Volume 3 of the + International Classification of Diseases, Ninth Revision, Clinical + Modification (ICD-9-CM). For more information about ICD-9-CM, see the + ICD-9-CM source synopsis. + + + ICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records. + example: 01N50ZZ + fairsharing: + abbreviation: ICD-10-PCS + description: The ICD-10 Procedure Coding System (ICD-10-PCS) is an international system of medical classification used for procedural coding. The ICD-10-PCS is a procedure classification published by the United States for classifying procedures performed in hospital inpatient health care settings. The ICD-10-PCS replaces the procedural coding portion (Volume 3) of ICD-9-CM. + id: '1522' + name: International Classification of Diseases Version 10 - Procedure Coding System + prefix: FAIRsharing.85k1jm + subjects: + - Health Science + - Biomedical Science + - Epidemiology + homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS + mappings: + bioportal: ICD10PCS + fairsharing: FAIRsharing.85k1jm + name: International Classification of Diseases, 10th Revision, Procedure Coding System + uri_format: https://www.findacode.com/code.php?set=ICD10PCS&c=$1 + wikidata: + prefix: P1690 +icd11: + description: Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease. + example: RA01.0 + fairsharing: + abbreviation: ICD 11 + description: The International Classification of Diseases (ICD) was created to allow the recording, reporting and grouping of conditions and factors that influence health. It contains categories for diseases, health related conditions, and external causes of illness or death. The purpose of the ICD is to allow the systematic recording, analysis, interpretation and comparison of mortality and morbidity data collected in different countries or areas and at different times. The ICD is used to translate diagnoses of diseases and other health problems into an alphanumeric code, which allows storage, retrieval, and analysis of the data. The ICD has become the international standard diagnostic classification for all general epidemiological and many health management purposes. ICD-11 was released in 2018 to allow Member States to prepare for implementation, including translating ICD into their national languages. Member States will start reporting using ICD-11 on 1 January 2022. + id: '1188' + name: International Classification of Diseases Version 11 + prefix: FAIRsharing.97805c + subjects: + - Health Science + - Global Health + - Biomedical Science + - Epidemiology + homepage: https://icd.who.int/ + mappings: + fairsharing: FAIRsharing.97805c + name: International Classification of Diseases, 11th Revision + synonyms: + - ICD-11 + uri_format: https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1 + wikidata: + prefix: P7807 +icd9: + biolink: + is_identifiers: false + is_obo: false + prefix: ICD9 + uri_format: http://translator.ncats.nih.gov/ICD9_$1 + description: The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics. + example: '277.9' + homepage: https://www.cdc.gov/nchs/icd/icd9.htm + mappings: + biolink: ICD9 + name: International Classification of Diseases, 9th Revision + synonyms: + - ICD9 + - ICD9_2005 + - MTHICD9_2006 + uri_format: http://www.icd9data.com/getICD9Code.ashx?icd9=$1 + wikidata: + prefix: P493 +icd9cm: + bioportal: + name: International Classification of Diseases, Version 9 - Clinical Modification + prefix: ICD9CM + description: ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. + example: '784' + fairsharing: + abbreviation: ICD-9-CM + description: The ICD is the international standard diagnostic classification for all general epidemiological, many health management purposes and clinical use. The International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) is an adaption created by the U.S. National Center for Health Statistics (NCHS) and used in assigning diagnostic and procedure codes associated with inpatient, outpatient, and physician office utilization in the United States. The ICD-9-CM is based on the ICD-9 but provides for additional morbidity detail. + id: '1208' + name: International Classification of Diseases, Ninth Revision, Clinical Modification + prefix: FAIRsharing.10zsxb + subjects: + - Medicine + - Health Science + - Biomedical Science + - Epidemiology + - Preclinical Studies + homepage: https://www.cdc.gov/nchs/icd/icd9cm.htm + mappings: + bioportal: ICD9CM + fairsharing: FAIRsharing.10zsxb + name: International Classification of Diseases, 9th Revision, Clinical Modification + pattern: ^([\dA-Z]\d{2}(\.\d{1,3}|))|(\d{2}(\.\d{1,2}|))$ + synonyms: + - IC9CM + - ICD9CM + - ICD9CM_2005 + - ICD9CM_2005 + - ICD9CM_2006 + - ICDCM_2005 + uri_format: http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1 + wikidata: + prefix: P1692 +icdc: + fairsharing: + abbreviation: ICDC + description: The Integrated Climate Data Center (ICDC) allows easy access to climate relevant data from in-situ measurements and satellite remote sensing. These data are important to determine the status and the changes in the climate system. Some relevant re-analysis data are included, which are modeled on the basis of observational data. + id: '3094' + name: Integrated Climate Data Center + prefix: FAIRsharing.d95034 + subjects: + - Social Science + - Meteorology + - Earth Science + - Atmospheric Science + - Remote Sensing + - Oceanography + mappings: + fairsharing: FAIRsharing.d95034 + miriam: icdc + miriam: + deprecated: false + description: The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer. + homepage: https://caninecommons.cancer.gov/#/ + id: '00000812' + name: Integrated Canine Data Commons + namespaceEmbeddedInLui: false + pattern: ^\d{6}$ + prefix: icdc + sampleId: '000009' + uri_format: https://caninecommons.cancer.gov/#/study/$1 +icdo: + description: The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases + example: 9861/3 + homepage: https://www.who.int/classifications/icd/adaptations/oncology/en/ + mappings: + prefixcommons: icdo + name: International Classification of Diseases for Oncology + pattern: ^[8-9]\d{3}(/[0-3])?$ + prefixcommons: + bioportal: '1670' + description: Ontology of Oncology as based on CDC SEER's ICDO-3 Code classification + example: M-8272/O + name: International Classification of Diseases for Oncology + pattern: ^[A-Z0-9]+\/[0-9]+$ + prefix: icdo + synonyms: + - ICD-O + - ICDO + uri_format: http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1 + wikidata: + prefix: P563 +iceberg.element: + biocontext: + is_identifiers: true + is_obo: false + prefix: ICEBERG.ELEMENT + uri_format: http://identifiers.org/iceberg.element/$1 + mappings: + biocontext: ICEBERG.ELEMENT + miriam: iceberg.element + n2t: iceberg.element + miriam: + deprecated: false + description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. + homepage: http://db-mml.sjtu.edu.cn/ICEberg/ + id: '00000469' + name: ICEberg element + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iceberg.element + sampleId: '100' + uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1 + n2t: + description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. + example: '100' + homepage: http://db-mml.sjtu.edu.cn/ICEberg/ + name: ICEberg element at Shanghai Jiaotong University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iceberg.element + uri_format: http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1 +iceberg.family: + biocontext: + is_identifiers: true + is_obo: false + prefix: ICEBERG.FAMILY + uri_format: http://identifiers.org/iceberg.family/$1 + mappings: + biocontext: ICEBERG.FAMILY + miriam: iceberg.family + n2t: iceberg.family + miriam: + deprecated: false + description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. + homepage: http://db-mml.sjtu.edu.cn/ICEberg/ + id: '00000470' + name: ICEberg family + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iceberg.family + sampleId: '1' + uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1 + n2t: + description: ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. + example: '1' + homepage: http://db-mml.sjtu.edu.cn/ICEberg/ + name: ICEberg family at Shanghai Jiaotong University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iceberg.family + uri_format: http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1 +iceo: + bioportal: + name: Integrative and Conjugative Element Ontology + prefix: ICEO + example: 0_0_0_0_7_1_2_1 + example_extras: + - '0000712' + mappings: + bioportal: ICEO + obofoundry: iceo + ols: iceo + ontobee: ICEO + obofoundry: + contact: liumeng94@sjtu.edu.cn + contact.github: Lemon-Liu + contact.label: Meng LIU + contact.orcid: 0000-0003-3781-6962 + deprecated: false + description: ICEO is an integrated biological ontology for the description of bacterial integrative and conjugative elements (ICEs). + download.owl: http://purl.obolibrary.org/obo/iceo.owl + homepage: https://github.com/ontoice/ICEO + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Integrative and Conjugative Element Ontology + preferredPrefix: ICEO + prefix: iceo + repository: https://github.com/ontoice/ICEO + ols: + description: A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. + download: http://purl.obolibrary.org/obo/iceo.owl + homepage: https://github.com/ontoice/ICEO + name: 'ICEO: Ontology of Integrative and Conjugative Elements' + prefix: iceo + version: '2.1' + ontobee: + library: Library + name: Integrative and Conjugative Element Ontology + prefix: ICEO + pattern: ^\d{7}(_\d)?$ +icepo: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ' + download_obo: https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo + example: '0000002' + homepage: https://download.nextprot.org/pub/current_release/controlled_vocabularies/ + name: Ion Channel Electrophysiology Ontology + pattern: ^\d{7}$ + references: + - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823818/ + twitter: neXtProt_news +iclc: + cellosaurus: + category: Cell line collections + homepage: http://www.iclc.it + name: Interlab Cell Line Collection + prefix: ICLC + uri_format: http://www.iclc.it/details/det_list.php?line_id=$1 + example: ATL98012 + mappings: + cellosaurus: ICLC +ico: + biocontext: + is_identifiers: false + is_obo: true + prefix: ICO + uri_format: http://purl.obolibrary.org/obo/ICO_$1 + bioportal: + name: Informed Consent Ontology + prefix: ICO + example: '0000066' + fairsharing: + abbreviation: ICO + description: Informed Consent Ontology (ICO) represents the documentations and processes involved in informed consent. ICO aims to support informed consent data integration and reasoning in the clinical research space. The core terms of ICO covers informed consent forms, the component inside the informed consent form, and various informed consent processes. + id: '651' + name: Informed Consent Ontology + prefix: FAIRsharing.b9znd5 + subjects: + - Medicine + - Health Science + - Biomedical Science + mappings: + biocontext: ICO + bioportal: ICO + fairsharing: FAIRsharing.b9znd5 + obofoundry: ico + ols: ico + ontobee: ICO + obofoundry: + appears_in: + - scdo + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqun Oliver He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: An ontology of clinical informed consents + download.owl: http://purl.obolibrary.org/obo/ico.owl + homepage: https://github.com/ICO-ontology/ICO + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Informed Consent Ontology + preferredPrefix: ICO + prefix: ico + repository: https://github.com/ICO-ontology/ICO + ols: + description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. + download: http://purl.obolibrary.org/obo/ico.owl + homepage: https://github.com/ICO-ontology/ICO + name: Informed Consent Ontology (ICO) + prefix: ico + version: 1.0.187 + version.iri: http://purl.obolibrary.org/obo/2020-08-27/ico.owl + ontobee: + library: Library + name: Informed Consent Ontology + prefix: ICO + pattern: ^\d{7}$ +ideal: + biocontext: + is_identifiers: true + is_obo: false + prefix: IDEAL + uri_format: http://identifiers.org/ideal/$1 + fairsharing: + abbreviation: IDEAL + description: IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature) is a collection of experimentally-verified intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and post-translational modification sites together with references and structural domain assignments. + id: '1597' + name: Intrinsically Disordered proteins with Extensive Annotations and Literature + prefix: FAIRsharing.h3y42f + subjects: + - Biology + homepage: https://www.ideal-db.org + mappings: + biocontext: IDEAL + fairsharing: FAIRsharing.h3y42f + miriam: ideal + n2t: ideal + uniprot: IDEAL + miriam: + deprecated: false + description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. + homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ + id: '00000398' + name: IDEAL + namespaceEmbeddedInLui: false + pattern: ^IID\d+$ + prefix: ideal + sampleId: IID00001 + uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 + n2t: + description: IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. + example: IID00001 + homepage: http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ + name: IDEAL at Maebashi Institute of Technology + namespaceEmbeddedInLui: false + pattern: ^IID\d+$ + prefix: ideal + uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$1 + name: Intrinsically Disordered proteins with Extensive Annotations and Literature + uniprot: + category: Family and domain databases + identifier: '251' + link_is_explicit: 'true' + name: Intrinsically Disordered proteins with Extensive Annotations and Literature + prefix: IDEAL + uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 +ido: + biocontext: + is_identifiers: false + is_obo: true + prefix: IDO + uri_format: http://purl.obolibrary.org/obo/IDO_$1 + bioportal: + name: Infectious Disease Ontology + prefix: IDO + fairsharing: + abbreviation: IDO + description: The IDO ontologies are designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases. + id: '1275' + name: Infectious Disease Ontology Core + prefix: FAIRsharing.aae3v6 + subjects: + - Molecular Infection Biology + - Biomedical Science + - Preclinical Studies + mappings: + biocontext: IDO + bioportal: IDO + fairsharing: FAIRsharing.aae3v6 + miriam: ido + n2t: ido + obofoundry: ido + ols: ido + ontobee: IDO + miriam: + deprecated: false + description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. + homepage: https://www.ebi.ac.uk/ols/ontologies/ido + id: '00000677' + name: Infectious Disease Ontology + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: ido + sampleId: '0000504' + uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 + n2t: + description: Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. + example: '0000504' + homepage: https://www.ebi.ac.uk/ols/ontologies/ido + name: IDO through OLS + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: ido + uri_format: https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 + obofoundry: + appears_in: + - scdo + contact: Lindsay.Cowell@utsouthwestern.edu + contact.github: lgcowell + contact.label: Lindsay Cowell + contact.orcid: 0000-0003-1617-8244 + deprecated: false + description: A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. + download.owl: http://purl.obolibrary.org/obo/ido.owl + homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Infectious Disease Ontology + preferredPrefix: IDO + prefix: ido + repository: https://github.com/infectious-disease-ontology/infectious-disease-ontology + ols: + description: A set of interoperable ontologies that will together provide coverage of the infectious disease domain. IDO core is the upper-level ontology that hosts terms of general relevance across the domain, while extension ontologies host terms to specific to a particular part of the domain. + download: http://purl.obolibrary.org/obo/ido.owl + homepage: http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology + name: Infectious Disease Ontology + prefix: ido + version: 2017-11-03 + version.iri: http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl + ontobee: + library: Library + name: Infectious Disease Ontology + prefix: IDO +idocovid19: + bioportal: + name: The COVID-19 Infectious Disease Ontology + prefix: IDO-COVID-19 + contact: + email: johnbeverley2021@u.northwestern.edu + github: johnbeve + name: John Beverly + orcid: 0000-0002-1118-1738 + example: '0001191' + mappings: + bioportal: IDO-COVID-19 + ols: idocovid19 + ols: + contact: johnbeverley2021@u.northwestern.edu + description: The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. + download: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19 + homepage: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 + name: The COVID-19 Infectious Disease Ontology + prefix: idocovid19 + version: 2020-07-21 + version.iri: http://purl.obolibrary.org/obo/2020-21-07/ido-covid-19.owl + pattern: ^\d{7}$ + repository: https://github.com/infectious-disease-ontology-extensions/ido-covid-19 +idoden: + bioportal: + name: Dengue Fever Ontology + prefix: IDODEN + description: An ontology for dengue fever. + example: '0003463' + fairsharing: + abbreviation: IDODEN + description: An ontology for dengue fever. + id: '756' + name: Dengue Fever Ontology + prefix: FAIRsharing.askzq4 + subjects: [] + homepage: https://bioportal.bioontology.org/ontologies/IDODEN + mappings: + bioportal: IDODEN + fairsharing: FAIRsharing.askzq4 + name: Dengue Fever Ontology + pattern: ^\d{7}$ + references: + - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479 +idomal: + biocontext: + is_identifiers: false + is_obo: true + prefix: IDOMAL + uri_format: http://purl.obolibrary.org/obo/IDOMAL_$1 + bioportal: + name: Malaria Ontology + prefix: IDOMAL + download_obo: http://purl.obolibrary.org/obo/idomal.obo + example: '0002350' + fairsharing: + abbreviation: IDOMAL + description: An application ontology for malaria extending the infectious disease ontology (IDO). With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated. + id: '549' + name: Infection Disease Ontology Malaria + prefix: FAIRsharing.2q8c28 + subjects: + - Molecular Infection Biology + - Life Science + - Biomedical Science + mappings: + biocontext: IDOMAL + bioportal: IDOMAL + fairsharing: FAIRsharing.2q8c28 + obofoundry: idomal + ols: idomal + ontobee: IDOMAL + obofoundry: + appears_in: + - scdo + contact: topalis@imbb.forth.gr + contact.label: Pantelis Topalis + deprecated: true + description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. + download.obo: http://purl.obolibrary.org/obo/idomal.obo + download.owl: http://purl.obolibrary.org/obo/idomal.owl + homepage: https://www.vectorbase.org/ontology-browser + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Malaria Ontology + prefix: idomal + repository: https://github.com/VEuPathDB-ontology/IDOMAL + ols: + description: An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. + download: http://purl.obolibrary.org/obo/idomal.owl + homepage: https://www.vectorbase.org/ontology-browser + name: Malaria Ontology + prefix: idomal + version: 2015-03-16 + version.iri: http://purl.obolibrary.org/obo/idomal/2015-03-16/idomal.owl + ontobee: + library: Library + name: Malaria Ontology + prefix: IDOMAL + pattern: ^\d{7}$ +idoo: + mappings: + miriam: idoo + n2t: idoo + miriam: + deprecated: false + description: Identifiers.org Ontology + homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology + id: '00000683' + name: Identifiers.org Ontology + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z]+$ + prefix: idoo + sampleId: DataCollection + uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 + n2t: + description: Identifiers.org Ontology + example: DataCollection + homepage: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology + name: Identifiers.org Ontology + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z]+$ + prefix: idoo + uri_format: http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 +idot: + biocontext: + is_identifiers: true + is_obo: false + prefix: IDOT + uri_format: http://identifiers.org/idot/$1 + homepage: http://biomodels.net/vocab/idot.rdf + mappings: + biocontext: IDOT + miriam: idot + n2t: idot + miriam: + deprecated: false + description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. + homepage: https://identifiers.org/ + id: '00000519' + name: Identifiers.org Terms + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+$ + prefix: idot + sampleId: identifierPattern + uri_format: https://biomodels.net/vocab/idot.rdf#$1 + n2t: + description: Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. + example: identifierPattern + homepage: https://identifiers.org/ + name: IdoT via biomodels.net + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+$ + prefix: idot + uri_format: https://biomodels.net/vocab/idot.rdf#$1 + uri_format: https://biomodels.net/vocab/idot.rdf#$1 +idpo: + contact: + email: f.quaglia@ibiom.cnr.it + github: federicaquaglia + name: Federica Quaglia + orcid: 0000-0002-0341-4888 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR. + example: '00056' + homepage: https://www.disprot.org/ontology + name: Intrinsically Disordered Proteins Ontology + pattern: ^\d{5}$ + uri_format: https://www.disprot.org/idpo/IDPO:$1 +idr: + fairsharing: + abbreviation: IDR + description: IDR is a prototype platform for publishing, mining and integrating bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy using the OMERO and Bio-Formats open source software built by the Open Microscopy Environment. Deployed on an OpenStack cloud running on the EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology. + id: '2303' + name: Image Data Resource + prefix: FAIRsharing.6wf1zw + subjects: + - Botany + - Life Science + - Biomedical Science + mappings: + fairsharing: FAIRsharing.6wf1zw + miriam: idr + miriam: + deprecated: false + description: Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools. + homepage: https://idr.openmicroscopy.org + id: '00000743' + name: Image Data Resource + namespaceEmbeddedInLui: false + pattern: ^[0-9]{4}$ + prefix: idr + sampleId: '0001' + uri_format: https://idr.openmicroscopy.org/search/?query=Name:idr$1 +iedb: + fairsharing: + abbreviation: IEDB + description: The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB. + id: '2346' + name: Immune Epitope Database + prefix: FAIRsharing.c886cd + subjects: + - Bioinformatics + - Immunology + - Life Science + mappings: + fairsharing: FAIRsharing.c886cd + miriam: iedb + miriam: + deprecated: false + description: The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes. + homepage: https://www.lji.org/ + id: '00000865' + name: Immune Epitope Database (IEDB) + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: iedb + sampleId: '1038233' + uri_format: https://www.iedb.org/reference/$1 + name: Immune Epitope Database +iev: + biocontext: + is_identifiers: false + is_obo: true + prefix: IEV + uri_format: http://purl.obolibrary.org/obo/IEV_$1 + example: '0000000' + mappings: + biocontext: IEV + obofoundry: iev + prefixcommons: iev + obofoundry: + deprecated: true + homepage: http://www.inoh.org + name: Event (INOH pathway ontology) + prefix: iev + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1011' + description: The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure. + example: IEV_0000913 + homepage: http://www.inoh.org + keywords: + - obo + - pathway + - structure + name: Event (INOH pathway ontology) + pattern: ^IEV_\d+$ + prefix: iev + uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1 +igrhcellid: + cellosaurus: + category: Cell line databases/resources + homepage: http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi + name: Integrated Genomic Resources of human Cell Lines for Identification + prefix: IGRhCellID + uri_format: http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1 + example: ACHN + mappings: + cellosaurus: IGRhCellID +igsn: + fairsharing: + abbreviation: IGSN + description: IGSN is a globally unique and persistent identifier for material samples. The IGSN registration service will facilitate the discovery, access, and sharing of samples, ensure preservation and access of sample data, aid identification of samples in the literature, and advance the exchange of digital sample data among interoperable data systems. + id: '51' + name: International GeoSample Number + prefix: FAIRsharing.Yvc76F + subjects: + - Geochemistry + - Hydrogeology + - Environmental Science + - Geology + - Earth Science + mappings: + fairsharing: FAIRsharing.Yvc76F + miriam: igsn + n2t: igsn + miriam: + deprecated: false + description: IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents. + homepage: http://www.geosamples.org/ + id: '00000806' + name: International Geo Sample Number + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$ + prefix: igsn + sampleId: AU124 + uri_format: http://igsn.org/$1 + n2t: + example: SSH000SUA + homepage: http://www.geosamples.org/ + name: International Geo Sample Number + namespaceEmbeddedInLui: false + prefix: igsn + uri_format: hdl.handle.net/10273/$1 +igsr: + cellosaurus: + category: Biological sample resources + homepage: https://www.internationalgenome.org/ + name: International Genome Sample Resource + prefix: IGSR + uri_format: https://www.internationalgenome.org/data-portal/sample/$1 + example: NA06985 + fairsharing: + abbreviation: IGSR + description: 'The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.' + id: '2737' + name: The International Genome Sample Resource + prefix: FAIRsharing.4Vs9VM + subjects: + - Genomics + - Comparative Genomics + mappings: + cellosaurus: IGSR + fairsharing: FAIRsharing.4Vs9VM +ihw: + cellosaurus: + category: Cell line databases/resources + homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html + name: International Histocompatibility Workshop cell lines + prefix: IHW + description: The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics. + example: IHW09326 + homepage: https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html + mappings: + cellosaurus: IHW + name: International Histocompatibility Workshop cell lines + pattern: ^IHW\d+$ +illumina.probe: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip. + example: ILMN_129894 + homepage: https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt + name: Illumina Probe Identifier + pattern: ^ILMN_\d+$ + references: + - https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt +imanis: + cellosaurus: + category: Cell line collections + homepage: https://www.imanislife.com/collections/cell-lines/ + name: Imanis Life Sciences cell line products + prefix: Imanis + uri_format: https://www.imanislife.com/?s=$1 + example: CL070 + mappings: + cellosaurus: Imanis +imdrf: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence. + homepage: http://www.imdrf.org/ + name: International Medical Device Regulators Forum + no_own_terms: true + references: + - https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes +imex: + biocontext: + is_identifiers: true + is_obo: false + prefix: IMEX + uri_format: http://identifiers.org/imex/$1 + mappings: + biocontext: IMEX + miriam: imex + n2t: imex + prefixcommons: imex + miriam: + deprecated: false + description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. + homepage: https://www.imexconsortium.org/ + id: '00000122' + name: IMEx + namespaceEmbeddedInLui: false + pattern: ^IM-\d+(-?)(\d+?)$ + prefix: imex + providers: + - code: CURATOR_REVIEW + description: IMEx Consortium though Intact + homepage: https://www.ebi.ac.uk/intact/ + name: IMEx Consortium though Intact + uri_format: https://imexcentral.org/icentral/imex/rec/$1 + sampleId: IM-19210-3 + uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1 + n2t: + description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. + example: IM-19210-3 + homepage: https://www.imexconsortium.org/ + name: IMEx Consortium running at EBI + namespaceEmbeddedInLui: false + pattern: ^IM-\d+(-?)(\d+?)$ + prefix: imex + uri_format: https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1 + name: International Molecular Exchange + prefixcommons: + description: The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. + example: IM-12080-80 + homepage: http://disber.net/imexdrupal/ + keywords: + - molecule + - interaction + name: International Molecular Exchange + pattern: ^IM-\d+(-?)(\d+?)$ + prefix: imex + pubmed_ids: + - '17893861' + uri_format: http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1 +img.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: IMG.GENE + uri_format: http://identifiers.org/img.gene/$1 + mappings: + biocontext: IMG.GENE + miriam: img.gene + n2t: img.gene + prefixcommons: img.gene + miriam: + deprecated: false + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. + homepage: http://img.jgi.doe.gov/ + id: '00000176' + name: Integrated Microbial Genomes Gene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: img.gene + sampleId: '638309541' + uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 + n2t: + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. + example: '638309541' + homepage: http://img.jgi.doe.gov/ + name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: img.gene + uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 + prefixcommons: + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. + example: '638309541' + keywords: + - gene + - genome + name: Integrated Microbial Genomes Gene + pattern: ^\d+$ + prefix: img.gene + pubmed_ids: + - '17933782' + uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1 +img.taxon: + biocontext: + is_identifiers: true + is_obo: false + prefix: IMG.TAXON + uri_format: http://identifiers.org/img.taxon/$1 + mappings: + biocontext: IMG.TAXON + miriam: img.taxon + n2t: img.taxon + prefixcommons: img.taxon + miriam: + deprecated: false + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. + homepage: http://img.jgi.doe.gov/ + id: '00000175' + name: Integrated Microbial Genomes Taxon + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: img.taxon + sampleId: '648028003' + uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 + n2t: + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. + example: '648028003' + homepage: http://img.jgi.doe.gov/ + name: Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: img.taxon + uri_format: http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 + prefixcommons: + description: The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. + example: '648028003' + keywords: + - genome + - taxonomy + name: Integrated Microbial Genomes Taxon + pattern: ^\d+$ + prefix: img.taxon + pubmed_ids: + - '17933782' + uri_format: http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&taxon_oid=$1 +imgt.hla: + biocontext: + is_identifiers: true + is_obo: false + prefix: IMGT.HLA + uri_format: http://identifiers.org/imgt.hla/$1 + cellosaurus: + category: Cell line databases/resources + homepage: https://www.ebi.ac.uk/ipd/imgt/hla/ + name: IPD-IMGT/HLA database + prefix: IPD-IMGT/HLA + uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/fetch_cell.cgi?$1 + fairsharing: + abbreviation: IPD-IMGT/HLA + description: The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IMGT/HLA Database was established to provide a locus-specific database (LSDB) for the allelic sequences of the genes in the HLA system, also known as the human MHC. The IMGT/HLA Database was first released in 1998 and subsequently incorporated as a module of IPD in 2012. + id: '1714' + name: IPD-IMGT/HLA - Human Leukocyte Antigen Sequence Database + prefix: FAIRsharing.e28v7g + subjects: + - Immunogenetics + - Immunology + - Biomedical Science + go: + homepage: http://www.ebi.ac.uk/imgt/hla + name: IMGT/HLA human major histocompatibility complex sequence database + prefix: IMGT_HLA + mappings: + biocontext: IMGT.HLA + cellosaurus: IPD-IMGT/HLA + fairsharing: FAIRsharing.e28v7g + go: IMGT_HLA + miriam: imgt.hla + n2t: imgt.hla + ncbi: IMGT/HLA + prefixcommons: imgthla + miriam: + deprecated: false + description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. + homepage: https://www.ebi.ac.uk/imgt/hla/allele.html + id: '00000331' + name: IMGT HLA + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9*:]+$ + prefix: imgt.hla + sampleId: A*01:01:01:01 + uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 + n2t: + description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. + example: A*01:01:01:01 + homepage: https://www.ebi.ac.uk/imgt/hla/allele.html + name: IMGT HLA at EBI + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9*:]+$ + prefix: imgt.hla + uri_format: https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 + ncbi: + example: HLA00031 + homepage: http://www.ebi.ac.uk/imgt/hla/ + name: Immunogenetics database, human MHC + prefix: IMGT/HLA + prefixcommons: + description: The IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. + example: A*01:01:01:01 + homepage: http://www.ebi.ac.uk/imgt/hla/ + keywords: + - DNA + - RNA + - protein + name: IMGT/HLA + pattern: ^[A-Z0-9*:]+$ + prefix: imgthla + pubmed_ids: + - '16381979' + uri_format: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele.cgi? + synonyms: + - IPD-IMGT/HLA +imgt.ligm: + biocontext: + is_identifiers: true + is_obo: false + prefix: IMGT.LIGM + uri_format: http://identifiers.org/imgt.ligm/$1 + go: + description: Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences. + homepage: http://www.imgt.org/ + name: ImMunoGeneTics database covering immunoglobulins and T-cell receptors + prefix: IMGT_LIGM + mappings: + biocontext: IMGT.LIGM + go: IMGT_LIGM + miriam: imgt.ligm + n2t: imgt.ligm + ncbi: IMGT/LIGM + prefixcommons: imgt.ligm + miriam: + deprecated: false + description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. + homepage: http://www.imgt.org/ + id: '00000287' + name: IMGT LIGM + namespaceEmbeddedInLui: false + pattern: ^M\d+$ + prefix: imgt.ligm + providers: + - code: CURATOR_REVIEW + description: IMGT LIGM through DKFZ (SRS) + homepage: http://genius.embnet.dkfz-heidelberg.de/ + name: IMGT LIGM through DKFZ (SRS) + uri_format: http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1'] + sampleId: M94112 + uri_format: http://www.imgt.org/ligmdb/view?id=$1 + n2t: + description: IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. + example: M94112 + homepage: http://www.imgt.org/ + name: IMGT LIGM at CNRS + namespaceEmbeddedInLui: false + pattern: ^M\d+$ + prefix: imgt.ligm + uri_format: http://www.imgt.org/ligmdb/view?id=$1 + ncbi: + example: U03895 + homepage: http://www.imgt.org/IMGTinformation/LIGM.html + name: Immunogenetics database, immunoglobulins and T-cell receptors + prefix: IMGT/LIGM + prefixcommons: + description: MGT/LIGM-DB is the IMGT comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species. + example: A68511 + homepage: http://imgt.cines.fr/cgi-bin/IMGTlect.jv + keywords: + - DNA + name: IMGT/LIGM-DB + pattern: ^[A-Z]\d+$ + prefix: imgt.ligm + pubmed_ids: + - '16381979' +imr: + biocontext: + is_identifiers: false + is_obo: true + prefix: IMR + uri_format: http://purl.obolibrary.org/obo/IMR_$1 + example: '0000001' + mappings: + biocontext: IMR + obofoundry: imr + prefixcommons: imr + obofoundry: + contact: curator@inoh.org + contact.label: INOH curators + deprecated: true + homepage: http://www.inoh.org + name: Molecule role (INOH Protein name/family name ontology) + prefix: imr + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1029' + description: MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data. + example: IMR_0800118 + homepage: http://www.inoh.org + keywords: + - ontology + - protein + - small molecule + name: MoleculeRole Ontology (INOH Protein name/family name ontology) + pattern: ^IMR_\d+$ + prefix: imr + uri_format: http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1 +inchi: + biocontext: + is_identifiers: true + is_obo: false + prefix: INCHI + uri_format: http://identifiers.org/inchi/$1 + fairsharing: + abbreviation: InChI + description: Originally developed by the International Union of Pure and Applied Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is a machine-readable string generated from a chemical structure. InChIs are unique to the compound they describe and can encode absolute stereochemistry making chemicals and chemistry machine-readable and discoverable. A simple analogy is that InChI is the bar-code for chemistry and chemical structures. A hashed fixed-length version of the InChI, the InChIKey, is also widely used. The InChI format and algorithm are non-proprietary and the software is open source, with ongoing development done by the community. A number of IUPAC working groups are working on extensions and new applications of the standard. + id: '1477' + name: IUPAC International Chemical Identifier + prefix: FAIRsharing.ddk9t9 + subjects: + - Knowledge and Information Systems + - Cheminformatics + - Chemistry + mappings: + biocontext: INCHI + fairsharing: FAIRsharing.ddk9t9 + miriam: inchi + n2t: inchi + miriam: + deprecated: false + description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. + homepage: http://www.chemspider.com/ + id: '00000383' + name: InChI + namespaceEmbeddedInLui: false + pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ + prefix: inchi + providers: + - code: CURATOR_REVIEW + description: InChI through NIST + homepage: http://webbook.nist.gov/chemistry + name: InChI through NIST + uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1 + - code: ebi + description: InChI through ChEBI + homepage: https://www.ebi.ac.uk/chebi/ + name: InChI through ChEBI + uri_format: https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1 + - code: um + description: InChI through RDF Open Molecules + homepage: http://rdf.openmolecules.net/ + name: InChI through RDF Open Molecules + uri_format: http://rdf.openmolecules.net/?$1 + sampleId: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + uri_format: http://www.chemspider.com/$1 + n2t: + description: The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. + example: InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 + homepage: http://webbook.nist.gov/chemistry + name: InChI through NIST + namespaceEmbeddedInLui: false + pattern: ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ + prefix: inchi + uri_format: http://webbook.nist.gov/cgi/cbook.cgi?$1 + wikidata: + prefix: P234 +inchikey: + biocontext: + is_identifiers: true + is_obo: false + prefix: INCHIKEY + uri_format: http://identifiers.org/inchikey/$1 + mappings: + biocontext: INCHIKEY + miriam: inchikey + n2t: inchikey + scholia: inchikey + miriam: + deprecated: false + description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. + homepage: http://www.chemspider.com/ + id: '00000387' + name: InChIKey + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? + prefix: inchikey + providers: + - code: scholia + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + homepage: https://scholia.toolforge.org/ + name: Scholia + uri_format: https://scholia.toolforge.org/inchikey/$1 + sampleId: RYYVLZVUVIJVGH-UHFFFAOYSA-N + uri_format: http://www.chemspider.com/inchikey=$1 + n2t: + description: The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. + example: RYYVLZVUVIJVGH-UHFFFAOYSA-N + homepage: http://cactus.nci.nih.gov/chemical/structure + name: InChiKey resolver at NCI + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? + prefix: inchikey + uri_format: http://cactus.nci.nih.gov/chemical/structure/$1/names + wikidata: + prefix: P235 +inhand: + comment: This nomenclature is available via email. Truly a disgrace. + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The standard reference for nomenclature and diagnostic criteria in toxicologic pathology. + fairsharing: + abbreviation: INHAND + description: Standard reference for nomenclature and diagnostic criteria in toxicologic pathology. + id: '392' + name: International Harmonization of Nomenclature and Diagnostic criteria + prefix: FAIRsharing.9gqfpm + subjects: + - Biomedical Science + homepage: https://www.goreni.org/gr3_nomenclature.php + mappings: + fairsharing: FAIRsharing.9gqfpm + name: The International Harmonization of Nomenclature and Diagnostic criteria + proprietary: true +inn: + comment: can not find a place to resolve to + description: Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. + example: fluticasone + homepage: https://www.who.int/teams/health-product-and-policy-standards/inn + name: International Nonproprietary Names + synonyms: + - INN_ID + uri_format: https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1 + wikidata: + prefix: P2275 +ino: + biolink: + is_identifiers: false + is_obo: true + prefix: INO + uri_format: http://purl.obolibrary.org/obo/INO_$1 + bioportal: + name: Interaction Network Ontology + prefix: INO + example: '0000003' + fairsharing: + abbreviation: INO + description: The Interaction Network Ontology (INO) aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It models general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies, and includes over 500 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms. + id: '891' + name: Interaction Network Ontology + prefix: FAIRsharing.mm72as + subjects: + - Life Science + mappings: + biolink: INO + bioportal: INO + fairsharing: FAIRsharing.mm72as + obofoundry: ino + ols: ino + ontobee: INO + obofoundry: + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqun Oliver He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: An ontology of interactions and interaction networks + download.owl: http://purl.obolibrary.org/obo/ino.owl + homepage: https://github.com/INO-ontology/ino + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Interaction Network Ontology + preferredPrefix: INO + prefix: ino + repository: https://github.com/INO-ontology/ino + ols: + description: he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. + download: http://purl.obolibrary.org/obo/ino.owl + homepage: https://github.com/INO-ontology/ino + name: 'INO: Interaction Network Ontology' + prefix: ino + version: 1.0.112 + ontobee: + library: Library + name: Interaction Network Ontology + prefix: INO + pattern: ^\d{7}$ +insdc: + biocontext: + is_identifiers: true + is_obo: false + prefix: INSDC + uri_format: http://identifiers.org/insdc/$1 + mappings: + biocontext: INSDC + miriam: insdc + n2t: insdc + prefixcommons: insdc + miriam: + deprecated: false + description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. + homepage: https://www.ncbi.nlm.nih.gov/Genbank/ + id: '00000029' + name: Nucleotide Sequence Database + namespaceEmbeddedInLui: false + pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ + prefix: insdc + providers: + - code: CURATOR_REVIEW + description: INSDC through DDBJ + homepage: http://www.ddbj.nig.ac.jp/ + name: INSDC through DDBJ + uri_format: http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1 + - code: ebi + description: INSDC through European Nucleotide Archive (ENA) + homepage: https://www.ebi.ac.uk/ena/ + name: INSDC through European Nucleotide Archive (ENA) + uri_format: https://www.ebi.ac.uk/ena/data/view/$1 + - code: ncbi + description: INSDC through Nucleotide database at NCBI + homepage: https://www.ncbi.nlm.nih.gov/nuccore/ + name: INSDC through Nucleotide database at NCBI + uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 + sampleId: X58356 + uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 + n2t: + description: The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. + example: X58356 + homepage: https://www.ncbi.nlm.nih.gov/nuccore/ + name: INSDC through Nucleotide database at NCBI + namespaceEmbeddedInLui: false + pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ + prefix: insdc + uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 + prefixcommons: + description: The International Nucleotide Sequence Databases (INSD) have been developed and maintained collaboratively between DDBJ, EMBL, and GenBank for over 18 years. + example: X58356 + homepage: http://www.insdc.org/ + keywords: + - DNA + name: International Nucleotide Sequence Database Collaboration (GenBank, EMBL, DDBJ) + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: insdc + pubmed_ids: + - '17148479' + - '17202161' + - '2326192' + - '12436968' +insdc.cds: + biocontext: + is_identifiers: true + is_obo: false + prefix: INSDC.CDS + uri_format: http://identifiers.org/insdc.cds/$1 + has_canonical: ncbiprotein + mappings: + biocontext: INSDC.CDS + miriam: insdc.cds + n2t: insdc.cds + miriam: + deprecated: false + description: The coding sequence or protein identifiers as maintained in INSDC. + homepage: http://getentry.ddbj.nig.ac.jp + id: '00000606' + name: INSDC CDS + namespaceEmbeddedInLui: false + pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ + prefix: insdc.cds + providers: + - code: CURATOR_REVIEW + description: INSDC CDS through ENA + homepage: https://www.ebi.ac.uk/ena + name: INSDC CDS through ENA + uri_format: https://www.ebi.ac.uk/ena/data/view/$1 + - code: CURATOR_REVIEW + description: INSDC CDS through NCBI + homepage: https://www.ncbi.nlm.nih.gov/protein/ + name: INSDC CDS through NCBI + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 + sampleId: AAA35559 + uri_format: http://getentry.ddbj.nig.ac.jp/getentry/dad/$1 + n2t: + description: The coding sequence or protein identifiers as maintained in INSDC. + example: AAA35559 + homepage: https://www.ncbi.nlm.nih.gov/protein/ + name: INSDC CDS through NCBI + namespaceEmbeddedInLui: false + pattern: ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ + prefix: insdc.cds + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 +insdc.gca: + biocontext: + is_identifiers: true + is_obo: false + prefix: INSDC.GCA + uri_format: http://identifiers.org/insdc.gca/$1 + mappings: + biocontext: INSDC.GCA + miriam: insdc.gca + n2t: insdc.gca + miriam: + deprecated: false + description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. + homepage: https://www.ebi.ac.uk/ena/browse/genome-assembly-database + id: '00000607' + name: Genome assembly database + namespaceEmbeddedInLui: false + pattern: ^GC[AF]_[0-9]{9}\.[0-9]+$ + prefix: insdc.gca + providers: + - code: ncbi + description: Genome assembly database NCBI + homepage: https://www.ncbi.nlm.nih.gov/assembly/ + name: Genome assembly database NCBI + uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 + sampleId: GCA_000155495.1 + uri_format: https://www.ebi.ac.uk/ena/data/view/$1 + n2t: + description: The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. + example: GCA_000155495.1 + homepage: https://www.ncbi.nlm.nih.gov/assembly/ + name: Genome assembly database NCBI + namespaceEmbeddedInLui: false + pattern: ^GCA_[0-9]{9}\.[0-9]$ + prefix: insdc.gca + uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 +insdc.run: + comment: "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --" + contributor: + email: cjmungall@lbl.gov + github: cmungall + name: Chris Mungall + orcid: 0000-0002-6601-2165 + description: An experimental run, served thrugh the ENA + example: ERR436051 + has_canonical: ena.embl + homepage: https://www.insdc.org/ + name: International Nucleotide Sequence Database Collaboration (INSDC) Run + pattern: ^(E|D|S)RR[0-9]{6,}$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: https://www.ebi.ac.uk/ena/browser/view/$1 +insdc.sra: + biocontext: + is_identifiers: true + is_obo: false + prefix: INSDC.SRA + uri_format: http://identifiers.org/insdc.sra/$1 + fairsharing: + abbreviation: SRA + description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' + id: '1978' + name: Sequence Read Archive + prefix: FAIRsharing.g7t2hv + subjects: + - Virology + - Life Science + - Epidemiology + mappings: + biocontext: INSDC.SRA + fairsharing: FAIRsharing.g7t2hv + miriam: insdc.sra + n2t: insdc.sra + miriam: + deprecated: false + description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' + homepage: https://www.ncbi.nlm.nih.gov/sra + id: '00000243' + name: Sequence Read Archive + namespaceEmbeddedInLui: false + pattern: ^[SED]R[APRSXZ]\d+$ + prefix: insdc.sra + providers: + - code: ebi + description: European Nucleotide Archive (ENA) + homepage: https://www.ebi.ac.uk/ena + name: European Nucleotide Archive (ENA) + uri_format: https://www.ebi.ac.uk/ena/data/view/$1 + - code: ddbj + description: DDBJ Sequence Read Archive (DRA) + homepage: http://trace.ddbj.nig.ac.jp/dra/ + name: DDBJ Sequence Read Archive (DRA) + uri_format: http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1 + sampleId: SRX000007 + uri_format: https://www.ncbi.nlm.nih.gov/sra/$1 + n2t: + description: 'The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.' + example: SRX000007 + homepage: https://www.ncbi.nlm.nih.gov/sra + name: Sequence Read Archive at NCBI + namespaceEmbeddedInLui: false + pattern: ^[SED]R[APRSXZ]\d+$ + prefix: insdc.sra + uri_format: https://www.ncbi.nlm.nih.gov/sra/$1 +intact: + biocontext: + is_identifiers: true + is_obo: false + prefix: INTACT + uri_format: http://identifiers.org/intact/$1 + fairsharing: + abbreviation: IntAct + description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. + id: '1599' + name: IntAct molecular interaction database + prefix: FAIRsharing.d05nwx + subjects: + - Biology + go: + homepage: https://www.ebi.ac.uk/intact/ + name: IntAct protein interaction database + prefix: IntAct + mappings: + biocontext: INTACT + fairsharing: FAIRsharing.d05nwx + go: IntAct + miriam: intact + n2t: intact + prefixcommons: intact + uniprot: IntAct + miriam: + deprecated: false + description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. + homepage: https://www.ebi.ac.uk/intact/ + id: '00000010' + name: IntAct + namespaceEmbeddedInLui: false + pattern: ^EBI\-[0-9]+$ + prefix: intact + sampleId: EBI-2307691 + uri_format: https://www.ebi.ac.uk/intact/interaction/$1 + n2t: + description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. + example: EBI-2307691 + homepage: https://www.ebi.ac.uk/intact/ + name: IntAct at EBI + namespaceEmbeddedInLui: false + pattern: ^EBI\-[0-9]+$ + prefix: intact + uri_format: https://www.ebi.ac.uk/intact/interaction/$1 + prefixcommons: + description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. + example: EBI-2307691 + homepage: http://www.ebi.ac.uk/intact + keywords: + - protein + - interaction + name: The IntAct molecular interaction database + pattern: ^EBI\-\d+$ + prefix: intact + pubmed_ids: + - '14681455' + uri_format: http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$1 + uniprot: + category: Protein-protein interaction databases + identifier: '51' + link_is_explicit: 'true' + name: Protein interaction database and analysis system + prefix: IntAct + uri_format: https://www.ebi.ac.uk/intact/interactors/id:$1* +intact.molecule: + biocontext: + is_identifiers: true + is_obo: false + prefix: INTACT.MOLECULE + uri_format: http://identifiers.org/intact.molecule/$1 + mappings: + biocontext: INTACT.MOLECULE + miriam: intact.molecule + n2t: intact.molecule + miriam: + deprecated: false + description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. + homepage: https://www.ebi.ac.uk/intact/ + id: '00000427' + name: IntAct Molecule + namespaceEmbeddedInLui: false + pattern: ^EBI\-[0-9]+$ + prefix: intact.molecule + sampleId: EBI-366083 + uri_format: https://www.ebi.ac.uk/intact/molecule/$1 + n2t: + description: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. + example: EBI-366083 + homepage: https://www.ebi.ac.uk/intact/ + name: IntAct Molecule at EBI + namespaceEmbeddedInLui: false + pattern: ^EBI\-[0-9]+$ + prefix: intact.molecule + uri_format: https://www.ebi.ac.uk/intact/molecule/$1 +interlex: + fairsharing: + abbreviation: InterLex + description: The InterLex terminology is a lexicon of biomedical terms built on the foundation of NeuroLex and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies and BIRNLex (Biomedical Informatics Research Network Project Lexicon). Final content review from NeuroLex is still ongoing. + id: '1118' + name: InterLex + prefix: FAIRsharing.67sssf + subjects: + - Anatomy + - Neurobiology + - Biomedical Science + mappings: + fairsharing: FAIRsharing.67sssf + miriam: ilx + miriam: + deprecated: false + description: 'InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ' + homepage: https://www.fdilab.org + id: '00000814' + name: InterLex + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: ilx + sampleId: '0101963' + uri_format: https://scicrunch.org/scicrunch/interlex/view/ilx_$1 + name: InterLex + references: + - https://github.com/AllenInstitute/nomenclature + synonyms: + - ILX +interpro: + biocontext: + is_identifiers: false + is_obo: true + prefix: IPR + uri_format: http://purl.obolibrary.org/obo/IPR_$1 + biolink: + is_identifiers: false + is_obo: false + prefix: interpro + uri_format: https://www.ebi.ac.uk/interpro/entry/$1 + deprecated: false + example: IPR016380 + fairsharing: + abbreviation: InterPro + description: InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium. + id: '1854' + name: Integrated resource of protein families, domains and functional sites + prefix: FAIRsharing.pda11d + subjects: + - Bioinformatics + - Biology + go: + homepage: http://www.ebi.ac.uk/interpro/ + name: InterPro database of protein domains and motifs + prefix: InterPro + synonyms: + - INTERPRO + - IPR + uri_format: http://www.ebi.ac.uk/interpro/entry/$1 + mappings: + biocontext: IPR + biolink: interpro + fairsharing: FAIRsharing.pda11d + go: InterPro + miriam: interpro + n2t: interpro + ncbi: InterPro + obofoundry: ipr + prefixcommons: interpro + uniprot: InterPro + miriam: + deprecated: false + description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. + homepage: https://www.ebi.ac.uk/interpro/ + id: '00000011' + name: InterPro + namespaceEmbeddedInLui: false + pattern: ^IPR\d{6}$ + prefix: interpro + providers: + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: http://interpro.bio2rdf.org/fct/ + name: Bio2RDF + uri_format: http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$1 + sampleId: IPR000100 + uri_format: https://www.ebi.ac.uk/interpro/entry/$1 + n2t: + description: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. + example: IPR000100 + homepage: https://www.ebi.ac.uk/interpro/ + name: InterPro + namespaceEmbeddedInLui: false + pattern: ^IPR\d{6}$ + prefix: interpro + uri_format: https://www.ebi.ac.uk/interpro/entry/$1 + name: InterPro + namespace_in_lui: false + ncbi: + example: IPR002928 + homepage: http://www.ebi.ac.uk/interpro/ + name: InterPro protein sequence database + prefix: InterPro + obofoundry: + contact: interhelp@ebi.ac.uk + contact.label: InterPro Help + deprecated: true + homepage: http://www.ebi.ac.uk/interpro/index.html + name: Protein Domains + prefix: ipr + preferred_prefix: interpro + prefixcommons: + description: InterPro is an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. + example: IPR000100 + homepage: http://www.ebi.ac.uk/interpro + keywords: + - domain + - protein + name: Integrated resource of protein families, domains and functional sites + pattern: ^IPR\d{6}$ + prefix: interpro + pubmed_ids: + - '15608177' + uri_format: http://www.ebi.ac.uk/interpro/IEntry?ac=$1 + synonyms: + - IP + - IPR + - InterPro + uniprot: + category: Family and domain databases + identifier: '52' + link_is_explicit: 'true' + name: Integrated resource of protein families, domains and functional sites + prefix: InterPro + uri_format: https://www.ebi.ac.uk/interpro/entry/$1 + wikidata: + prefix: P2926 +ird.segment: + biocontext: + is_identifiers: true + is_obo: false + prefix: IRD.SEGMENT + uri_format: http://identifiers.org/ird.segment/$1 + mappings: + biocontext: IRD.SEGMENT + miriam: ird.segment + n2t: ird.segment + prefixcommons: ird.segment + miriam: + deprecated: false + description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). + homepage: http://www.fludb.org/ + id: '00000172' + name: IRD Segment Sequence + namespaceEmbeddedInLui: false + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: ird.segment + sampleId: CY077097 + uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 + n2t: + description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). + example: CY077097 + homepage: http://www.fludb.org/ + name: IRD at BioHealthBase + namespaceEmbeddedInLui: false + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: ird.segment + uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 + prefixcommons: + description: Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). + example: CY077097 + keywords: + - gene + - protein + name: IRD Segment Sequence + pattern: ^\w+(\_)?\d+(\.\d+)?$ + prefix: ird.segment + pubmed_ids: + - '17965094' + uri_format: http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 +irefweb: + biocontext: + is_identifiers: true + is_obo: false + prefix: IREFWEB + uri_format: http://identifiers.org/irefweb/$1 + fairsharing: + abbreviation: iRefWeb + description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.' + id: '2071' + name: Interaction Reference Index Web Interface + prefix: FAIRsharing.t31wcb + subjects: + - Life Science + mappings: + biocontext: IREFWEB + fairsharing: FAIRsharing.t31wcb + miriam: irefweb + n2t: irefweb + prefixcommons: irefweb + miriam: + deprecated: false + description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' + homepage: http://wodaklab.org/iRefWeb/ + id: '00000123' + name: iRefWeb + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: irefweb + sampleId: '617102' + uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1 + n2t: + description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.' + example: '617102' + homepage: http://wodaklab.org/iRefWeb/ + name: iRefWeb Protein Interaction Reference Index + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: irefweb + uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1 + prefixcommons: + description: 'iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.' + example: '617102' + homepage: http://wodaklab.org/iRefWeb/ + keywords: + - interaction + - protein + name: Interaction Reference Index Web Interface + pattern: ^\d+$ + prefix: irefweb + uri_format: http://wodaklab.org/iRefWeb/interaction/show/$1 +iro: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + example: '0000008' + name: Insect Resistance Ontology + pattern: ^\d{7}$ + uri_format: https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1 +isbn: + biocontext: + is_identifiers: false + is_obo: false + prefix: ISBN-13 + uri_format: https://monarchinitiative.org/ISBN13_$1 + biolink: + is_identifiers: false + is_obo: false + prefix: isbn + uri_format: https://www.isbn-international.org/identifier/$1 + go: + homepage: https://www.worldcat.org + name: International Standard Book Number + prefix: ISBN + uri_format: https://www.worldcat.org/search?q=bn%3A$1 + mappings: + biocontext: ISBN-13 + biolink: isbn + go: ISBN + miriam: isbn + n2t: isbn + prefixcommons: isbn + miriam: + deprecated: false + description: The International Standard Book Number (ISBN) is for identifying printed books. + homepage: http://isbndb.com/ + id: '00000064' + name: ISBN + namespaceEmbeddedInLui: false + pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ + prefix: isbn + providers: + - code: CURATOR_REVIEW + description: ISBN database at WorldCat + homepage: http://www.worldcat.org/ + name: ISBN database at WorldCat + uri_format: http://www.worldcat.org/isbn/$1 + sampleId: '9781584885658' + uri_format: http://isbndb.com/search-all.html?kw=$1 + n2t: + description: The International Standard Book Number (ISBN) is for identifying printed books. + example: '9781584885658' + homepage: http://isbndb.com/ + name: ISBNDB - ISBN Database + namespaceEmbeddedInLui: false + pattern: ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ + prefix: isbn + uri_format: http://isbndb.com/search-all.html?kw=$1 + prefixcommons: + description: The International Standard Book Number (ISBN) is for identifying printed books. + example: '9781584885658' + homepage: http://isbndb.com/ + keywords: + - bibliography + name: International Standard Book Number + pattern: ^\d+$ + prefix: isbn + uri_format: http://isbndb.com/search-all.html?kw=$1 + synonyms: + - ISBN-10 + - ISBN-13 +isfinder: + biocontext: + is_identifiers: true + is_obo: false + prefix: ISFINDER + uri_format: http://identifiers.org/isfinder/$1 + fairsharing: + abbreviation: IS Finder + description: This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Some of the entries have been identified as individual elements by their insertion activities but a growing number are included from their description in sequenced bacterial genomes. It also includes certain transposons, in particular, members of the Tn3 family of replicative transposons. + id: '1836' + name: Insertion Sequence Finder + prefix: FAIRsharing.xhpc3h + subjects: + - Life Science + mappings: + biocontext: ISFINDER + fairsharing: FAIRsharing.xhpc3h + miriam: isfinder + n2t: isfinder + ncbi: ISFinder + prefixcommons: isfinder + miriam: + deprecated: false + description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. + homepage: http://www-is.biotoul.fr/i + id: '00000173' + name: ISFinder + namespaceEmbeddedInLui: false + pattern: ^IS\w+(\-\d)?$ + prefix: isfinder + sampleId: ISA1083-2 + uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1 + n2t: + description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. + example: ISA1083-2 + homepage: http://www-is.biotoul.fr/i + name: IS Finder at CNRS + namespaceEmbeddedInLui: false + pattern: ^IS\w+(\-\d)?$ + prefix: isfinder + uri_format: https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1 + ncbi: + example: ISA1083-2 + homepage: http://www-is.biotoul.fr/ + name: Insertion sequence elements database + prefix: ISFinder + prefixcommons: + description: ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. + example: ISA1083-2 + homepage: http://www-is.biotoul.fr + keywords: + - gene + - sequence + name: IS Finder + pattern: ^IS\w+(\-\d)?$ + prefix: isfinder + pubmed_ids: + - '16381877' + uri_format: http://www-is.biotoul.fr/index.html?is_special_name=$1 +isni: + biolink: + is_identifiers: false + is_obo: false + prefix: isni + uri_format: https://isni.org/isni/$1 + mappings: + biolink: isni + miriam: isni + n2t: isni + miriam: + deprecated: false + description: "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described." + homepage: http://www.isni.org + id: '00000684' + name: International Standard Name Identifier + namespaceEmbeddedInLui: false + pattern: ^[0-9]{15}[0-9X]{1}$ + prefix: isni + sampleId: 000000012281955X + uri_format: http://www.isni.org/isni/$1 + n2t: + description: ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC. The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described. + example: 000000012281955X + homepage: http://www.isni.org + name: International Standard Name Identifier + namespaceEmbeddedInLui: false + pattern: ^[0-9]{15}[0-9X]{1}$ + prefix: isni + uri_format: http://www.isni.org/isni/$1 +issn: + biocontext: + is_identifiers: true + is_obo: false + prefix: ISSN + uri_format: http://identifiers.org/issn/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: issn + uri_format: https://portal.issn.org/resource/ISSN/$1 + go: + homepage: http://www.issn.org/ + name: International Standard Serial Number + prefix: ISSN + mappings: + biocontext: ISSN + biolink: issn + go: ISSN + miriam: issn + n2t: issn + miriam: + deprecated: false + description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. + homepage: https://portal.issn.org + id: '00000301' + name: ISSN + namespaceEmbeddedInLui: false + pattern: ^\d{4}-\d{3}[\dX]$ + prefix: issn + providers: + - code: CURATOR_REVIEW + description: ISSN at Library of Congress + homepage: http://catalog.loc.gov/webvoy.htm + name: ISSN at Library of Congress + uri_format: https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$1&searchType=1&recCount=25 + sampleId: 0745-4570 + uri_format: https://portal.issn.org/resource/ISSN/$1 + n2t: + description: The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. + example: 1776-3045 + homepage: https://portal.issn.org + name: ISSN Portal + namespaceEmbeddedInLui: false + pattern: ^\d{4}-\d{3}[\dX]$ + prefix: issn + uri_format: https://portal.issn.org/resource/ISSN/$1 +itis: + description: Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world. + example: '589462' + fairsharing: + abbreviation: ITIS + description: The Integrated Taxonomic Information System (ITIS) provides taxonomic information on plants, animals, fungi, and microbes of North America and the world. The goal is to create an easily accessible database with reliable information on species names and their hierarchical classification. The database will be reviewed periodically to ensure high quality with valid classifications, revisions, and additions of newly described species. The ITIS includes documented taxonomic information of flora and fauna from both aquatic and terrestrial habitats. + id: '2127' + name: Integrated Taxonomic Information System + prefix: FAIRsharing.t19hpa + subjects: + - Taxonomy + - Biodiversity + - Life Science + homepage: https://www.itis.gov/ + mappings: + fairsharing: FAIRsharing.t19hpa + name: Integrated Taxonomic Information System + pattern: ^\d+$ + uri_format: https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1 + wikidata: + prefix: P815 +ito: + bioportal: + name: Intelligence Task Ontology + prefix: ITO + mappings: + bioportal: ITO + miriam: ito + miriam: + deprecated: false + description: The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks. + homepage: https://bioportal.bioontology.org/ + id: '00000802' + name: Intelligence Task Ontology + namespaceEmbeddedInLui: false + pattern: ^.+$ + prefix: ito + sampleId: ITO_01625 + uri_format: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1 +iuphar.family: + biocontext: + is_identifiers: true + is_obo: false + prefix: IUPHAR.FAMILY + uri_format: http://identifiers.org/iuphar.family/$1 + mappings: + biocontext: IUPHAR.FAMILY + miriam: iuphar.family + n2t: iuphar.family + prefixcommons: iuphar.family + miriam: + deprecated: false + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. + homepage: http://www.guidetopharmacology.org/ + id: '00000317' + name: IUPHAR family + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.family + sampleId: '78' + uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1 + n2t: + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. + example: '78' + homepage: http://www.guidetopharmacology.org/ + name: The IUPHAR/BPS Guide to PHARMACOLOGY + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.family + uri_format: http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1 + prefixcommons: + description: IUPHAR G protein-coupled receptors database + example: '78' + homepage: http://www.iuphar-db.org/DATABASE/ReceptorFamiliesForward?type=GPCR + keywords: + - protein + name: G protein-coupled receptors database + pattern: ^\d+$ + prefix: iuphar.family + uri_format: http://www.iuphar-db.org/DATABASE/FamilyIntroductionForward?familyId=$1 + synonyms: + - IUPHARfam +iuphar.ligand: + biocontext: + is_identifiers: true + is_obo: false + prefix: IUPHAR.LIGAND + uri_format: http://identifiers.org/iuphar.ligand/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: GTOPDB + uri_format: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 + mappings: + biocontext: IUPHAR.LIGAND + biolink: GTOPDB + miriam: iuphar.ligand + n2t: iuphar.ligand + wikidata: P595 + miriam: + deprecated: false + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. + homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all + id: '00000457' + name: IUPHAR ligand + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.ligand + sampleId: '1755' + uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 + n2t: + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. + example: '1755' + homepage: http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all + name: IUPHAR ligand at University of Edinburgh + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.ligand + uri_format: http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 + name: Guide to Pharmacology Ligand + synonyms: + - IUPHAR_LIGAND + - IUPHAR_LIGAND_ID + wikidata: + database: Q17091219 + database.homepage: http://www.guidetopharmacology.org + database.label: IUPHAR/BPS Guide to PHARMACOLOGY + homepage: https://www.guidetopharmacology.org/ + name: Guide to Pharmacology Ligand ID + pattern: \d{1,4} + prefix: P595 + uri_format: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1 +iuphar.receptor: + biocontext: + is_identifiers: true + is_obo: false + prefix: IUPHAR.RECEPTOR + uri_format: http://identifiers.org/iuphar.receptor/$1 + go: + homepage: http://www.iuphar.org/ + name: International Union of Pharmacology + prefix: IUPHAR_RECEPTOR + uri_format: https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 + mappings: + biocontext: IUPHAR.RECEPTOR + go: IUPHAR_RECEPTOR + miriam: iuphar.receptor + n2t: iuphar.receptor + wikidata: P5458 + miriam: + deprecated: false + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. + homepage: http://www.guidetopharmacology.org/targets.jsp + id: '00000281' + name: IUPHAR receptor + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.receptor + sampleId: '101' + uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 + n2t: + description: The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. + example: '101' + homepage: http://www.guidetopharmacology.org/targets.jsp + name: IUPHAR Receptor at University of Edinburgh + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: iuphar.receptor + uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 + name: Guide to Pharmacology Target + synonyms: + - IUPHAR_GPCR + - IUPHARobj + wikidata: + database: Q17091219 + database.homepage: http://www.guidetopharmacology.org + database.label: IUPHAR/BPS Guide to PHARMACOLOGY + homepage: http://www.guidetopharmacology.org/GRAC/ + name: Guide to Pharmacology Target ID + pattern: '[1-9]\d{0,3}' + prefix: P5458 + uri_format: http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1 +jax: + biocontext: + is_identifiers: false + is_obo: false + prefix: JAX + uri_format: http://jaxmice.jax.org/strain/$1 + description: Information about the C57BL/6J. Includes genetic background and disease data. + example: '004435' + fairsharing: + abbreviation: JAX + description: JAX® Mice are the industry standard for animal model research, using precise genome solutions to better understand human disease. Our rigorous Animal Health Programs and stringent genetic quality standards ensure the reproducibility and validity of your experimental data. + id: '2067' + name: JAX Mice Database + prefix: FAIRsharing.5701h1 + subjects: + - Life Science + homepage: https://www.jax.org/strain + mappings: + biocontext: JAX + fairsharing: FAIRsharing.5701h1 + name: Jackson Laboratories Strain + pattern: ^\d{6}$ + uri_format: https://www.jax.org/strain/$1 +jaxmice: + biocontext: + is_identifiers: true + is_obo: false + prefix: JAXMICE + uri_format: http://identifiers.org/jaxmice/$1 + mappings: + biocontext: JAXMICE + miriam: jaxmice + n2t: jaxmice + miriam: + deprecated: false + description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. + homepage: http://jaxmice.jax.org/ + id: '00000337' + name: JAX Mice + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jaxmice + sampleId: '005012' + uri_format: http://jaxmice.jax.org/strain/$1.html + n2t: + description: JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. + example: '005012' + homepage: http://jaxmice.jax.org/ + name: JAX Mice at Jackson Laboratory + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jaxmice + uri_format: http://jaxmice.jax.org/strain/$1.html +jcggdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: JCGGDB + uri_format: http://identifiers.org/jcggdb/$1 + mappings: + biocontext: JCGGDB + miriam: jcggdb + n2t: jcggdb + miriam: + deprecated: false + description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. + homepage: http://jcggdb.jp/index_en.html + id: '00000479' + name: JCGGDB + namespaceEmbeddedInLui: false + pattern: ^JCGG-STR\d{6}$ + prefix: jcggdb + sampleId: JCGG-STR008690 + uri_format: http://jcggdb.jp/idb/jcggdb/$1 + n2t: + description: JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. + example: JCGG-STR008690 + homepage: http://jcggdb.jp/index_en.html + name: JCGGDB at Advanced Science Institute (Japan) + namespaceEmbeddedInLui: false + pattern: ^JCGG-STR\d{6}$ + prefix: jcggdb + uri_format: http://jcggdb.jp/idb/jcggdb/$1 + name: Japan Consortium for Glycobiology and Glycotechnology Database +jcm: + biocontext: + is_identifiers: true + is_obo: false + prefix: JCM + uri_format: http://identifiers.org/jcm/$1 + fairsharing: + abbreviation: JCM + description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. + id: '2038' + name: Japan Collection of Microorganisms + prefix: FAIRsharing.h2wrt2 + subjects: + - Life Science + mappings: + biocontext: JCM + fairsharing: FAIRsharing.h2wrt2 + miriam: jcm + n2t: jcm + ncbi: JCM + prefixcommons: jcm + miriam: + deprecated: false + description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. + homepage: http://www.jcm.riken.go.jp/ + id: '00000174' + name: Japan Collection of Microorganisms + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jcm + sampleId: '17254' + uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 + n2t: + description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. + example: '17254' + homepage: http://www.jcm.riken.go.jp/ + name: JCM at RIKEN BioResource Center + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jcm + uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 + ncbi: + example: '1339' + homepage: http://www.jcm.riken.go.jp/ + name: Japan Collection of Microorganisms + prefix: JCM + prefixcommons: + description: The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. + example: '17254' + homepage: http://www.jcm.riken.go.jp/ + keywords: + - microbial + - taxonomy + name: Japan Collection of Microorganisms + pattern: ^\d+$ + prefix: jcm + uri_format: http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1 +jcrb: + cellosaurus: + category: Cell line collections + homepage: http://cellbank.nibiohn.go.jp/english/ + name: Japanese Collection of Research Bioresources Cell Bank + prefix: JCRB + uri_format: http://cellbank.nibiohn.go.jp//~cellbank/en/search_res_det.cgi?RNO=$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: JCRB1355 + homepage: https://cellbank.nibiohn.go.jp + mappings: + cellosaurus: JCRB + name: JRBC Cell Bank + uri_format: https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1 +jcsd: + biocontext: + is_identifiers: true + is_obo: false + prefix: JCSD + uri_format: http://identifiers.org/jcsd/$1 + mappings: + biocontext: JCSD + miriam: jcsd + n2t: jcsd + prefixcommons: jcsd + miriam: + deprecated: false + description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). + homepage: http://jglobal.jst.go.jp/en/ + id: '00000241' + name: Japan Chemical Substance Dictionary + namespaceEmbeddedInLui: false + pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ + prefix: jcsd + sampleId: J55.713G + uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1 + n2t: + description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). + example: J55.713G + homepage: http://jglobal.jst.go.jp/en/ + name: Japan Chemical Substance Dictionary + namespaceEmbeddedInLui: false + pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ + prefix: jcsd + uri_format: http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1 + prefixcommons: + description: The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). + example: J55.713G + keywords: + - chemical + - structure + name: Japan Chemical Substance Dictionary + pattern: ^J\d{1,3}(\.\d{3})?(\.\d{1,3})?[A-Za-z]$ + prefix: jcsd + uri_format: http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp?CONTENT=syosai&SN=$1 +jstor: + biocontext: + is_identifiers: true + is_obo: false + prefix: JSTOR + uri_format: http://identifiers.org/jstor/$1 + go: + homepage: https://www.jstor.org/ + name: Digital archive of scholarly articles + prefix: JSTOR + uri_format: https://www.jstor.org/stable/$1 + mappings: + biocontext: JSTOR + go: JSTOR + miriam: jstor + n2t: jstor + miriam: + deprecated: false + description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. + homepage: http://www.jstor.org/ + id: '00000444' + name: JSTOR + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jstor + sampleId: '3075966' + uri_format: http://www.jstor.org/stable/$1 + n2t: + description: JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. + example: '3075966' + homepage: http://www.jstor.org/ + name: JSTOR Online + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: jstor + uri_format: http://www.jstor.org/stable/$1 +jws: + biocontext: + is_identifiers: true + is_obo: false + prefix: JWS + uri_format: http://identifiers.org/jws/$1 + example: achcar11 + mappings: + biocontext: JWS + miriam: jws + n2t: jws + prefixcommons: jws + miriam: + deprecated: false + description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. + homepage: http://jjj.biochem.sun.ac.za/models/ + id: '00000130' + name: JWS Online + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: jws + providers: + - code: CURATOR_REVIEW + description: JWS Online Model Repository at Manchester + homepage: http://jjj.mib.ac.uk/index.html + name: JWS Online Model Repository at Manchester + uri_format: http://jjj.mib.ac.uk/models/$1 + - code: CURATOR_REVIEW + description: JWS Online Model Repository at Amsterdam + homepage: http://jjj.bio.vu.nl/models/ + name: JWS Online Model Repository at Amsterdam + uri_format: http://jjj.bio.vu.nl/models/$1/ + sampleId: curien + uri_format: http://jjj.biochem.sun.ac.za/models/$1/ + n2t: + description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. + example: curien + homepage: http://jjj.mib.ac.uk/index.html + name: JWS Online Model Repository at Manchester + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: jws + uri_format: http://jjj.mib.ac.uk/models/$1 + prefixcommons: + description: JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. + example: curien + homepage: http://jjj.mib.ac.uk/index.html + keywords: + - model + - pathway + name: JWS Online Model Repository + pattern: ^\w+$ + prefix: jws + pubmed_ids: + - '15072998' + uri_format: http://jjj.mib.ac.uk/cgi-bin/processModelSelection.py?keytype=modelname&keyword=$1 + uri_format: https://jjj.bio.vu.nl/models/$1 +kaggle: + mappings: + miriam: kaggle + n2t: kaggle + miriam: + deprecated: false + description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. + homepage: https://kaggle.com + id: '00000682' + name: Kaggle + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ + prefix: kaggle + sampleId: nasa/kepler-exoplanet-search-results + uri_format: https://www.kaggle.com/$1 + n2t: + description: Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions. + example: nasa/kepler-exoplanet-search-results + homepage: https://kaggle.com + name: Kaggle + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z\-]+\/[0-9a-zA-Z\-]+$ + prefix: kaggle + uri_format: https://www.kaggle.com/$1 +kclb: + cellosaurus: + category: Cell line collections + homepage: https://cellbank.snu.ac.kr/main/index.html + name: Korean Cell Line Bank + prefix: KCLB + uri_format: https://cellbank.snu.ac.kr/english/sub/catalog.php?page=detail&CatNo=59&strQ=$1&submit1=Find+it + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: '10020.2' + homepage: https://cellbank.snu.ac.kr/english + mappings: + cellosaurus: KCLB + name: Korean Cell Line Bank + uri_format: https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1 +kegg: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG + uri_format: http://identifiers.org/kegg/$1 + cheminf: + description: Database identifier used by KEGG. + name: KEGG + obsolete: false + prefix: '000409' + comment: KEGG prefix has been split into several others + deprecated: true + go: + homepage: http://www.genome.ad.jp/kegg/ + name: Kyoto Encyclopedia of Genes and Genomes + prefix: KEGG + mappings: + biocontext: KEGG + cheminf: '000409' + go: KEGG + miriam: kegg + n2t: kegg + uniprot: KEGG + miriam: + deprecated: false + description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. + homepage: http://www.kegg.jp/ + id: '00000578' + name: Kyoto Encyclopedia of Genes and Genomes + namespaceEmbeddedInLui: false + pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ + prefix: kegg + sampleId: hsa00190 + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. + example: hsa00190 + homepage: http://www.kegg.jp/ + name: KEGG at Kyoto University Bioinformatics Center + namespaceEmbeddedInLui: false + pattern: ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$ + prefix: kegg + uri_format: http://www.kegg.jp/entry/$1 + synonyms: + - KEGG + uniprot: + category: Genome annotation databases + identifier: '53' + link_is_explicit: 'true' + name: 'KEGG: Kyoto Encyclopedia of Genes and Genomes' + prefix: KEGG + uri_format: https://www.genome.jp/dbget-bin/www_bget?$1 +kegg.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.COMPOUND + uri_format: http://identifiers.org/kegg.compound/$1 + mappings: + biocontext: KEGG.COMPOUND + miriam: kegg.compound + n2t: kegg.compound + prefixcommons: kegg.compound + miriam: + deprecated: false + description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. + homepage: https://www.genome.jp/kegg/ligand.html + id: '00000013' + name: KEGG Compound + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: kegg.compound + sampleId: C12345 + uri_format: https://www.kegg.jp/entry/$1 + n2t: + description: KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. + example: C12345 + homepage: https://www.genome.jp/kegg/ligand.html + name: KEGG LIGAND Database + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: kegg.compound + uri_format: https://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: KEGG COMPOUND is a chemical structure database for metabolic compounds and other chemical substances that are relevant to biological systems. + example: C12345 + homepage: http://www.genome.jp/kegg/compound/ + keywords: + - small molecule + name: KEGG Compound + pattern: ^C\d+$ + prefix: kegg.compound + pubmed_ids: + - '22700311' + uri_format: http://www.genome.jp/dbget-bin/www_bget?cpd:$1 + synonyms: + - KEGG COMPOUND + - KEGG.COMPOUND + wikidata: + prefix: P665 +kegg.dgroup: + biolink: + is_identifiers: false + is_obo: false + prefix: KEGG.DGROUP + uri_format: http://www.kegg.jp/entry/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: >2- + KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups. + + Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc. + Structure - grouped as similar chemical structures having the same skeleton, etc. + Target - grouped by drug targets + Class - drug classes often representing similar mechanisms of action + Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters + + Chemical groups are often used for identifying essentially the same active ingredients of drugs in different countries. + example: DG00301 + homepage: http://www.genome.jp/kegg/reaction/ + mappings: + biolink: KEGG.DGROUP + name: KEGG Drug Group + part_of: kegg + pattern: ^DG\d+$ + references: + - https://github.com/prefixcommons/prefixes/pull/4 + synonyms: + - KEGG_DGROUP + - KEGG_DRUG_GROUP +kegg.disease: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.DISEASE + uri_format: http://identifiers.org/kegg.disease/$1 + mappings: + biocontext: KEGG.DISEASE + miriam: kegg.disease + n2t: kegg.disease + prefixcommons: kegg.disease + miriam: + deprecated: false + description: The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. + homepage: http://www.genome.jp/kegg/disease/ + id: '00000475' + name: KEGG Disease + namespaceEmbeddedInLui: false + pattern: ^H\d+$ + prefix: kegg.disease + sampleId: H00076 + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. + example: H00076 + homepage: http://www.genome.jp/kegg/disease/ + name: KEGG Disease at Kyoto University Bioinformatics Center + namespaceEmbeddedInLui: false + pattern: ^H\d+$ + prefix: kegg.disease + uri_format: http://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: The KEGG DISEASE database is a new collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry is identified by the H number and contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. + example: H00047 + homepage: http://www.genome.jp/kegg/disease/ + keywords: + - classification + name: KEGG Disease + pattern: ^H\d+$ + prefix: kegg.disease + uri_format: http://www.genome.jp/dbget-bin/www_bget?ds:$1 +kegg.drug: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.DRUG + uri_format: http://identifiers.org/kegg.drug/$1 + mappings: + biocontext: KEGG.DRUG + miriam: kegg.drug + n2t: kegg.drug + prefixcommons: kegg.drug + miriam: + deprecated: false + description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. + homepage: https://www.genome.jp/kegg/drug/ + id: '00000025' + name: KEGG Drug + namespaceEmbeddedInLui: false + pattern: ^D\d+$ + prefix: kegg.drug + sampleId: D00123 + uri_format: https://www.kegg.jp/entry/$1 + n2t: + description: KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. + example: D00123 + homepage: https://www.genome.jp/kegg/drug/ + name: KEGG DRUG Database + namespaceEmbeddedInLui: false + pattern: ^D\d+$ + prefix: kegg.drug + uri_format: https://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: KEGG DRUG is a unified drug information resource that contains chemical structures and/or chemical components of all prescription and OTC drugs in Japan, most prescription drugs in the USA, and many prescription drugs in Europe. + example: D00123 + homepage: http://www.genome.jp/kegg/drug/ + keywords: + - small molecule + name: KEGG Drug + pattern: ^D\d+$ + prefix: kegg.drug + pubmed_ids: + - '16381885' + uri_format: http://www.genome.jp/dbget-bin/www_bget?dr:$1 + synonyms: + - KEGG DRUG + - KEGG.DRUG + wikidata: + prefix: P665 +kegg.environ: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.ENVIRON + uri_format: http://identifiers.org/kegg.environ/$1 + mappings: + biocontext: KEGG.ENVIRON + miriam: kegg.environ + n2t: kegg.environ + miriam: + deprecated: false + description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. + homepage: http://www.genome.jp/kegg/drug/environ.html + id: '00000389' + name: KEGG Environ + namespaceEmbeddedInLui: false + pattern: ^(ev\:)?E\d+$ + prefix: kegg.environ + sampleId: ev:E00032 + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. + example: ev:E00032 + homepage: http://www.genome.jp/kegg/drug/environ.html + name: KEGG ENVIRON Database + namespaceEmbeddedInLui: false + pattern: ^(ev\:)?E\d+$ + prefix: kegg.environ + uri_format: http://www.kegg.jp/entry/$1 + part_of: kegg +kegg.enzyme: + biolink: + is_identifiers: false + is_obo: false + prefix: KEGG.ENZYME + uri_format: http://www.kegg.jp/entry/$1 + description: KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links. + go: + homepage: http://www.genome.jp/dbget-bin/www_bfind?enzyme + name: KEGG Enzyme Database + prefix: KEGG_ENZYME + uri_format: http://www.genome.jp/dbget-bin/www_bget?ec:$1 + mappings: + biolink: KEGG.ENZYME + go: KEGG_ENZYME + name: KEGG Enzyme + part_of: kegg + provides: eccode +kegg.genes: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.GENES + uri_format: http://identifiers.org/kegg.genes/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: KEGG.GENE + uri_format: http://www.kegg.jp/entry/$1 + example: bsu:BSU01340 + mappings: + biocontext: KEGG.GENES + biolink: KEGG.GENE + miriam: kegg.genes + n2t: kegg.genes + miriam: + deprecated: false + description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. + homepage: http://www.genome.jp/kegg/genes.html + id: '00000070' + name: KEGG Genes + namespaceEmbeddedInLui: false + pattern: ^\w+:[\w\d\.-]*$ + prefix: kegg.genes + sampleId: syn:ssr3451 + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. + example: syn:ssr3451 + homepage: http://www.genome.jp/kegg/genes.html + name: KEGG GENES Database + namespaceEmbeddedInLui: false + pattern: ^\w+:[\w\d\.-]*$ + prefix: kegg.genes + uri_format: http://www.kegg.jp/entry/$1 + part_of: kegg + wikidata: + prefix: P665 +kegg.genome: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.GENOME + uri_format: http://identifiers.org/kegg.genome/$1 + example: T06648 + mappings: + biocontext: KEGG.GENOME + miriam: kegg.genome + n2t: kegg.genome + prefixcommons: kegg.genome + miriam: + deprecated: false + description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced. + homepage: http://www.genome.jp/kegg/catalog/org_list.html + id: '00000238' + name: KEGG Genome + namespaceEmbeddedInLui: false + pattern: ^(T0\d+|\w{3,5})$ + prefix: kegg.genome + sampleId: eco + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: KEGG Genome is a collection of organisms whose genomes have been completely sequenced. + example: eco + homepage: http://www.genome.jp/kegg/catalog/org_list.html + name: KEGG Genome Database + namespaceEmbeddedInLui: false + pattern: ^(T0\d+|\w{3,5})$ + prefix: kegg.genome + uri_format: http://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: Complete organism genomes + example: T00047 + homepage: http://www.genome.jp/kegg/catalog/org_list.html + name: KEGG Genome + pattern: ^T\d+$ + prefix: kegg.genome + pubmed_ids: + - '22080510' + uri_format: http://www.genome.jp/dbget-bin/www_bget?gn:$1 + synonyms: + - kegg_genome + - kegg_genomes + wikidata: + prefix: P665 +kegg.glycan: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.GLYCAN + uri_format: http://identifiers.org/kegg.glycan/$1 + mappings: + biocontext: KEGG.GLYCAN + miriam: kegg.glycan + n2t: kegg.glycan + prefixcommons: kegg.glycan + miriam: + deprecated: false + description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. + homepage: https://www.genome.jp/kegg/glycan/ + id: '00000026' + name: KEGG Glycan + namespaceEmbeddedInLui: false + pattern: ^G\d+$ + prefix: kegg.glycan + sampleId: G00123 + uri_format: https://www.kegg.jp/entry/$1 + n2t: + description: KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. + example: G00123 + homepage: https://www.genome.jp/kegg/glycan/ + name: KEGG GLYCAN Database + namespaceEmbeddedInLui: false + pattern: ^G\d+$ + prefix: kegg.glycan + uri_format: https://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: The KEGG GLYCAN structure database is a collection of experimentally determined glycan structures [1]. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. + example: G00123 + homepage: http://www.genome.jp/kegg/glycan/ + keywords: + - small molecule + name: KEGG Glycan + pattern: ^G\d+$ + prefix: kegg.glycan + pubmed_ids: + - '16014746' + uri_format: http://www.genome.jp/dbget-bin/www_bget?gl:$1 +kegg.ligand: + comment: This database has been discontinued by KEGG. It now lives inside the compound database + deprecated: true + go: + homepage: http://www.genome.ad.jp/kegg/docs/upd_ligand.html + name: KEGG LIGAND Database + prefix: KEGG_LIGAND + uri_format: http://www.genome.jp/dbget-bin/www_bget?cpd:$1 + mappings: + go: KEGG_LIGAND + name: KEGG LIGAND + part_of: kegg +kegg.metagenome: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.METAGENOME + uri_format: http://identifiers.org/kegg.metagenome/$1 + mappings: + biocontext: KEGG.METAGENOME + miriam: kegg.metagenome + n2t: kegg.metagenome + prefixcommons: kegg.metagenome + miriam: + deprecated: false + description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. + homepage: http://www.genome.jp/kegg/catalog/org_list3.html + id: '00000239' + name: KEGG Metagenome + namespaceEmbeddedInLui: false + pattern: ^T3\d+$ + prefix: kegg.metagenome + sampleId: T30002 + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. + example: T30002 + homepage: http://www.genome.jp/kegg/catalog/org_list3.html + name: KEGG Metagenome Database + namespaceEmbeddedInLui: false + pattern: ^T3\d+$ + prefix: kegg.metagenome + uri_format: http://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. + example: T30002 + keywords: + - genome + name: KEGG Metagenome + pattern: ^T3\d+$ + prefix: kegg.metagenome + pubmed_ids: + - '22080510' + uri_format: http://www.genome.jp/kegg-bin/show_organism?org=$1 +kegg.module: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.MODULE + uri_format: http://identifiers.org/kegg.module/$1 + mappings: + biocontext: KEGG.MODULE + miriam: kegg.module + n2t: kegg.module + miriam: + deprecated: false + description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. + homepage: http://www.kegg.jp/kegg/module.html + id: '00000474' + name: KEGG Module + namespaceEmbeddedInLui: false + pattern: ^([a-z]{3,5}_)?M\d{5}$ + prefix: kegg.module + sampleId: M00002 + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. + example: M00002 + homepage: http://www.kegg.jp/kegg/module.html + name: KEGG Module at Kyoto University Bioinformatics Center + namespaceEmbeddedInLui: false + pattern: ^([a-z]{3,5}_)?M\d{5}$ + prefix: kegg.module + uri_format: http://www.kegg.jp/entry/$1 + part_of: kegg +kegg.orthology: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.ORTHOLOGY + uri_format: http://identifiers.org/kegg.orthology/$1 + mappings: + biocontext: KEGG.ORTHOLOGY + miriam: kegg.orthology + n2t: kegg.orthology + prefixcommons: kegg.orthology + miriam: + deprecated: false + description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. + homepage: http://www.genome.jp/kegg/ko.html + id: '00000116' + name: KEGG Orthology + namespaceEmbeddedInLui: false + pattern: ^K\d+$ + prefix: kegg.orthology + sampleId: K00001 + uri_format: http://www.kegg.jp/entry/$1 + n2t: + description: KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. + example: K00001 + homepage: http://www.genome.jp/kegg/ko.html + name: KEGG Orthology Database + namespaceEmbeddedInLui: false + pattern: ^K\d+$ + prefix: kegg.orthology + uri_format: http://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: The KEGG reference pathway maps and BRITE functional hierarchies are represented in a general way to be applicable to all organisms. KEGG Orthology (KO) is the basis for this representation, consisting of manually defined ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes. + example: K00001 + homepage: http://www.genome.jp/kegg/ko.html + keywords: + - classification + - pathway + name: KEGG Orthology + pattern: ^K\d+$ + prefix: kegg.orthology + uri_format: http://www.genome.jp/dbget-bin/www_bget?ko:$1 +kegg.pathway: + biocontext: + is_identifiers: false + is_obo: false + prefix: KEGG-path + uri_format: http://www.kegg.jp/dbget-bin/www_bget?path:$1 + biolink: + is_identifiers: false + is_obo: false + prefix: KEGG.PATHWAY + uri_format: https://www.kegg.jp/entry/$1 + example: rsk00410 + go: + homepage: http://www.genome.jp/kegg/pathway.html + name: KEGG Pathways Database + prefix: KEGG_PATHWAY + uri_format: http://www.genome.jp/dbget-bin/www_bget?path:$1 + mappings: + biocontext: KEGG-path + biolink: KEGG.PATHWAY + go: KEGG_PATHWAY + miriam: kegg.pathway + n2t: kegg.pathway + prefixcommons: kegg.pathway + miriam: + deprecated: false + description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. + homepage: https://www.genome.jp/kegg/pathway.html + id: '00000012' + name: KEGG Pathway + namespaceEmbeddedInLui: false + pattern: ^\w{2,4}\d{5}$ + prefix: kegg.pathway + sampleId: hsa00620 + uri_format: https://www.kegg.jp/entry/$1 + n2t: + description: KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. + example: hsa00620 + homepage: https://www.genome.jp/kegg/pathway.html + name: KEGG PATHWAY Database + namespaceEmbeddedInLui: false + pattern: ^\w{2,4}\d{5}$ + prefix: kegg.pathway + uri_format: https://www.kegg.jp/entry/$1 + part_of: kegg + prefixcommons: + description: KEGG PATHWAY is a collection of manually drawn pathway maps (see new maps, change history, and last updates) representing our knowledge on the molecular interaction and reaction networks + example: map00071 + homepage: http://www.genome.jp/kegg/pathway.html + keywords: + - pathway + name: KEGG Pathway + pattern: ^map\d+$ + prefix: kegg.pathway + pubmed_ids: + - '22700311' + uri_format: http://www.genome.jp/dbget-bin/www_bget?map$1 + synonyms: + - KEGG-path + - KEGG_PATHWAY + wikidata: + prefix: P665 +kegg.rclass: + biolink: + is_identifiers: false + is_obo: false + prefix: KEGG.RCLASS + uri_format: http://www.kegg.jp/entry/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns. + example: RC00001 + homepage: http://www.genome.jp/kegg/reaction/ + mappings: + biolink: KEGG.RCLASS + name: KEGG Reaction Class + part_of: kegg + pattern: ^RC\d+$ + references: + - https://github.com/prefixcommons/prefixes/pull/2 + synonyms: + - KEGG_RCLASS + - KEGG_REACTION_CLASS +kegg.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: KEGG.REACTION + uri_format: http://identifiers.org/kegg.reaction/$1 + go: + homepage: http://www.genome.jp/kegg/reaction/ + name: KEGG Reaction Database + prefix: KEGG_REACTION + uri_format: http://www.genome.jp/dbget-bin/www_bget?rn:$1 + mappings: + biocontext: KEGG.REACTION + go: KEGG_REACTION + miriam: kegg.reaction + n2t: kegg.reaction + prefixcommons: kegg.reaction + wikidata: P665 + miriam: + deprecated: false + description: KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. + homepage: https://www.genome.jp/kegg/reaction/ + id: '00000014' + name: KEGG Reaction + namespaceEmbeddedInLui: false + pattern: ^R\d+$ + prefix: kegg.reaction + sampleId: R00100 + uri_format: https://www.kegg.jp/entry/$1 + n2t: + description: KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. + example: R00100 + homepage: https://www.genome.jp/kegg/reaction/ + name: KEGG Reaction Database + namespaceEmbeddedInLui: false + pattern: ^R\d+$ + prefix: kegg.reaction + uri_format: https://www.kegg.jp/entry/$1 + name: KEGG Reaction + part_of: kegg + prefixcommons: + description: KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the metabolic pathway maps in KEGG PATHWAY. + example: R00047 + homepage: http://www.genome.jp/kegg/reaction/ + keywords: + - enzyme + - pathway + name: KEGG Reaction + pattern: ^R\d+$ + prefix: kegg.reaction + pubmed_ids: + - '22700311' + uri_format: http://www.genome.jp/dbget-bin/www_bget?rn:$1 + synonyms: + - KEGG_REACTION + wikidata: + database: Q909442 + database.homepage: http://www.genome.jp/kegg/ + database.label: Kyoto Encyclopedia of Genes and Genomes + format.rdf: https://www.kegg.jp/entry/$1 + homepage: https://www.kegg.jp/ + name: KEGG ID + pattern: '[A-Z]\d+' + prefix: P665 + uri_format: https://www.kegg.jp/entry/$1 +kerafast: + cellosaurus: + category: Cell line collections + homepage: https://www.kerafast.com/ + name: Kerafast cell lines + prefix: Kerafast + uri_format: https://www.kerafast.com/Search?SearchTerm="$1" + example: EJH014 + mappings: + cellosaurus: Kerafast +knapsack: + biocontext: + is_identifiers: true + is_obo: false + prefix: KNAPSACK + uri_format: http://identifiers.org/knapsack/$1 + mappings: + biocontext: KNAPSACK + miriam: knapsack + n2t: knapsack + wikidata: P2064 + miriam: + deprecated: false + description: |- + KNApSAcK provides information on metabolites and the + taxonomic class with which they are associated. + homepage: http://www.knapsackfamily.com/KNApSAcK/ + id: '00000271' + name: KNApSAcK + namespaceEmbeddedInLui: false + pattern: ^C\d{8} + prefix: knapsack + sampleId: C00000001 + uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?word=$1 + n2t: + description: Knapsack provides information on metabolites and the taxonomic class with which they are associated. + example: C00000001 + homepage: http://kanaya.aist-nara.ac.jp/KNApSAcK/ + name: KnapSack at Nara Institute + namespaceEmbeddedInLui: false + pattern: ^C\d{8} + prefix: knapsack + uri_format: http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$1 + name: KNApSAcK + wikidata: + database: Q20900436 + database.homepage: http://kanaya.naist.jp/KNApSAcK/ + database.label: KNApSAcK + name: KNApSAcK ID + pattern: C\d{8} + prefix: P2064 + uri_format: http://www.knapsackfamily.com/knapsack_core/information.php?sname=C_ID&word=$1 +kupo: + appears_in: + - cl + comment: Website is down, now it redirects to something else that is not related + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + example: '0001009' + homepage: http://www.kupkb.org/ + name: Kidney and Urinary Pathway Ontology + pattern: ^\d{7}$ + references: + - https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7 +kyinno: + cellosaurus: + category: Cell line collections + homepage: https://www.kyinno.com/ + name: KYinno cell lines + prefix: KYinno + uri_format: https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf + example: KC-0979 + mappings: + cellosaurus: KYinno +labo: + bioportal: + name: clinical LABoratory Ontology + prefix: LABO + example: '0000124' + mappings: + bioportal: LABO + obofoundry: labo + ols: labo + ontobee: LABO + obofoundry: + contact: paul.fabry@usherbrooke.ca + contact.github: pfabry + contact.label: Paul Fabry + contact.orcid: 0000-0002-3336-2476 + depends_on: + - iao + - obi + - ogms + - omiabis + - omrse + - opmi + deprecated: false + description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. + download.owl: http://purl.obolibrary.org/obo/labo.owl + homepage: https://github.com/OpenLHS/LABO + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: clinical LABoratory Ontology + preferredPrefix: LABO + prefix: labo + publications: + - id: https://doi.org/10.5281/zenodo.6522019 + title: 'LABO: An Ontology for Laboratory Test Prescription and Reporting' + repository: https://github.com/OpenLHS/LABO + ols: + description: LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. + download: http://purl.obolibrary.org/obo/labo.owl + homepage: https://github.com/OpenLHS/LABO + name: clinical LABoratory Ontology + prefix: labo + version: 2021-06-08 + version.iri: http://purl.obolibrary.org/obo/labo/2021-06-08/labo.owl + ontobee: + library: Library + name: clinical LABoratory Ontology + prefix: LABO + pattern: ^\d{7}$ +lbo: + bioportal: + name: Livestock Breed Ontology + prefix: LBO + contact: + email: caripark@iastate.edu + github: caripark + name: Carissa Park + orcid: 0000-0002-2346-5201 + download_obo: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo + download_owl: https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl + example: '0000487' + fairsharing: + abbreviation: LBO + description: A vocabulary for buffalo, cattle, chicken, goat, horse, pig, and sheep breeds. + id: '349' + name: Livestock Breed Ontology + prefix: FAIRsharing.309v57 + subjects: [] + mappings: + bioportal: LBO + fairsharing: FAIRsharing.309v57 + ols: lbo + ols: + contact: jreecy@iastate.edu + description: A vocabulary for cattle, chicken, horse, pig, and sheep breeds. + download: http://data.bioontology.org/ontologies/LBO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb + homepage: http://bioportal.bioontology.org/ontologies/LBO + name: Livestock Breed Ontology + prefix: lbo + pattern: ^\d{7}$ + repository: https://github.com/AnimalGenome/livestock-breed-ontology +lei: + mappings: + miriam: lei + n2t: lei + miriam: + deprecated: false + description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. + homepage: https://www.gleif.org/ + id: '00000686' + name: Global LEI Index + namespaceEmbeddedInLui: false + pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ + prefix: lei + sampleId: HWUPKR0MPOU8FGXBT394 + uri_format: https://www.gleif.org/lei/$1 + n2t: + description: Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. + example: HWUPKR0MPOU8FGXBT394 + homepage: https://www.gleif.org/ + name: Global LEI Index + namespaceEmbeddedInLui: false + pattern: ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ + prefix: lei + uri_format: https://www.gleif.org/lei/$1 +lepao: + bioportal: + name: Lepidoptera Anatomy Ontology + prefix: LEPAO + example: '0000005' + mappings: + bioportal: LEPAO + obofoundry: lepao + ols: lepao + obofoundry: + contact: lagonzalezmo@unal.edu.co + contact.github: luis-gonzalez-m + contact.label: Luis A. Gonzalez-Montana + contact.orcid: 0000-0002-9136-9932 + depends_on: + - aism + - bfo + - bspo + - caro + - pato + - ro + - uberon + deprecated: false + description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research). + download.obo: http://purl.obolibrary.org/obo/lepao.obo + download.owl: http://purl.obolibrary.org/obo/lepao.owl + homepage: https://github.com/insect-morphology/lepao + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Lepidoptera Anatomy Ontology + preferredPrefix: LEPAO + prefix: lepao + repository: https://github.com/insect-morphology/lepao + ols: + description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. + download: http://purl.obolibrary.org/obo/lepao.owl + homepage: https://github.com/insect-morphology/lepao + name: Lepidoptera Anatomy Ontology + prefix: lepao + version: 2021-11-20 + version.iri: http://purl.obolibrary.org/obo/lepao/releases/2021-11-20/lepao.owl + pattern: ^\d{7}$ +lgai.cede: + mappings: + miriam: lgai.cede + miriam: + deprecated: false + description: LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR). + homepage: https://www.lgresearch.ai + id: '00000867' + name: LG Chemical Entity Detection Dataset (LGCEDe) + namespaceEmbeddedInLui: false + pattern: ^LGCEDe-S-\d{9}$ + prefix: lgai.cede + sampleId: LGCEDe-S-000002244 + uri_format: https://s3.us-east-2.amazonaws.com/lg.cede/$1 +lgic: + biocontext: + is_identifiers: true + is_obo: false + prefix: LGIC + uri_format: http://identifiers.org/lgic/$1 + comment: Website is gone + deprecated: true + mappings: + biocontext: LGIC + miriam: lgic + n2t: lgic + miriam: + deprecated: false + description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. + homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php + id: '00000087' + name: Ligand-Gated Ion Channel database + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: lgic + sampleId: 5HT3Arano + uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php + n2t: + description: The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. + example: 5HT3Arano + homepage: https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php + name: Ligand-Gated Ion Channel database at EBI + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: lgic + uri_format: https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php +licebase: + biocontext: + is_identifiers: true + is_obo: false + prefix: LICEBASE + uri_format: http://identifiers.org/licebase/$1 + fairsharing: + abbreviation: LiceBase + description: LiceBase is a database for sea lice genomics. LiceBase provides the genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, Blast functionality and access to related high-thoughput genomics data. + id: '2389' + name: LiceBase + prefix: FAIRsharing.c7w81a + subjects: + - Life Science + mappings: + biocontext: LICEBASE + fairsharing: FAIRsharing.c7w81a + miriam: licebase + n2t: licebase + miriam: + deprecated: false + description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. + homepage: https://licebase.org + id: '00000628' + name: LiceBase + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\-\/]+$ + prefix: licebase + sampleId: EMLSAT00000003403 + uri_format: https://licebase.org/?q=$1 + n2t: + description: Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. + example: EMLSAT00000003403 + homepage: https://licebase.org + name: LiceBase + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\-\/]+$ + prefix: licebase + uri_format: https://licebase.org/?q=$1 +ligandbook: + mappings: + miriam: ligandbook + n2t: ligandbook + miriam: + deprecated: false + description: Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community. + homepage: https://ligandbook.org/ + id: '00000681' + name: LigandBook + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: ligandbook + sampleId: '785' + uri_format: https://ligandbook.org/package/$1 + n2t: + description: Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community. + example: '785' + homepage: https://ligandbook.org/ + name: LigandBook + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: ligandbook + uri_format: https://ligandbook.org/package/$1 +ligandbox: + biocontext: + is_identifiers: true + is_obo: false + prefix: LIGANDBOX + uri_format: http://identifiers.org/ligandbox/$1 + mappings: + biocontext: LIGANDBOX + miriam: ligandbox + n2t: ligandbox + miriam: + deprecated: false + description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. + homepage: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en + id: '00000477' + name: LigandBox + namespaceEmbeddedInLui: false + pattern: ^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$ + prefix: ligandbox + sampleId: D00001 + uri_format: http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1 + n2t: + description: LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. + example: D00001 + homepage: http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en + name: LigandBox at + namespaceEmbeddedInLui: false + pattern: ^D\d{5} + prefix: ligandbox + uri_format: http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$1 +ligandexpo: + biocontext: + is_identifiers: true + is_obo: false + prefix: LIGANDEXPO + uri_format: http://identifiers.org/ligandexpo/$1 + fairsharing: + abbreviation: Ligand Expo + description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. + id: '2043' + name: Ligand Expo + prefix: FAIRsharing.2ma4gq + subjects: + - Life Science + mappings: + biocontext: LIGANDEXPO + fairsharing: FAIRsharing.2ma4gq + miriam: ligandexpo + n2t: ligandexpo + prefixcommons: ligandexpo + miriam: + deprecated: false + description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. + homepage: http://ligand-depot.rutgers.edu/index.html + id: '00000062' + name: Ligand Expo + namespaceEmbeddedInLui: false + pattern: ^(\w){3}$ + prefix: ligandexpo + providers: + - code: CURATOR_REVIEW + description: Ligand Expo at Rutgers + homepage: http://ligand-expo.rcsb.org/ + name: Ligand Expo at Rutgers + uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid + sampleId: ABC + uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid + n2t: + description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. + example: ABC + homepage: http://ligand-expo.rcsb.org/ + name: Ligand Expo at Rutgers + namespaceEmbeddedInLui: false + pattern: ^(\w){3}$ + prefix: ligandexpo + uri_format: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid + prefixcommons: + description: Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. + example: ABC + homepage: http://ligand-depot.rutgers.edu/ + keywords: + - interaction + - structure + - protein + - chemical + - nucleic acid + name: Ligand Expo + pattern: ^(\w){3}$ + prefix: ligandexpo + pubmed_ids: + - '15059838' + uri_format: http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid +ligea: + cellosaurus: + category: Polymorphism and mutation databases + homepage: http://hpc-bioinformatics.cineca.it/fusion/main + name: Cancer cell LInes GEne fusions portAl + prefix: LiGeA + uri_format: http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1 + comment: This might just be a provider for CCLE + example: CCLE_867 + mappings: + cellosaurus: LiGeA +limore: + cellosaurus: + category: Cell line databases/resources + homepage: https://www.picb.ac.cn/limore/home + name: Liver Cancer Model Repository + prefix: LIMORE + uri_format: https://www.picb.ac.cn/limore/cellLines/single?para=$1 + example: Li7 + mappings: + cellosaurus: LIMORE +lincs.cell: + biocontext: + is_identifiers: true + is_obo: false + prefix: LINCS.CELL + uri_format: http://identifiers.org/lincs.cell/$1 + cellosaurus: + category: Cell line databases/resources + homepage: http://lincsportal.ccs.miami.edu/cells/ + name: LINCS Data Portal + prefix: LINCS_LDP + uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1 + mappings: + biocontext: LINCS.CELL + cellosaurus: LINCS_LDP + miriam: lincs.cell + n2t: lincs.cell + miriam: + deprecated: false + description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.' + homepage: http://lincsportal.ccs.miami.edu/cells/ + id: '00000544' + name: LINCS Cell + namespaceEmbeddedInLui: false + pattern: (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$) + prefix: lincs.cell + sampleId: LCL-2085 + uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1 + n2t: + description: 'The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.' + example: LCL-2085 + homepage: http://lincsportal.ccs.miami.edu/cells/ + name: LINCS Portal + namespaceEmbeddedInLui: false + pattern: (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$) + prefix: lincs.cell + uri_format: http://lincsportal.ccs.miami.edu/cells/#/view/$1 + pattern: ^(LCL|LDC|ES|LSC|LPC)-\d+$ + synonyms: + - LINCS_LDP +lincs.data: + biocontext: + is_identifiers: true + is_obo: false + prefix: LINCS.DATA + uri_format: http://identifiers.org/lincs.data/$1 + mappings: + biocontext: LINCS.DATA + miriam: lincs.data + n2t: lincs.data + miriam: + deprecated: false + description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). + homepage: http://lincsportal.ccs.miami.edu/datasets/ + id: '00000588' + name: LINCS Data + namespaceEmbeddedInLui: false + pattern: ^[EL]D[SG]-\d+$ + prefix: lincs.data + providers: + - code: omicsdi + description: Lincs through OmicsDI + homepage: https://www.omicsdi.org/ + name: Lincs through OmicsDI + uri_format: https://www.omicsdi.org/dataset/lincs/$1 + sampleId: LDS-1110 + uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1 + n2t: + description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). + example: LDS-1110 + homepage: http://lincsportal.ccs.miami.edu/datasets/ + name: LINCS Data at University of Miami + namespaceEmbeddedInLui: false + pattern: ^[EL]D[SG]-\d+$ + prefix: lincs.data + uri_format: http://lincsportal.ccs.miami.edu/datasets/#/view/$1 +lincs.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: LINCS.PROTEIN + uri_format: http://identifiers.org/lincs.protein/$1 + mappings: + biocontext: LINCS.PROTEIN + miriam: lincs.protein + n2t: lincs.protein + miriam: + deprecated: false + description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. + homepage: http://lincs.hms.harvard.edu/db/proteins/ + id: '00000545' + name: LINCS Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: lincs.protein + sampleId: '200282' + uri_format: http://lincs.hms.harvard.edu/db/proteins/$1/ + n2t: + description: The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. + example: '200282' + homepage: http://lincs.hms.harvard.edu/db/proteins/ + name: LINCS Protein at Harvard Medical School + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: lincs.protein + uri_format: http://lincs.hms.harvard.edu/db/proteins/$1/ + uri_format: https://lincs.hms.harvard.edu/db/proteins/$1 +lincs.smallmolecule: + biocontext: + is_identifiers: true + is_obo: false + prefix: LINCS.SMALLMOLECULE + uri_format: http://identifiers.org/lincs.smallmolecule/$1 + mappings: + biocontext: LINCS.SMALLMOLECULE + miriam: lincs.smallmolecule + n2t: lincs.smallmolecule + miriam: + deprecated: false + description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). + homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/ + id: '00000546' + name: LINCS Small Molecule + namespaceEmbeddedInLui: false + pattern: ^LSM-\d+$ + prefix: lincs.smallmolecule + sampleId: LSM-6306 + uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 + n2t: + description: The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). + example: LSM-6306 + homepage: http://lincsportal.ccs.miami.edu/SmallMolecules/ + name: LINCS Portal + namespaceEmbeddedInLui: false + pattern: ^LSM-\d+$ + prefix: lincs.smallmolecule + uri_format: http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 + synonyms: + - lincs +linguist: + homepage: https://github.com/github/linguist + mappings: + miriam: linguist + miriam: + deprecated: false + description: Registry of programming languages for the Linguist program for detecting and highlighting programming languages. + homepage: https://github.com/ + id: '00000849' + name: Linguist + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9 +#'*]+$ + prefix: linguist + sampleId: Python + uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 + repository: https://github.com/github/linguist +lipidbank: + biocontext: + is_identifiers: true + is_obo: false + prefix: LIPIDBANK + uri_format: http://identifiers.org/lipidbank/$1 + fairsharing: + abbreviation: LipidBank + description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. + id: '2111' + name: LipidBank + prefix: FAIRsharing.bdn9br + subjects: + - Life Science + mappings: + biocontext: LIPIDBANK + fairsharing: FAIRsharing.bdn9br + miriam: lipidbank + n2t: lipidbank + prefixcommons: lipidbank + miriam: + deprecated: false + description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. + homepage: http://lipidbank.jp/index.html + id: '00000115' + name: LipidBank + namespaceEmbeddedInLui: false + pattern: ^\w+\d+$ + prefix: lipidbank + sampleId: BBA0001 + uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 + n2t: + description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. + example: BBA0001 + homepage: http://lipidbank.jp/index.html + name: LipidBank the Lipid database + namespaceEmbeddedInLui: false + pattern: ^\w+\d+$ + prefix: lipidbank + uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 + prefixcommons: + description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. + example: BBA0001 + homepage: http://lipidbank.jp/index.html + keywords: + - lipid + - molecule + - structure + name: LipidBank + pattern: ^\w+\d+$ + prefix: lipidbank + pubmed_ids: + - '12058481' + uri_format: http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 +lipidmaps: + biocontext: + is_identifiers: true + is_obo: false + prefix: LIPIDMAPS + uri_format: http://identifiers.org/lipidmaps/$1 + cheminf: + description: Identifier used by the LipidMaps database, http://www.lipidmaps.org/. + name: LipidMaps + obsolete: false + prefix: '000564' + fairsharing: + abbreviation: LIPID MAPS + description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. + id: '2090' + name: LIPID MAPS + prefix: FAIRsharing.cpneh8 + subjects: + - Endocrinology + - Life Science + - Biomedical Science + - Systems Biology + mappings: + biocontext: LIPIDMAPS + cheminf: '000564' + fairsharing: FAIRsharing.cpneh8 + miriam: lipidmaps + n2t: lipidmaps + prefixcommons: lipidmaps + scholia: lipidmaps + miriam: + deprecated: false + description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. + homepage: http://www.lipidmaps.org + id: '00000052' + name: LIPID MAPS + namespaceEmbeddedInLui: false + pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ + prefix: lipidmaps + providers: + - code: scholia + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + homepage: https://scholia.toolforge.org/ + name: Scholia + uri_format: https://scholia.toolforge.org/lipidmaps/$1 + sampleId: LMPR0102010012 + uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 + n2t: + description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. + example: LMPR0102010012 + homepage: http://www.lipidmaps.org + name: Department of Bioengineering and the San Diego Supercomputer Center + namespaceEmbeddedInLui: false + pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ + prefix: lipidmaps + uri_format: http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 + prefixcommons: + description: The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. + example: LMPR0102010012 + homepage: http://www.lipidmaps.org + keywords: + - lipid + - structure + - taxonomy + name: LIPID MAPS + pattern: ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ + prefix: lipidmaps + pubmed_ids: + - '17098933' + - '15722563' + uri_format: http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=$1 + synonyms: + - LIPID MAPS + - LIPID_MAPS_class + - LIPID_MAPS_instance + wikidata: + prefix: P2063 +lipro: + biocontext: + is_identifiers: false + is_obo: true + prefix: LIPRO + uri_format: http://purl.obolibrary.org/obo/LIPRO_$1 + bioportal: + name: Lipid Ontology + prefix: LIPRO + mappings: + biocontext: LIPRO + bioportal: LIPRO + obofoundry: lipro + obofoundry: + contact: bakerc@unb.ca + contact.label: Christipher Baker + deprecated: true + description: An ontology representation of the LIPIDMAPS nomenclature classification. + name: Lipid Ontology + prefix: lipro +lncipedia: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A comprehensive compendium of human long non-coding RNAs + example: SNHG3 + fairsharing: + abbreviation: LNCipedia + description: LNCipedia is a database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. + id: '2647' + name: LNCipedia + prefix: FAIRsharing.84c1a7 + subjects: + - Life Science + homepage: https://lncipedia.org + mappings: + fairsharing: FAIRsharing.84c1a7 + name: LNCipedia +loggerhead: + biocontext: + is_identifiers: false + is_obo: true + prefix: LOGGERHEAD + uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1 + mappings: + biocontext: LOGGERHEAD + obofoundry: loggerhead + obofoundry: + contact: peteremidford@yahoo.com + contact.label: Peter Midford + contact.orcid: 0000-0001-6512-3296 + deprecated: true + homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html + name: Loggerhead nesting + prefix: loggerhead +loinc: + biolink: + is_identifiers: false + is_obo: false + prefix: LOINC + uri_format: http://loinc.org/rdf/$1 + bioportal: + name: Logical Observation Identifier Names and Codes + prefix: LOINC + description: The international standard for identifying health measurements, observations, and documents. + example: LL379-9 + fairsharing: + abbreviation: LOINC + description: LOINC is a common language (set of identifiers, names, and codes) for clinical and laboratory observations. LOINC is a catalog of measurements, including laboratory tests, clinical measures like vital signs and anthropomorphic measures, standardized survey instruments, and more. LOINC enables the exchange and aggregation of clinical results for care delivery, outcomes management, and research by providing a set of universal codes and structured names to unambiguously identify things you can measure or observe. + id: '2' + name: Logical Observation Identifier Names and Codes + prefix: FAIRsharing.2mk2zb + subjects: + - Life Science + - Biomedical Science + - Preclinical Studies + homepage: https://loinc.org/ + mappings: + biolink: LOINC + bioportal: LOINC + fairsharing: FAIRsharing.2mk2zb + name: Logical Observation Identifiers Names and Codes + synonyms: + - LNC + uri_format: https://loinc.org/$1 +lonza: + cellosaurus: + category: Cell line databases/resources + homepage: https://knowledge.lonza.com + name: Lonza Cell and Transfection Database + prefix: Lonza + uri_format: https://knowledge.lonza.com/cell?id=$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Contains information about cells and data sheets related to transfection. + example: '968' + homepage: https://knowledge.lonza.com + mappings: + cellosaurus: Lonza + name: Lonza + pattern: ^\d+$ + uri_format: https://knowledge.lonza.com/cell?id=$1 +lotus: + comment: IDs are actually leading to the structural part of LOTUS only, which might change in the future. Will adapt the regexp in case. + contact: + email: adriano.rutz@ik.me + github: adafede + name: Adriano Rutz + orcid: 0000-0003-0443-9902 + contributor: + github: adafede + name: Adriano Rutz + orcid: 0000-0003-0443-9902 + description: LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry. + example: LTS0004651 + homepage: https://lotus.naturalproducts.net + name: LOTUS Initiative for Open Natural Products Research + pattern: ^LTS\d{7}$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: https://lotus.naturalproducts.net/compound/lotus_id/$1 + wikidata: + database: Q104225190 +lpt: + biocontext: + is_identifiers: false + is_obo: true + prefix: LPT + uri_format: http://purl.obolibrary.org/obo/LPT_$1 + bioportal: + name: Livestock Product Trait Ontology + prefix: LPT + contact: + email: caripark@iastate.edu + github: caripark + name: Carissa Park + orcid: 0000-0002-2346-5201 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit. + download_obo: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.obo + download_owl: https://github.com/AnimalGenome/livestock-product-trait-ontology/raw/master/current_release/lpt.owl + example: '0000001' + fairsharing: + abbreviation: LPT + description: The Livestock Product Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit. + id: '739' + name: Livestock Product Trait Ontology + prefix: FAIRsharing.g78mbm + subjects: [] + homepage: https://github.com/AnimalGenome/livestock-product-trait-ontology + mappings: + biocontext: LPT + bioportal: LPT + fairsharing: FAIRsharing.g78mbm + name: Livestock Product Trait Ontology + pattern: ^\d+$ + repository: https://github.com/AnimalGenome/livestock-product-trait-ontology +lrg: + biocontext: + is_identifiers: true + is_obo: false + prefix: LRG + uri_format: http://identifiers.org/lrg/$1 + mappings: + biocontext: LRG + miriam: lrg + n2t: lrg + miriam: + deprecated: false + description: A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. + homepage: http://www.lrg-sequence.org/ + id: '00000376' + name: Locus Reference Genomic + namespaceEmbeddedInLui: false + pattern: ^LRG_\d+$ + prefix: lrg + providers: + - code: CURATOR_REVIEW + description: Locus Reference Genomic through Ensembl + homepage: http://www.ensembl.org/ + name: Locus Reference Genomic through Ensembl + uri_format: http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 + - code: CURATOR_REVIEW + description: Locus Reference Genomic through Ensembl mirror (asia) + homepage: http://asia.ensembl.org/ + name: Locus Reference Genomic through Ensembl mirror (asia) + uri_format: http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 + - code: CURATOR_REVIEW + description: Locus Reference Genomic through Ensembl mirror (US west) + homepage: http://uswest.ensembl.org/ + name: Locus Reference Genomic through Ensembl mirror (US west) + uri_format: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 + - code: CURATOR_REVIEW + description: Locus Reference Genomic through Ensembl mirror (US east) + homepage: http://useast.ensembl.org/ + name: Locus Reference Genomic through Ensembl mirror (US east) + uri_format: http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 + sampleId: LRG_1 + uri_format: ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml + n2t: + description: Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI). + example: LRG_1 + homepage: http://uswest.ensembl.org/ + name: Locus Reference Genomic through Ensembl mirror (US west) + namespaceEmbeddedInLui: false + pattern: ^LRG_\d+$ + prefix: lrg + uri_format: http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1 +lspci: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions) + example: '1' + homepage: https://labsyspharm.github.io/lspci/ + name: Laboratory of Systems Pharmacology Compound + pattern: ^\d+$ + uri_format: https://labsyspharm.github.io/lspci/$1 +lter: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Ecological terms + example: '182' + homepage: https://vocab.lternet.edu/vocab/vocab/index.php + name: Long Term Ecological Research Controlled Vocabulary + pattern: ^\d+$ + uri_format: https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1 +ma: + biocontext: + is_identifiers: false + is_obo: true + prefix: MA + uri_format: http://purl.obolibrary.org/obo/MA_$1 + bioportal: + name: Mouse Adult Gross Anatomy Ontology + prefix: MA + fairsharing: + abbreviation: MA + description: The Mouse Adult Gross Anatomy ontology also has aliases of 'Mouse Anatomy' or 'Mouse anatomical entity'. The resource is a standard, providing a structured vocabulary for the adult anatomy of the mouse. This ontology is part of the Gene Expression Database (GDX) Project of the Jackson Laboratory. + id: '13' + name: Mouse Adult Gross Anatomy Ontology + prefix: FAIRsharing.pdwqcr + subjects: + - Anatomy + - Life Science + go: + description: Adult Mouse Anatomical Dictionary; part of Gene Expression Database + homepage: http://www.informatics.jax.org/ + name: Adult Mouse Anatomical Dictionary + prefix: MA + uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 + mappings: + biocontext: MA + bioportal: MA + fairsharing: FAIRsharing.pdwqcr + go: MA + miriam: ma + n2t: ma + obofoundry: ma + ols: ma + ontobee: MA + prefixcommons: ma + miriam: + deprecated: false + description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) + homepage: http://www.informatics.jax.org/ + id: '00000445' + name: Mouse Adult Gross Anatomy + namespaceEmbeddedInLui: true + pattern: ^MA:\d+$ + prefix: ma + sampleId: '0002502' + uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 + n2t: + description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus) + example: '0002502' + homepage: http://www.informatics.jax.org/ + name: Mouse Adult Gross Anatomy at The Jackson Laboratory + namespaceEmbeddedInLui: true + pattern: ^MA:\d+$ + prefix: ma + uri_format: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 + obofoundry: + contact: Terry.Hayamizu@jax.org + contact.github: tfhayamizu + contact.label: Terry Hayamizu + contact.orcid: 0000-0002-0956-8634 + deprecated: false + description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). + download.obo: http://purl.obolibrary.org/obo/ma.obo + download.owl: http://purl.obolibrary.org/obo/ma.owl + homepage: https://github.com/obophenotype/mouse-anatomy-ontology + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Mouse adult gross anatomy + preferredPrefix: MA + prefix: ma + repository: https://github.com/obophenotype/mouse-anatomy-ontology + ols: + description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). + download: http://purl.obolibrary.org/obo/ma.owl + homepage: https://github.com/obophenotype/mouse-anatomy-ontology + name: Mouse adult gross anatomy + prefix: ma + version: 2017-02-07 + version.iri: http://purl.obolibrary.org/obo/ma/releases/2017-02-07/ma.owl + ontobee: + library: Library + name: Mouse adult gross anatomy + prefix: MA + pattern: ^\d+$ + prefixcommons: + bioportal: '1000' + description: A structured controlled vocabulary of the adult anatomy of the mouse (Mus). + example: MA:0000021 + homepage: http://www.informatics.jax.org/searches/AMA_form.shtml + keywords: + - obo + - anatomy + - mouse + name: Mouse adult gross anatomy + pattern: ^MA:\d+$ + prefix: ma +macie: + biocontext: + is_identifiers: true + is_obo: false + prefix: MACIE + uri_format: http://identifiers.org/macie/$1 + fairsharing: + abbreviation: MACiE + description: MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. The database contains the reaction mechanisms for 100 individual enzymes; this includes the overall reactions and the multiple steps that constitute them. + id: '1602' + name: Mechanism, Annotation and Classification in Enzymes + prefix: FAIRsharing.7xkx69 + subjects: + - Life Science + mappings: + biocontext: MACIE + fairsharing: FAIRsharing.7xkx69 + miriam: macie + n2t: macie + prefixcommons: macie + miriam: + deprecated: false + description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. + homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html + id: '00000077' + name: MACiE + namespaceEmbeddedInLui: false + pattern: ^M\d{4}$ + prefix: macie + sampleId: M0001 + uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 + n2t: + description: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. + example: M0001 + homepage: https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html + name: MACiE database of mechanisms, annotation and classification in enzymes + namespaceEmbeddedInLui: false + pattern: ^M\d{4}$ + prefix: macie + uri_format: https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 + name: Mechanism, Annotation and Classification in Enzymes + prefixcommons: + description: MACiE is an electronic database of well-characterised enzymatic reactions. MACiE is the result of more than three years' collaboration between the Mitchell and Murray-Rust groups in the Unilever Centre and Prof. Janet Thornton at the European Bioinformatics Institute. The database contains the reaction mechanisms for 100 individual enzymes; this includes the overall reactions and the multiple steps that constitute them. + example: M0001 + homepage: http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ + keywords: + - enzyme + - pathway + name: MACiE + pattern: ^M\d{4}$ + prefix: macie + pubmed_ids: + - '17082206' + uri_format: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/getPage.pl?id=$1 +maizegdb.locus: + biocontext: + is_identifiers: true + is_obo: false + prefix: MAIZEGDB.LOCUS + uri_format: http://identifiers.org/maizegdb.locus/$1 + fairsharing: + abbreviation: MaizeGDB + description: MaizeGDB is the maize research community's central repository for genetics and genomics information. + id: '1948' + name: Maize Genetics and Genomics Database + prefix: FAIRsharing.aq280w + subjects: + - Genomics + - Genetics + - Life Science + go: + homepage: https://www.maizegdb.org/ + name: MaizeGDB + prefix: MaizeGDB_Locus + uri_format: https://www.maizegdb.org/gene_center/gene/$1 + mappings: + biocontext: MAIZEGDB.LOCUS + fairsharing: FAIRsharing.aq280w + go: MaizeGDB_Locus + miriam: maizegdb.locus + n2t: maizegdb.locus + ncbi: MaizeGDB + prefixcommons: maizegdb + uniprot: MaizeGDB + miriam: + deprecated: false + description: MaizeGDB is the maize research community's central repository for genetics and genomics information. + homepage: http://www.maizegdb.org/ + id: '00000177' + name: MaizeGDB Locus + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: maizegdb.locus + sampleId: '25011' + uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 + n2t: + description: MaizeGDB is the maize research community's central repository for genetics and genomics information. + example: '25011' + homepage: http://www.maizegdb.org/ + name: MaizeGDB at Missouri + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: maizegdb.locus + uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 + name: MaizeGDB Locus + ncbi: + example: '635633' + homepage: http://www.maizegdb.org/ + name: Maize Genome Database unique identifiers + prefix: MaizeGDB + prefixcommons: + description: MaizeGDB is the maize research community's central repository for genetics and genomics information. + example: '25011' + homepage: http://www.maizegdb.org + keywords: + - genome + - DNA + name: Maize Genetics and Genomics Database + pattern: ^\d+$ + prefix: maizegdb + pubmed_ids: + - '18769488' + uri_format: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 + synonyms: + - MaizeGDB + uniprot: + category: Organism-specific databases + comment: Replacement for MaizeDB + identifier: '58' + link_is_explicit: 'true' + name: Maize Genetics and Genomics Database + prefix: MaizeGDB + uri_format: https://www.maizegdb.org/data_center/gene_product?id=$1 +mamo: + biocontext: + is_identifiers: false + is_obo: true + prefix: MAMO + uri_format: http://purl.obolibrary.org/obo/MAMO_$1 + bioportal: + name: Mathematical Modelling Ontology + prefix: MAMO + example: '0000026' + fairsharing: + abbreviation: MAMO + description: Classification of the types of mathematical models used mostly in the life sciences, the types of variables, the types of readout and other relevant features. + id: '178' + name: Mathematical Modelling Ontology + prefix: FAIRsharing.kbz5jh + subjects: + - Mathematics + - Computational Biology + - Systems Biology + mappings: + biocontext: MAMO + bioportal: MAMO + fairsharing: FAIRsharing.kbz5jh + miriam: mamo + n2t: mamo + obofoundry: mamo + ols: mamo + ontobee: MAMO + miriam: + deprecated: false + description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. + homepage: http://bioportal.bioontology.org/ontologies/MAMO + id: '00000517' + name: Mathematical Modelling Ontology + namespaceEmbeddedInLui: false + pattern: ^MAMO_\d{7}$ + prefix: mamo + sampleId: MAMO_0000026 + uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1 + n2t: + description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. + example: MAMO_0000026 + homepage: http://bioportal.bioontology.org/ontologies/MAMO + name: MAMO through BioPortal + namespaceEmbeddedInLui: false + pattern: ^MAMO_\d{7}$ + prefix: mamo + uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$1 + obofoundry: + contact: nicolas@ascistance.co.uk + contact.github: gambardella + contact.label: Nicolas Gambardella + contact.orcid: 0000-0002-6309-7327 + deprecated: false + description: The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. + download.owl: http://purl.obolibrary.org/obo/mamo.owl + homepage: http://sourceforge.net/p/mamo-ontology/wiki/Home/ + license: Artistic License 2.0 + license.url: http://opensource.org/licenses/Artistic-2.0 + name: Mathematical modeling ontology + preferredPrefix: MAMO + prefix: mamo + repository: http://sourceforge.net/p/mamo-ontology + ols: + download: http://purl.obolibrary.org/obo/mamo.owl + name: Mathematical Modelling Ontology + prefix: mamo + version: 2020-08-24 + ontobee: + library: Library + name: Mathematical modeling ontology + prefix: MAMO + pattern: ^\d{7}$ + uri_format: http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1 +mao: + biocontext: + is_identifiers: false + is_obo: true + prefix: MAO + uri_format: http://purl.obolibrary.org/obo/MAO_$1 + mappings: + biocontext: MAO + obofoundry: mao + prefixcommons: mao + obofoundry: + contact: julie@igbmc.u-strasbg.fr + contact.label: Julie Thompson + deprecated: true + homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html + name: Multiple alignment + prefix: mao + prefixcommons: + bioportal: '1026' + description: An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment. + example: MAO:0000061 + homepage: http://bips.u-strasbg.fr/LBGI/MAO/mao.html + keywords: + - obo + - sequence + - alignment + name: Multiple Alignment Ontology + pattern: ^MAO_\d+$ + prefix: mao +massbank: + biocontext: + is_identifiers: true + is_obo: false + prefix: MASSBANK + uri_format: http://identifiers.org/massbank/$1 + fairsharing: + abbreviation: MassBank + description: MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry. + id: '2349' + name: MassBank Europe + prefix: FAIRsharing.dk451a + subjects: + - Chemistry + - Life Science + - Physics + mappings: + biocontext: MASSBANK + fairsharing: FAIRsharing.dk451a + miriam: massbank + n2t: massbank + miriam: + deprecated: false + description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). + homepage: http://www.massbank.jp + id: '00000273' + name: MassBank + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$ + prefix: massbank + providers: + - code: CURATOR_REVIEW + description: MassBank in Europe + homepage: https://massbank.eu/ + name: MassBank in Europe + uri_format: https://massbank.eu/MassBank/RecordDisplay?id=$1 + sampleId: PB000166 + uri_format: http://www.massbank.jp/RecordDisplay?id=$1 + n2t: + description: MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). + example: PB000166 + homepage: http://www.massbank.jp + name: MassBank in Japan + namespaceEmbeddedInLui: false + pattern: ^[A-Z]{2}[A-Z0-9][0-9]{5}$ + prefix: massbank + uri_format: http://www.massbank.jp/jsp/FwdRecord.jsp?id=$1 + wikidata: + database: Q24088019 + prefix: P6689 +massive: + biocontext: + is_identifiers: true + is_obo: false + prefix: MASSIVE + uri_format: http://identifiers.org/massive/$1 + fairsharing: + abbreviation: MassIVE + description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements. + id: '2671' + name: Mass Spectrometry Interactive Virtual Environment + prefix: FAIRsharing.LYsiMd + subjects: + - Proteomics + - Metabolomics + - Transcriptomics + mappings: + biocontext: MASSIVE + fairsharing: FAIRsharing.LYsiMd + miriam: massive + n2t: massive + uniprot: MassIVE + miriam: + deprecated: false + description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. + homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp + id: '00000650' + name: MassIVE + namespaceEmbeddedInLui: false + pattern: ^MSV\d+$ + prefix: massive + providers: + - code: omicsdi + description: MassIVE through OmicsDI + homepage: https://www.omicsdi.org/ + name: MassIVE through OmicsDI + uri_format: https://www.omicsdi.org/dataset/massive/$1 + sampleId: MSV000082131 + uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 + n2t: + description: MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. + example: MSV000082131 + homepage: https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp + name: MassIVE + namespaceEmbeddedInLui: false + pattern: ^MSV\d+$ + prefix: massive + uri_format: https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 + uniprot: + category: Proteomic databases + identifier: '241' + link_is_explicit: 'true' + name: MassIVE - Mass Spectrometry Interactive Virtual Environment + prefix: MassIVE + uri_format: https://massive.ucsd.edu/ProteoSAFe/protein_explorer.jsp?libraries=2&protein_name=$1 +mat: + biocontext: + is_identifiers: false + is_obo: true + prefix: MAT + uri_format: http://purl.obolibrary.org/obo/MAT_$1 + bioportal: + name: Minimal Anatomical Terminology + prefix: MAT + example: '0000000' + mappings: + biocontext: MAT + bioportal: MAT + obofoundry: mat + name: Minimal Anatomical Terminology + obofoundry: + contact: j.bard@ed.ac.uk + contact.label: Jonathan Bard + deprecated: true + name: Minimal anatomical terminology + prefix: mat + pattern: ^\d{7}$ +matrixdb: + appears_in: + - complexportal + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides + example: MULT_4_VAR1_bovine + fairsharing: + abbreviation: MatrixDB + description: MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondins) when appropriate. Multimers are treated as permanent complexes, referencing EBI identifiers when possible. Human interactions were inferred from non-human homologous interactions when available. + id: '1893' + name: Extracellular Matrix Interaction Database + prefix: FAIRsharing.91yrz6 + subjects: + - Biology + homepage: http://matrixdb.univ-lyon1.fr/ + mappings: + fairsharing: FAIRsharing.91yrz6 + prefixcommons: matrixdb + name: MatrixDB + prefixcommons: + description: MatrixDB is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. Full-length molecules, fragments and multimers present in the extracellular matrix are all included in the database. + example: P00747_P07355 + homepage: http://matrixdb.ibcp.fr + keywords: + - protein + - small molecule + - interaction + name: 'MatrixDB: Extracellular Matrix interactions database' + pattern: ^[A-Z]\d+_[A-Z]\d+$ + prefix: matrixdb + pubmed_ids: + - '19147664' + uri_format: http://matrixdb.ibcp.fr/cgi-bin/model/report/default?name=$1&class=Association + uri_format: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1 +matrixdb.association: + biocontext: + is_identifiers: true + is_obo: false + prefix: MATRIXDB.ASSOCIATION + uri_format: http://identifiers.org/matrixdb.association/$1 + mappings: + biocontext: MATRIXDB.ASSOCIATION + miriam: matrixdb.association + n2t: matrixdb.association + miriam: + deprecated: false + description: MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. + homepage: http://matrixdb.univ-lyon1.fr/ + id: '00000068' + name: MatrixDB + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ + prefix: matrixdb.association + sampleId: P00747__P07355 + uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association + n2t: + description: MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. + example: P00747__P07355 + homepage: http://matrixdb.univ-lyon1.fr/ + name: MatrixDB Association + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ + prefix: matrixdb.association + uri_format: http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association + name: MatrixDB Association +maxo: + biolink: + is_identifiers: false + is_obo: true + prefix: MAXO + uri_format: http://purl.obolibrary.org/obo/MAXO_$1 + bioportal: + name: Medical Action Ontology + prefix: MAXO + example: '0000008' + mappings: + biolink: MAXO + bioportal: MAXO + obofoundry: maxo + ols: maxo + ontobee: MAXO + obofoundry: + appears_in: + - ecto + contact: Leigh.Carmody@jax.org + contact.github: LCCarmody + contact.label: Leigh Carmody + contact.orcid: 0000-0001-7941-2961 + depends_on: + - chebi + - foodon + - go + - iao + - ro + - uberon + deprecated: false + description: Medical Action Ontology is an ontology... + download.json: http://purl.obolibrary.org/obo/maxo.json + download.obo: http://purl.obolibrary.org/obo/maxo.obo + download.owl: http://purl.obolibrary.org/obo/maxo.owl + homepage: https://github.com/monarch-initiative/MAxO + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Medical Action Ontology + preferredPrefix: MAXO + prefix: maxo + repository: https://github.com/monarch-initiative/MAxO + ols: + description: An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. + download: http://purl.obolibrary.org/obo/maxo.owl + homepage: https://github.com/monarch-initiative/MAxO + name: Medical Action Ontology + prefix: maxo + version: 2022-04-11 + version.iri: http://purl.obolibrary.org/obo/maxo/releases/2022-04-11/maxo.owl + ontobee: + library: Library + name: Medical Action Ontology + prefix: MAXO + pattern: ^\d{7}$ + twitter: MonarchInit +mba: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A controlled vocabulary to support the study of transcription in the mouse brain + download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo + example: '688' + homepage: https://mouse.brain-map.org + name: Mouse Brain Atlas + pattern: ^\d+$ + preferred_prefix: MBA +mcc: + bioportal: + name: Cell Line Ontology [by Mahadevan] + prefix: MCCL + deprecated: true + mappings: + bioportal: MCCL + name: Cell Line Ontology [derivative] +mco: + bioportal: + name: Microbial Conditions Ontology + prefix: MCO + example: '0000858' + mappings: + bioportal: MCO + obofoundry: mco + ols: mco + ontobee: MCO + obofoundry: + contact: citlalli.mejiaalmonte@gmail.com + contact.github: citmejia + contact.label: Citlalli Mejía-Almonte + contact.orcid: 0000-0002-0142-5591 + depends_on: + - bfo + - chebi + - cl + - clo + - micro + - ncbitaxon + - ncit + - obi + - omit + - omp + - pato + - peco + - uberon + - zeco + deprecated: false + description: Microbial Conditions Ontology is an ontology... + download.obo: http://purl.obolibrary.org/obo/mco.obo + download.owl: http://purl.obolibrary.org/obo/mco.owl + homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Microbial Conditions Ontology + preferredPrefix: MCO + prefix: mco + repository: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology + ols: + description: Microbial Conditions Ontology is an ontology... + download: http://purl.obolibrary.org/obo/mco.owl + homepage: https://github.com/microbial-conditions-ontology/microbial-conditions-ontology + name: Microbial Conditions Ontology + prefix: mco + version: 2019-05-15 + version.iri: http://purl.obolibrary.org/obo/mco/releases/2019-05-15/mco.owl + ontobee: + library: Library + name: Microbial Conditions Ontology + prefix: MCO + pattern: ^\d+$ +mdm: + biocontext: + is_identifiers: true + is_obo: false + prefix: MDM + uri_format: http://identifiers.org/mdm/$1 + bioportal: + name: Mapping of Drug Names and MeSH 2022 + prefix: MDM + fairsharing: + abbreviation: MDM + description: MDM-Portal (Medical Data-Models) is a meta-data registry for creating, analysing, sharing and reusing medical forms, developed by the Institute of Medical Informatics, University of Muenster in Germany. see also http://www.ncbi.nlm.nih.gov/pubmed/26868052 Electronic forms for documentation of patient data are an integral part within the workflow of physicians. A huge amount of data is collected either through routine documentation forms (EHRs) for electronic health records or as case report forms (CRFs) for clinical trials. This raises major scientific challenges for health care, since different health information systems are not necessarily compatible with each other and thus information exchange of structured data is hampered. Software vendors provide a variety of individual documentation forms according to their standard contracts, which function as isolated applications. Furthermore, free availability of those forms is rarely the case. Currently less than 5 % of medical forms are freely accessible. Based on this lack of transparency harmonization of data models in health care is extremely cumbersome, thus work and know-how of completed clinical trials and routine documentation in hospitals are hard to be re-used. The MDM-Portal serves as an infrastructure for academic (non-commercial) medical research to contribute a solution to this problem. It already contains more than 6,000 system-independent forms (CDISC ODM Format, www.cdisc.org, Operational Data Model) with more than 470,000 data-elements. This enables researchers to view, discuss, download and export forms in most common technical formats such as PDF, CSV, Excel, SQL, SPSS, R, etc. A growing user community will lead to a growing database of medical forms. In this matter, we would like to encourage all medical researchers to register and add forms and discuss existing forms. + id: '2297' + name: Medical Data Models + prefix: FAIRsharing.wnk2eq + subjects: + - Medicine + - Biomedical Science + - Translational Medicine + mappings: + biocontext: MDM + bioportal: MDM + fairsharing: FAIRsharing.wnk2eq + miriam: mdm + n2t: mdm + miriam: + deprecated: false + description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. + homepage: https://medical-data-models.org/ + id: '00000574' + name: MDM + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mdm + sampleId: '4776' + uri_format: https://medical-data-models.org/forms/$1 + n2t: + description: The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. + example: '4776' + homepage: https://medical-data-models.org/ + name: MDM at University of Muenster + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mdm + uri_format: https://medical-data-models.org/forms/$1 + name: Medical Data Models +meddra: + biocontext: + is_identifiers: false + is_obo: false + prefix: MEDDRA + uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1 + bioportal: + name: Medical Dictionary for Regulatory Activities Terminology (MedDRA) + prefix: MEDDRA + fairsharing: + abbreviation: MedDRA + description: 'MedDRA is a multilingual terminology allowing most users to operate in their native languages. MedDRA can be used to analyse individual medical events (e.g., “Influenza”) or issues involving a system, organ or etiology (e.g., infections) using its hierarchical structure. MedDRA can be used for signal detection and monitoring of clinical syndromes whose symptoms encompass numerous systems or organs using its multi-axial hierarchy or through the special feature of Standardised MedDRA Queries. The ability to communicate adverse event data is another strength of MedDRA and has lead to MedDRA being an integral part of the ICH e-submission standards: eCTD (ICH M8) and ICSRs (ICH E2B).' + id: '1022' + name: Medical Dictionary for Regulatory Activities Terminology + prefix: FAIRsharing.ad3137 + subjects: + - Medicine + - Biomedical Science + - Preclinical Studies + mappings: + biocontext: MEDDRA + bioportal: MEDDRA + fairsharing: FAIRsharing.ad3137 + miriam: meddra + n2t: meddra + miriam: + deprecated: false + description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). + homepage: http://bioportal.bioontology.org/ontologies/MEDDRA + id: '00000563' + name: MedDRA + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: meddra + sampleId: '10015919' + uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1 + n2t: + description: The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). + example: '10015919' + homepage: http://bioportal.bioontology.org/ontologies/MEDDRA + name: MedDRA through BioPortal + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: meddra + uri_format: http://purl.bioontology.org/ontology/MEDDRA/$1 + name: Medical Dictionary for Regulatory Activities Terminology + synonyms: + - MEDRA + - MeDRA + - MedDRA + - Medical Dictionary for Regulatory Activities + wikidata: + prefix: P3201 +medgen: + biocontext: + is_identifiers: false + is_obo: false + prefix: MedGen + uri_format: http://www.ncbi.nlm.nih.gov/medgen/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: medgen + uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 + mappings: + biocontext: MedGen + biolink: medgen + miriam: medgen + n2t: medgen + ncbi: MedGen + miriam: + deprecated: false + description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. + homepage: https://www.ncbi.nlm.nih.gov/medgen/ + id: '00000594' + name: MedGen + namespaceEmbeddedInLui: false + pattern: ^[CN]*\d{4,7}$ + prefix: medgen + sampleId: '760050' + uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 + n2t: + description: MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. + example: '760050' + homepage: https://www.ncbi.nlm.nih.gov/medgen/ + name: MedGen at NCBI + namespaceEmbeddedInLui: false + pattern: ^[CN]*\d{4,7}$ + prefix: medgen + uri_format: https://www.ncbi.nlm.nih.gov/medgen/$1 + ncbi: + example: C0010674 + homepage: https://www.ncbi.nlm.nih.gov/medgen + name: Human Medical Genetics + prefix: MedGen +medlineplus: + biocontext: + is_identifiers: true + is_obo: false + prefix: MEDLINEPLUS + uri_format: http://identifiers.org/medlineplus/$1 + bioportal: + name: MedlinePlus Health Topics + prefix: MEDLINEPLUS + fairsharing: + abbreviation: MEDLINEPLUS + description: This resource provides information on the symptoms, causes, treatment and prevention for a wide range of diseases, illnesses, health conditions and wellness issues. MedlinePlus health topics are regularly reviewed, and links are updated daily. + id: '884' + name: MedlinePlus Health Topics + prefix: FAIRsharing.bf8dsb + subjects: + - Medicine + - Health Science + - Biomedical Science + mappings: + biocontext: MEDLINEPLUS + bioportal: MEDLINEPLUS + fairsharing: FAIRsharing.bf8dsb + miriam: medlineplus + n2t: medlineplus + miriam: + deprecated: false + description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. + homepage: http://www.nlm.nih.gov/medlineplus/ + id: '00000476' + name: MedlinePlus + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: medlineplus + sampleId: '002804' + uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm + n2t: + description: MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. + example: '002804' + homepage: http://www.nlm.nih.gov/medlineplus/ + name: MedlinePlus at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: medlineplus + uri_format: http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm +merops: + biocontext: + is_identifiers: true + is_obo: false + prefix: MEROPS + uri_format: http://identifiers.org/merops/$1 + fairsharing: + abbreviation: MEROPS + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. + id: '2047' + name: MEROPS + prefix: FAIRsharing.2s4n8r + subjects: + - Life Science + - Biomedical Science + go: + homepage: https://www.ebi.ac.uk/merops/ + name: MEROPS peptidase database + prefix: MEROPS + uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1 + mappings: + biocontext: MEROPS + fairsharing: FAIRsharing.2s4n8r + go: MEROPS + miriam: merops + n2t: merops + prefixcommons: merops + uniprot: MEROPS + miriam: + deprecated: false + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. + homepage: http://merops.sanger.ac.uk/index.htm + id: '00000059' + name: MEROPS + namespaceEmbeddedInLui: false + pattern: ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$ + prefix: merops + sampleId: S01.001 + uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$1 + n2t: + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. + example: S01.001 + homepage: http://merops.sanger.ac.uk/index.htm + name: MEROPS database at Sanger Institute + namespaceEmbeddedInLui: false + pattern: ^[SCTAGMNU]\d{2}\.([AB]\d{2}|\d{3})$ + prefix: merops + uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$1 + prefixcommons: + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. + example: S01.001 + homepage: http://merops.sanger.ac.uk/ + keywords: + - protein + - enzyme + - structure + name: MEROPS - the Peptidase Database + pattern: ^S\d{2}\.\d{3}$ + prefix: merops + pubmed_ids: + - '17991683' + uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1 + uniprot: + category: Protein family/group databases + identifier: '59' + link_is_explicit: 'true' + name: MEROPS protease database + prefix: MEROPS + uri_format: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?mid=$1 +merops.family: + biocontext: + is_identifiers: true + is_obo: false + prefix: MEROPS.FAMILY + uri_format: http://identifiers.org/merops.family/$1 + mappings: + biocontext: MEROPS.FAMILY + miriam: merops.family + n2t: merops.family + miriam: + deprecated: false + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. + homepage: http://merops.sanger.ac.uk/index.htm + id: '00000302' + name: MEROPS Family + namespaceEmbeddedInLui: false + pattern: ^[SCTAGMNU]\d+$ + prefix: merops.family + sampleId: S1 + uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1 + n2t: + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. + example: S1 + homepage: http://merops.sanger.ac.uk/index.htm + name: Merops Family at Sanger Institute + namespaceEmbeddedInLui: false + pattern: ^[SCTAGMNU]\d+$ + prefix: merops.family + uri_format: http://merops.sanger.ac.uk/cgi-bin/famsum?family=$1 +merops.inhibitor: + biocontext: + is_identifiers: true + is_obo: false + prefix: MEROPS.INHIBITOR + uri_format: http://identifiers.org/merops.inhibitor/$1 + mappings: + biocontext: MEROPS.INHIBITOR + miriam: merops.inhibitor + n2t: merops.inhibitor + miriam: + deprecated: false + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. + homepage: http://merops.sanger.ac.uk/index.htm + id: '00000491' + name: MEROPS Inhibitor + namespaceEmbeddedInLui: false + pattern: ^I\d{2}\.\d{3}$ + prefix: merops.inhibitor + sampleId: I31.952 + uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1 + n2t: + description: The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. + example: I31.952 + homepage: http://merops.sanger.ac.uk/index.htm + name: MEROPS Inhibitor at Sanger Institute + namespaceEmbeddedInLui: false + pattern: ^I\d{2}\.\d{3}$ + prefix: merops.inhibitor + uri_format: http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$1 +mesh: + biocontext: + is_identifiers: false + is_obo: true + prefix: MESH + uri_format: http://purl.obolibrary.org/obo/MESH_$1 + biolink: + is_identifiers: false + is_obo: false + prefix: MESH + uri_format: http://id.nlm.nih.gov/mesh/$1 + bioportal: + name: Medical Subject Headings + prefix: MESH + cellosaurus: + category: Medical resources + homepage: https://www.ncbi.nlm.nih.gov/mesh + name: Medical Subject Headings + prefix: MeSH + uri_format: https://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?field=uid&term=$1 + example: C063233 + example_extras: + - D000001 + fairsharing: + abbreviation: MESH + description: MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as "Anatomy" or "Mental Disorders." More specific headings are found at more narrow levels of the thirteen-level hierarchy, such as "Ankle" and "Conduct Disorder." There are 27,883 descriptors in 2016 MeSH with over 87,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, "Vitamin C" is an entry term to "Ascorbic Acid." In addition to these headings, there are more than 232,000 Supplementary Concept Records (SCRs) within a separate file. Generally SCR records contain specific examples of chemicals, diseases, and drug protocols. They are updated more frequently than descriptors. Each SCR is assigned to a related descriptor via the Heading Map (HM) field. The HM is used to rapidly identify the most specific descriptor class and include it in the citation. If you work on the project responsible for "Medical Subject Headings" then please consider helping us by claiming this record and updating it appropriately. + id: '1265' + name: Medical Subject Headings + prefix: FAIRsharing.qnkw45 + subjects: + - Bioinformatics + - Life Science + - Biomedical Science + go: + homepage: https://meshb.nlm.nih.gov + name: Medical Subject Headings + prefix: MeSH + synonyms: + - MESH + - MSH + uri_format: http://id.nlm.nih.gov/mesh/$1 + mappings: + biocontext: MESH + biolink: MESH + bioportal: MESH + cellosaurus: MeSH + fairsharing: FAIRsharing.qnkw45 + go: MeSH + miriam: mesh + n2t: mesh + prefixcommons: mesh + scholia: mesh + miriam: + deprecated: false + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. + homepage: http://id.nlm.nih.gov/mesh/ + id: '00000560' + name: MeSH + namespaceEmbeddedInLui: false + pattern: ^(C|D)\d{6,9}$ + prefix: mesh + sampleId: C000100 + uri_format: http://id.nlm.nih.gov/mesh/$1 + n2t: + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. + example: C000100 + homepage: http://id.nlm.nih.gov/mesh/ + name: MeSH Linked Data at National Library of Medicine + namespaceEmbeddedInLui: false + pattern: ^(C|D)\d{6}$ + prefix: mesh + uri_format: http://id.nlm.nih.gov/mesh/$1 + name: Medical Subject Headings + prefixcommons: + bioportal: '1351' + description: MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity + example: D018377 + homepage: http://www.nlm.nih.gov/mesh/meshhome.html + keywords: + - classification + name: Medical Subject Headings + pattern: ^[A-Za-z0-9]+$ + prefix: mesh + synonyms: + - MESH + - MESHA + - MESHC + - MESHCS + - MESHD + - MESHPP + - MESH_DESCRIPTOR_UI + - MESH_SUPPLEMENTAL_RECORD_UI + - MSH + uri_format: https://meshb.nlm.nih.gov/record/ui?ui=$1 + wikidata: + database: Q199897 + database.label: Medical Subject Headings + homepage: https://www.wikidata.org/wiki/Q6589563 + name: MeSH descriptor ID + pattern: ^[CD]\w{6}(\w{3}|)$ + prefix: P486 + uri_format: http://id.nlm.nih.gov/mesh/$1 +mesh.2012: + biocontext: + is_identifiers: true + is_obo: false + prefix: MESH.2012 + uri_format: http://identifiers.org/mesh.2012/$1 + mappings: + biocontext: MESH.2012 + miriam: mesh.2012 + n2t: mesh.2012 + miriam: + deprecated: false + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. + homepage: http://www.nlm.nih.gov/mesh/ + id: '00000270' + name: MeSH 2012 + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: mesh.2012 + sampleId: '17186' + uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded + n2t: + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. + example: '17186' + homepage: http://www.nlm.nih.gov/mesh/ + name: MeSH at National Library of Medicine + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: mesh.2012 + uri_format: http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded +mesh.2013: + biocontext: + is_identifiers: true + is_obo: false + prefix: MESH.2013 + uri_format: http://identifiers.org/mesh.2013/$1 + mappings: + biocontext: MESH.2013 + miriam: mesh.2013 + n2t: mesh.2013 + miriam: + deprecated: false + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. + homepage: http://www.nlm.nih.gov/mesh/ + id: '00000473' + name: MeSH 2013 + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: mesh.2013 + sampleId: '17165' + uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded + n2t: + description: MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. + example: '17165' + homepage: http://www.nlm.nih.gov/mesh/ + name: MeSH 2013 at National Library of Medicine + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: mesh.2013 + uri_format: http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded +metabolights: + biocontext: + is_identifiers: true + is_obo: false + prefix: METABOLIGHTS + uri_format: http://identifiers.org/metabolights/$1 + cellosaurus: + category: Metabolomic databases + homepage: https://www.ebi.ac.uk/metabolights/ + name: MetaboLights database for metabolomics experiments and derived information + prefix: MetaboLights + uri_format: https://www.ebi.ac.uk/metabolights/$1 + mappings: + biocontext: METABOLIGHTS + cellosaurus: MetaboLights + miriam: metabolights + n2t: metabolights + wikidata: P3890 + miriam: + deprecated: false + description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. + homepage: https://www.ebi.ac.uk/metabolights/ + id: '00000380' + name: MetaboLights + namespaceEmbeddedInLui: false + pattern: ^MTBLS\d+$ + prefix: metabolights + providers: + - code: omicsdi + description: MataboLights through OmicsDI + homepage: https://www.omicsdi.org/ + name: MataboLights through OmicsDI + uri_format: https://www.omicsdi.org/dataset/metabolights_dataset/$1 + sampleId: MTBLS1 + uri_format: https://www.ebi.ac.uk/metabolights/$1 + n2t: + description: MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. + example: MTBLS1 + homepage: https://www.ebi.ac.uk/metabolights/ + name: MetaboLights at EBI + namespaceEmbeddedInLui: false + pattern: ^MTBLS\d+$ + prefix: metabolights + uri_format: https://www.ebi.ac.uk/metabolights/$1 + name: MetaboLights Compound + wikidata: + database: Q24174701 + database.homepage: http://www.ebi.ac.uk/metabolights + database.label: MetaboLights + name: MetaboLights Compound ID + pattern: MTBLC\d+ + prefix: P3890 + uri_format: http://www.ebi.ac.uk/metabolights/$1 +metacyc.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: METACYC.COMPOUND + uri_format: http://identifiers.org/metacyc.compound/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: MetaCyc + uri_format: http://translator.ncats.nih.gov/MetaCyc_$1 + fairsharing: + abbreviation: MetaCyc + description: MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways, and are curated from the primary scientific literature. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. + id: '1680' + name: MetaCyc + prefix: FAIRsharing.yytevr + subjects: + - Life Science + - Metabolomics + - Systems Biology + go: + homepage: http://metacyc.org/ + name: Metabolic Encyclopedia of metabolic and other pathways + prefix: MetaCyc + synonyms: + - METACYC + uri_format: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=$1 + mappings: + biocontext: METACYC.COMPOUND + biolink: MetaCyc + fairsharing: FAIRsharing.yytevr + go: MetaCyc + miriam: metacyc.compound + n2t: metacyc.compound + miriam: + deprecated: false + description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. + homepage: https://metacyc.org + id: '00000609' + name: MetaCyc Compound + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9+_.%-:]+$ + prefix: metacyc.compound + sampleId: CPD-10330 + uri_format: https://metacyc.org/compound?orgid=META&id=$1 + n2t: + description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. + example: CPD-10330 + homepage: https://metacyc.org + name: MetaCyc Metabolic Pathway Database + namespaceEmbeddedInLui: false + pattern: ^CPD-\d{5}$ + prefix: metacyc.compound + uri_format: https://metacyc.org/compound?orgid=META&id=$1 + synonyms: + - MetaCyc +metacyc.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: METACYC.REACTION + uri_format: http://identifiers.org/metacyc.reaction/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: metacyc.reaction + uri_format: https://identifiers.org/metacyc.reaction:$1 + mappings: + biocontext: METACYC.REACTION + biolink: metacyc.reaction + miriam: metacyc.reaction + n2t: metacyc.reaction + miriam: + deprecated: false + description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. + homepage: https://metacyc.org + id: '00000610' + name: MetaCyc Reaction + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9+_.%-:]+$ + prefix: metacyc.reaction + sampleId: RXN-14904 + uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1 + n2t: + description: MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. + example: RXN-14904 + homepage: https://metacyc.org + name: MetaCyc Metabolic Pathway Database - Reaction + namespaceEmbeddedInLui: false + pattern: ^RXN-\d{5}$ + prefix: metacyc.reaction + uri_format: https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1 +metanetx.chemical: + biocontext: + is_identifiers: true + is_obo: false + prefix: METANETX.CHEMICAL + uri_format: http://identifiers.org/metanetx.chemical/$1 + mappings: + biocontext: METANETX.CHEMICAL + miriam: metanetx.chemical + n2t: metanetx.chemical + miriam: + deprecated: false + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. + homepage: https://www.metanetx.org/ + id: '00000567' + name: MetaNetX chemical + namespaceEmbeddedInLui: false + pattern: ^(MNXM\d+|BIOMASS|WATER)$ + prefix: metanetx.chemical + sampleId: MNXM1723 + uri_format: https://www.metanetx.org/chem_info/$1 + n2t: + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. + example: MNXM1723 + homepage: http://www.metanetx.org/ + name: MetaNetX chemical at SIB Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^(MNXM\d+|BIOMASS)$ + prefix: metanetx.chemical + uri_format: https://www.metanetx.org/chem_info/$1 +metanetx.compartment: + biocontext: + is_identifiers: true + is_obo: false + prefix: METANETX.COMPARTMENT + uri_format: http://identifiers.org/metanetx.compartment/$1 + mappings: + biocontext: METANETX.COMPARTMENT + miriam: metanetx.compartment + n2t: metanetx.compartment + miriam: + deprecated: false + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. + homepage: https://www.metanetx.org/ + id: '00000569' + name: MetaNetX compartment + namespaceEmbeddedInLui: false + pattern: ^(MNX[CD]\d+|BOUNDARY|IN|OUT)$ + prefix: metanetx.compartment + sampleId: MNXC15 + uri_format: https://www.metanetx.org/comp_info/$1 + n2t: + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. + example: MNXC15 + homepage: http://www.metanetx.org/ + name: MetaNetX compartment at SIB Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^(MNX[CD]\d+|BOUNDARY)$ + prefix: metanetx.compartment + uri_format: http://www.metanetx.org/comp_info/$1 +metanetx.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: METANETX.REACTION + uri_format: http://identifiers.org/metanetx.reaction/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: METANETX.REACTION + uri_format: https://www.metanetx.org/equa_info/$1 + mappings: + biocontext: METANETX.REACTION + biolink: METANETX.REACTION + miriam: metanetx.reaction + n2t: metanetx.reaction + miriam: + deprecated: false + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. + homepage: https://www.metanetx.org/ + id: '00000568' + name: MetaNetX reaction + namespaceEmbeddedInLui: false + pattern: ^(MNXR\d+|EMPTY)$ + prefix: metanetx.reaction + sampleId: MNXR101574 + uri_format: https://www.metanetx.org/equa_info/$1 + n2t: + description: MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. + example: MNXR101574 + homepage: http://www.metanetx.org/ + name: MetaNetX reaction at SIB Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^MNXR\d+$ + prefix: metanetx.reaction + uri_format: http://www.metanetx.org/equa_info/$1 +metlin: + biocontext: + is_identifiers: true + is_obo: false + prefix: METLIN + uri_format: http://identifiers.org/metlin/$1 + mappings: + biocontext: METLIN + miriam: metlin + n2t: metlin + miriam: + deprecated: false + description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. + homepage: http://masspec.scripps.edu/ + id: '00000322' + name: METLIN + namespaceEmbeddedInLui: false + pattern: ^\d{4}$ + prefix: metlin + sampleId: '1455' + uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1 + n2t: + description: The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. + example: '1455' + homepage: http://masspec.scripps.edu/ + name: METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry, La Jolla + namespaceEmbeddedInLui: false + pattern: ^\d{4}$ + prefix: metlin + uri_format: http://metlin.scripps.edu/metabo_info.php?molid=$1 + name: Metabolite and Tandem Mass Spectrometry Database +mex: + biocontext: + is_identifiers: true + is_obo: false + prefix: MEX + uri_format: http://identifiers.org/mex/$1 + mappings: + biocontext: MEX + miriam: mex + n2t: mex + miriam: + deprecated: false + description: A public place to process, interpret and share GC/MS metabolomics datasets. + homepage: https://www.metabolome-express.org/ + id: '00000648' + name: Metabolome Express + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mex + providers: + - code: omicsdi + description: Metabolome Express through OmicsDI + homepage: https://www.omicsdi.org/ + name: Metabolome Express through OmicsDI + uri_format: https://www.omicsdi.org/dataset/metabolome_express/MEX$1 + sampleId: '36' + uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1 + n2t: + description: A public place to process, interpret and share GC/MS metabolomics datasets. + example: '36' + homepage: https://www.metabolome-express.org/ + name: Metabolome Express + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mex + uri_format: https://www.metabolome-express.org/datasetview.php?datasetid=$1 +mf: + biocontext: + is_identifiers: false + is_obo: true + prefix: MF + uri_format: http://purl.obolibrary.org/obo/MF_$1 + bioportal: + name: Mental Functioning Ontology + prefix: MF + example: '0000091' + fairsharing: + abbreviation: MF + description: The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies. + id: '244' + name: Mental Functioning Ontology + prefix: FAIRsharing.4gm9gt + subjects: + - Cognitive Neuroscience + - Biomedical Science + mappings: + biocontext: MF + bioportal: MF + fairsharing: FAIRsharing.4gm9gt + obofoundry: mf + ols: mf + ontobee: MF + obofoundry: + contact: janna.hastings@gmail.com + contact.github: jannahastings + contact.label: Janna Hastings + contact.orcid: 0000-0002-3469-4923 + deprecated: false + description: The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. + download.owl: http://purl.obolibrary.org/obo/mf.owl + homepage: https://github.com/jannahastings/mental-functioning-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Mental Functioning Ontology + preferredPrefix: MF + prefix: mf + repository: https://github.com/jannahastings/mental-functioning-ontology + ols: + download: http://purl.obolibrary.org/obo/mf.owl + name: Mental Functioning Ontology + prefix: mf + version: 2021-11-17 + version.iri: http://purl.obolibrary.org/obo/MF/2021-11-17/MF.owl + ontobee: + library: Library + name: Mental Functioning Ontology + prefix: MF + pattern: ^\d{7}$ +mfmo: + biocontext: + is_identifiers: false + is_obo: true + prefix: MFMO + uri_format: http://purl.obolibrary.org/obo/MFMO_$1 + bioportal: + name: Mammalian Feeding Muscle Ontology + prefix: MFMO + example: '0000208' + fairsharing: + abbreviation: MFMO + description: An antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. + id: '719' + name: Mammalian Feeding Muscle Ontology + prefix: FAIRsharing.669cnk + subjects: [] + mappings: + biocontext: MFMO + bioportal: MFMO + fairsharing: FAIRsharing.669cnk + obofoundry: mfmo + ols: mfmo + ontobee: MFMO + obofoundry: + contact: druzinsk@uic.edu + contact.github: RDruzinsky + contact.label: Robert Druzinsky + contact.orcid: 0000-0002-1572-1316 + depends_on: + - uberon + deprecated: false + description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. + download.owl: http://purl.obolibrary.org/obo/mfmo.owl + homepage: https://github.com/rdruzinsky/feedontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Mammalian Feeding Muscle Ontology + preferredPrefix: MFMO + prefix: mfmo + repository: https://github.com/RDruzinsky/feedontology + ols: + description: The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. + download: http://purl.obolibrary.org/obo/mfmo.owl + homepage: https://github.com/rdruzinsky/feedontology + name: Mammalian Feeding Muscle Ontology + prefix: mfmo + version: 2013-11-16 + version.iri: http://purl.obolibrary.org/obo/mfmo/2013-11-16/mfmo.owl + ontobee: + library: Library + name: Mammalian Feeding Muscle Ontology + prefix: MFMO + pattern: ^\d{7}$ +mfo: + biocontext: + is_identifiers: false + is_obo: true + prefix: MFO + uri_format: http://purl.obolibrary.org/obo/MFO_$1 + bioportal: + name: Medaka Fish Anatomy and Development Ontology + prefix: MFO + mappings: + biocontext: MFO + bioportal: MFO + obofoundry: mfo + prefixcommons: mfo + obofoundry: + contact: Thorsten.Henrich@embl-heidelberg.de + contact.label: Thorsten Henrich + deprecated: true + description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. + download.owl: http://purl.obolibrary.org/obo/mfo.owl + name: Medaka fish anatomy and development + prefix: mfo + prefixcommons: + bioportal: '1027' + description: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. + example: MFO_0000001 + homepage: http://ani.embl.de:8080/mepd/ + keywords: + - obo + - anatomy + - development + - fish + name: Medaka fish anatomy and development + pattern: ^MFO_\d+$ + prefix: mfo +mfoem: + biocontext: + is_identifiers: false + is_obo: true + prefix: MFOEM + uri_format: http://purl.obolibrary.org/obo/MFOEM_$1 + bioportal: + name: Emotion Ontology + prefix: MFOEM + example: '000204' + fairsharing: + abbreviation: MFOEM + description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialisation of the broader Mental Functioning Ontology. + id: '234' + name: Emotion Ontology + prefix: FAIRsharing.dx30m8 + subjects: + - Biomedical Science + mappings: + biocontext: MFOEM + bioportal: MFOEM + fairsharing: FAIRsharing.dx30m8 + obofoundry: mfoem + ols: mfoem + ontobee: MFOEM + obofoundry: + contact: janna.hastings@gmail.com + contact.github: jannahastings + contact.label: Janna Hastings + contact.orcid: 0000-0002-3469-4923 + deprecated: false + description: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. + download.owl: http://purl.obolibrary.org/obo/mfoem.owl + homepage: https://github.com/jannahastings/emotion-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Emotion Ontology + preferredPrefix: MFOEM + prefix: mfoem + repository: https://github.com/jannahastings/emotion-ontology + ols: + download: http://purl.obolibrary.org/obo/mfoem.owl + name: Emotion Ontology + prefix: mfoem + version: 2021-11-17 + version.iri: http://purl.obolibrary.org/obo/MFOEM/2021-11-17/MFOEM.owl + ontobee: + library: Library + name: Emotion Ontology + prefix: MFOEM + pattern: ^\d{6}$ +mfomd: + biocontext: + is_identifiers: false + is_obo: true + prefix: MFOMD + uri_format: http://purl.obolibrary.org/obo/MFOMD_$1 + bioportal: + name: MFO Mental Disease Ontology + prefix: MFOMD + example: '0000046' + fairsharing: + abbreviation: MFOMD + description: An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable. + id: '776' + name: MFO Mental Disease Ontology + prefix: FAIRsharing.q053vb + subjects: [] + mappings: + biocontext: MFOMD + bioportal: MFOMD + fairsharing: FAIRsharing.q053vb + obofoundry: mfomd + ols: mfomd + ontobee: MFOMD + obofoundry: + contact: janna.hastings@gmail.com + contact.github: jannahastings + contact.label: Janna Hastings + contact.orcid: 0000-0002-3469-4923 + deprecated: false + description: An ontology to describe and classify mental diseases such as schizophrenia, annotated with DSM-IV and ICD codes where applicable + download.owl: http://purl.obolibrary.org/obo/mfomd.owl + homepage: https://github.com/jannahastings/mental-functioning-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Mental Disease Ontology + preferredPrefix: MFOMD + prefix: mfomd + repository: https://github.com/jannahastings/mental-functioning-ontology + ols: + description: The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). + download: http://purl.obolibrary.org/obo/mfomd.owl + homepage: https://github.com/jannahastings/mental-functioning-ontology + name: Mental Disease Ontology + prefix: mfomd + version: 2020-04-26 + version.iri: http://purl.obolibrary.org/obo/MFOMD/2020-04-26/MFOMD.owl + ontobee: + library: Library + name: Mental Disease Ontology + prefix: MFOMD + pattern: ^\d{7}$ +mge: + banana: mge + mappings: + miriam: mge + n2t: mge + miriam: + deprecated: false + description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. + homepage: http://aclame.ulb.ac.be/ + id: '00000063' + name: Aclame + namespaceEmbeddedInLui: true + pattern: ^mge:\d+$ + prefix: mge + sampleId: '2' + uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 + n2t: + description: ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. + example: '2' + homepage: http://aclame.ulb.ac.be/ + name: Aclame database of mobile genetic elements + namespaceEmbeddedInLui: true + pattern: ^mge:\d+$ + prefix: mge + uri_format: http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 + pattern: ^\d+$ +mgi: + banana: MGI + biocontext: + is_identifiers: false + is_obo: false + prefix: MGI + uri_format: http://www.informatics.jax.org/accession/MGI:$1 + cellosaurus: + category: Organism-specific databases + homepage: http://www.informatics.jax.org + name: Mouse Genome Database (MGD) from Mouse Genome Informatics + prefix: MGI + uri_format: http://www.informatics.jax.org/marker/$1 + example: '6017782' + fairsharing: + abbreviation: MGI + description: MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. + id: '1955' + name: Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource + prefix: FAIRsharing.fcwyhz + subjects: + - Life Science + - Ontology and Terminology + go: + homepage: http://www.informatics.jax.org/ + name: Mouse Genome Informatics + prefix: MGI + mappings: + biocontext: MGI + cellosaurus: MGI + fairsharing: FAIRsharing.fcwyhz + go: MGI + miriam: mgi + n2t: mgi + ncbi: MGI + prefixcommons: mgi + uniprot: MGI + wikidata: P671 + miriam: + deprecated: false + description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. + homepage: http://www.informatics.jax.org/ + id: '00000037' + name: Mouse Genome Database + namespaceEmbeddedInLui: true + pattern: ^MGI:\d+$ + prefix: mgi + providers: + - code: bioentitylink + description: MGD through BioEntity Link + homepage: https://bioentity.link/ + name: MGD through BioEntity Link + uri_format: https://bioentity.link/#/lexicon/public/MGI:$1 + - code: agr + description: MGI through the Alliance of Genome Resources + homepage: https://www.alliancegenome.org + name: MGI through the Alliance of Genome Resources + uri_format: https://www.alliancegenome.org/gene/MGI:$1 + sampleId: '2442292' + uri_format: http://www.informatics.jax.org/accession/MGI:$1 + n2t: + description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. + example: '2442292' + homepage: http://www.informatics.jax.org/ + name: Mouse Genome Informatics Database + namespaceEmbeddedInLui: true + pattern: ^MGI:\d+$ + prefix: mgi + uri_format: http://www.informatics.jax.org/accession/MGI:$1 + name: Mouse Genome Informatics + ncbi: + example: MGI:1894891 + homepage: http://www.informatics.jax.org/ + name: Mouse Genome Informatics + prefix: MGI + pattern: ^\d+$ + preferred_prefix: MGI + prefixcommons: + description: The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. + example: '95484' + homepage: http://www.informatics.jax.org/ + keywords: + - expression + - phenotype + - sequence + name: Mouse genome database (MGD) from Mouse Genome Informatics (MGI) + pattern: ^\d+$ + prefix: mgi + pubmed_ids: + - '15608240' + uri_format: http://www.informatics.jax.org/searches/accession_report.cgi?id=mgi:$1 + synonyms: + - MGD + - MGI + uniprot: + category: Organism-specific databases + comment: Replacement for MGD + identifier: '60' + link_is_explicit: 'true' + name: Mouse genome database (MGD) from Mouse Genome Informatics (MGI) + prefix: MGI + uri_format: http://www.informatics.jax.org/marker/$1 + wikidata: + database: Q1951035 + database.homepage: http://www.informatics.jax.org/ + database.label: Mouse Genome Informatics + homepage: http://www.informatics.jax.org/ + name: Mouse Genome Informatics ID + pattern: MGI:\d{1,7} + prefix: P671 + uri_format: http://www.informatics.jax.org/accession/$1 +mgnify.analysis: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Analyses of microbiome data within MGnify + example: MGYA00002270 + homepage: https://www.ebi.ac.uk/metagenomics/ + name: MGnify Analysis + pattern: ^MGYA\d+$ + uri_format: https://www.ebi.ac.uk/metagenomics/analyses/$1 +mgnify.proj: + mappings: + miriam: mgnify.proj + n2t: mgnify.proj + miriam: + deprecated: false + description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. + homepage: https://www.ebi.ac.uk/metagenomics + id: '00000535' + name: MGnify Project + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+$ + prefix: mgnify.proj + sampleId: ERP004492 + uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1 + n2t: + description: MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. + example: ERP004492 + homepage: https://www.ebi.ac.uk/metagenomics + name: MGnify Project + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+$ + prefix: mgnify.proj + uri_format: https://www.ebi.ac.uk/metagenomics/projects/$1 +mgnify.samp: + mappings: + miriam: mgnify.samp + n2t: mgnify.samp + miriam: + deprecated: false + description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. + homepage: https://www.ebi.ac.uk/metagenomics + id: '00000510' + name: MGnify Sample + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+$ + prefix: mgnify.samp + sampleId: SRS086444 + uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1 + n2t: + description: The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. + example: SRS086444 + homepage: https://www.ebi.ac.uk/metagenomics + name: MGnify Sample + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+[0-9]+$ + prefix: mgnify.samp + uri_format: https://www.ebi.ac.uk/metagenomics/samples/$1 +mi: + biocontext: + is_identifiers: false + is_obo: true + prefix: MI + uri_format: http://purl.obolibrary.org/obo/MI_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: MI + uri_format: http://purl.obolibrary.org/obo/MI_$1 + bioportal: + name: Molecular Interactions + prefix: MI + example: '0058' + go: + homepage: http://www.psidev.info/ + name: Proteomic Standard Initiative for Molecular Interaction + prefix: PSI-MI + synonyms: + - MI + mappings: + biocontext: MI + biolink: MI + bioportal: MI + go: PSI-MI + miriam: mi + n2t: psimi + obofoundry: mi + ols: mi + ontobee: MI + prefixcommons: psi.mi + miriam: + deprecated: false + description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. + homepage: https://www.ebi.ac.uk/ols/ontologies/mi + id: '00000109' + name: Molecular Interactions Ontology + namespaceEmbeddedInLui: true + pattern: ^MI:\d{4}$ + prefix: mi + sampleId: '0308' + uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1 + n2t: + description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. + example: '0308' + homepage: https://www.ebi.ac.uk/ols/ontologies/mi + name: Molecular Interactions Ontology through OLS + namespaceEmbeddedInLui: true + pattern: ^MI:\d{4}$ + prefix: psimi + uri_format: https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1 + obofoundry: + contact: pporras@ebi.ac.uk + contact.github: pporrasebi + contact.label: Pablo Porras Millán + contact.orcid: 0000-0002-8429-8793 + deprecated: false + description: A structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. + download.obo: http://purl.obolibrary.org/obo/mi.obo + download.owl: http://purl.obolibrary.org/obo/mi.owl + homepage: https://github.com/HUPO-PSI/psi-mi-CV + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Molecular Interactions Controlled Vocabulary + preferredPrefix: MI + prefix: mi + repository: https://github.com/HUPO-PSI/psi-mi-CV + ols: + download: https://raw.githubusercontent.com/HUPO-PSI/psi-mi-CV/master/psi-mi.obo + name: mi + prefix: mi + version.iri: http://purl.obolibrary.org/obo/mi/releases/2020-04-13/mi.owl + ontobee: + library: Library + name: Molecular Interactions Controlled Vocabulary + prefix: MI + pattern: ^\d{4}$ + prefixcommons: + bioportal: '1040' + description: The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. + example: MI:0308 + homepage: http://psidev.sf.net + keywords: + - obo + - interaction + - molecule + name: Proteomic Standard Initiative for Molecular Interaction + pattern: ^MI:\d{4}$ + prefix: psi.mi + pubmed_ids: + - '14755292' + synonyms: + - PSI-MI +miaa: + comment: same as MAT + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + name: Minimal Information About Anatomy ontology + references: + - https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf +miapa: + biocontext: + is_identifiers: false + is_obo: true + prefix: MIAPA + uri_format: http://purl.obolibrary.org/obo/MIAPA_$1 + bioportal: + name: MIAPA Ontology + prefix: MIAPA + example: '0000010' + fairsharing: + abbreviation: MIAPA + description: The MIAPA (minimum information about a phylogenetic analysis) checklist details the list of metadata necessary for researchers to evaluate or reuse a published phylogeny. + id: '94' + name: Minimal Information About a Phylogenetic Analysis + prefix: FAIRsharing.ca48xs + subjects: + - Phylogeny + - Phylogenetics + - Life Science + mappings: + biocontext: MIAPA + bioportal: MIAPA + fairsharing: FAIRsharing.ca48xs + obofoundry: miapa + ols: miapa + ontobee: MIAPA + name: Minimum Anformation About a Phylogenetic Analysis Ontology + obofoundry: + contact: hilmar.lapp@duke.edu + contact.github: hlapp + contact.label: Hilmar Lapp + contact.orcid: 0000-0001-9107-0714 + deprecated: false + description: An application ontology to formalize annotation of phylogenetic data. + download.owl: http://purl.obolibrary.org/obo/miapa.owl + homepage: http://www.evoio.org/wiki/MIAPA + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: MIAPA Ontology + preferredPrefix: MIAPA + prefix: miapa + repository: https://github.com/evoinfo/miapa + ols: + description: >- + The MIAPA ontology is intended to be an application ontology for the + purpose of semantic annotation of phylogenetic data according to the + requirements and recommendations of the Minimum Information for A + Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology + leverages (imports) primarily from the CDAO (Comparative Data Analysis + Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, + which includes the EDAM ontologies) ontologies. It adds some assertions of + its own, as well as some classes and individuals that may eventually get + pushed down into one of the respective source ontologies. + + + This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA. + download: http://purl.obolibrary.org/obo/miapa.owl + homepage: http://www.evoio.org/wiki/MIAPA + name: Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology + prefix: miapa + version: 2017-05-09 + version.iri: http://purl.obolibrary.org/obo/miapa/2013-02-01/miapa.owl + ontobee: + library: Library + name: MIAPA Ontology + prefix: MIAPA + pattern: ^\d{7}$ +micro: + biocontext: + is_identifiers: false + is_obo: true + prefix: MICRO + uri_format: http://purl.obolibrary.org/obo/MICRO_$1 + example: '0002999' + fairsharing: + abbreviation: MicrO + description: MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource. + id: '1150' + name: Ontology of Prokaryotic Phenotypic and Metabolic Characters + prefix: FAIRsharing.brhpb0 + subjects: + - Bioinformatics + - Microbiology + mappings: + biocontext: MICRO + fairsharing: FAIRsharing.brhpb0 + obofoundry: micro + ols: micro + ontobee: MicrO + obofoundry: + appears_in: + - mco + contact: carrine.blank@umontana.edu + contact.github: carrineblank + contact.label: Carrine Blank + contact.orcid: 0000-0002-2100-6351 + deprecated: false + description: An ontology of prokaryotic phenotypic and metabolic characters + download.owl: http://purl.obolibrary.org/obo/micro.owl + homepage: https://github.com/carrineblank/MicrO + license: CC BY 2.0 + license.url: https://creativecommons.org/licenses/by/2.0/ + name: Ontology of Prokaryotic Phenotypic and Metabolic Characters + preferredPrefix: MICRO + prefix: micro + repository: https://github.com/carrineblank/MicrO + ols: + description: An ontology of prokaryotic phenotypic and metabolic characters + download: http://purl.obolibrary.org/obo/micro.owl + homepage: https://github.com/carrineblank/MicrO + name: Ontology of Prokaryotic Phenotypic and Metabolic Characters + prefix: micro + version: 1.5.1 + ontobee: + library: Library + name: Ontology of Prokaryotic Phenotypic and Metabolic Characters + prefix: MicrO + pattern: ^\d{7}$ +microscope: + biocontext: + is_identifiers: true + is_obo: false + prefix: MICROSCOPE + uri_format: http://identifiers.org/microscope/$1 + fairsharing: + abbreviation: MicroScope + description: MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and metabolic analysis specific to each genome. + id: '2390' + name: Microbial Genome Annotation & Analysis Platform + prefix: FAIRsharing.3t5qc3 + subjects: + - Life Science + - Comparative Genomics + mappings: + biocontext: MICROSCOPE + fairsharing: FAIRsharing.3t5qc3 + miriam: microscope + n2t: microscope + miriam: + deprecated: false + description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. + homepage: http://www.genoscope.cns.fr/agc/microscope + id: '00000631' + name: MicroScope + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: microscope + sampleId: '5601141' + uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 + n2t: + description: MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. + example: '5601141' + homepage: http://www.genoscope.cns.fr/agc/microscope + name: MicroScope + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: microscope + uri_format: http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 +microsporidia: + biocontext: + is_identifiers: true + is_obo: false + prefix: MICROSPORIDIA + uri_format: http://identifiers.org/microsporidia/$1 + mappings: + biocontext: MICROSPORIDIA + miriam: microsporidia + n2t: microsporidia + prefixcommons: microsporidia + miriam: + deprecated: false + description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: http://microsporidiadb.org/micro/ + id: '00000152' + name: MicrosporidiaDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: microsporidia + sampleId: ECU03_0820i + uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + n2t: + description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: ECU03_0820i + homepage: http://microsporidiadb.org/micro/ + name: MicrosporidiaDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: microsporidia + uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + prefixcommons: + description: MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: ECU03_0820i + homepage: http://microsporidiadb.org/micro/ + keywords: + - eukaryotic + - genome + name: MicrosporidiaDB + pattern: ^\w+$ + prefix: microsporidia + pubmed_ids: + - '19914931' + uri_format: http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +millipore: + cellosaurus: + category: Cell line collections + homepage: https://www.merckmillipore.com/ + name: Merck Millipore (EMD Millipore) + prefix: Millipore + uri_format: https://www.merckmillipore.com/catalogue/item/$1 + example: SCC111 + mappings: + cellosaurus: Millipore +mimodb: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIMODB + uri_format: http://identifiers.org/mimodb/$1 + fairsharing: + abbreviation: MimoDB + description: Mimotope database, active site-mimicking peptides selected from phage-display libraries. It is a database which stores information on peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues, organs, and even entire organisms through phage display technology. Besides the peptide sequences, other information such as the corresponding target, template, library, and structures are also stored. All entries are manually extracted from published peer review articles and other public data sources such as Uniprot, GenBank and PDBSum. + id: '1606' + name: Mimotope Database + prefix: FAIRsharing.bv0zjz + subjects: + - Life Science + mappings: + biocontext: MIMODB + fairsharing: FAIRsharing.bv0zjz + miriam: mimodb + n2t: mimodb + prefixcommons: mimodb + miriam: + deprecated: false + description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. + homepage: http://immunet.cn/bdb/ + id: '00000251' + name: MimoDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mimodb + sampleId: '1' + uri_format: http://immunet.cn/bdb/index.php/mimoset/$1 + n2t: + description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. + example: '1' + homepage: http://immunet.cn/bdb/ + name: BDB at University of Electronic Science and Technology of China + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mimodb + uri_format: http://immunet.cn/bdb/index.php/mimoset/$1 + prefixcommons: + description: MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. + example: '1' + homepage: http://immunet.cn/mimodb/ + keywords: + - interaction + - protein + name: MimoDB + pattern: ^\d+$ + prefix: mimodb + pubmed_ids: + - '22053087' + uri_format: http://immunet.cn/mimodb/browse.php?table=mimoset&ID=$1 +minid: + biocontext: + is_identifiers: true + is_obo: false + prefix: MINID + uri_format: http://identifiers.org/minid/$1 + mappings: + biocontext: MINID + miriam: minid + n2t: minid + miriam: + deprecated: false + description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. + homepage: https://fair-research.org + id: '00000645' + name: Minimal Viable Identifier + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: minid + sampleId: b97957 + uri_format: https://hdl.handle.net/hdl:20.500.12582/$1 + n2t: + description: Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. + example: b97957 + homepage: http://minid.bd2k.org + name: Minimal Identifiers for Transient Data + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: minid + uri_format: http://n2t.net/ark:/57799/$1 +minid.test: + mappings: + miriam: minid.test + miriam: + deprecated: false + description: 'Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ' + homepage: https://fair-research.org + id: '00000707' + name: MINID Test + namespaceEmbeddedInLui: false + pattern: '[A-Za-z0-9]+$' + prefix: minid.test + sampleId: 3SBPLMKKVEVR + uri_format: https://hdl.handle.net/hdl:20.500.12633/$1 +mint: + biocontext: + is_identifiers: true + is_obo: false + prefix: MINT + uri_format: http://identifiers.org/mint/$1 + fairsharing: + abbreviation: MINT + description: MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT is an ELIXIR Core Resource. + id: '1609' + name: Molecular INTeraction Database + prefix: FAIRsharing.2bdvmk + subjects: + - Proteomics + - Life Science + mappings: + biocontext: MINT + fairsharing: FAIRsharing.2bdvmk + miriam: mint + n2t: mint + prefixcommons: mint + uniprot: MINT + miriam: + deprecated: false + description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. + homepage: http://mint.bio.uniroma2.it/mint/ + id: '00000042' + name: MINT + namespaceEmbeddedInLui: false + pattern: ^MINT\-\d{1,7}$ + prefix: mint + providers: + - code: ebi + description: MINT subset through IntAct + homepage: https://www.ebi.ac.uk/intact/ + name: MINT subset through IntAct + uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1 + sampleId: MINT-10000 + uri_format: http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$1 + n2t: + description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. + example: MINT-7905142 + homepage: https://www.ebi.ac.uk/intact/ + name: MINT subset through IntAct + namespaceEmbeddedInLui: false + pattern: ^MINT\-\d{1,7}$ + prefix: mint + uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:$1 + name: Molecular Interaction Database + prefixcommons: + description: The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. + example: MINT-10000 + homepage: http://mint.bio.uniroma2.it/mint/ + keywords: + - protein + - interaction + name: Molecular INTeraction Database + pattern: ^MINT\-\d{1,5}$ + prefix: mint + pubmed_ids: + - '17135203' + uri_format: http://mint.bio.uniroma2.it/mint/search/interactor.do?queryType=protein&interactorAc=$1 + uniprot: + category: Protein-protein interaction databases + identifier: '158' + link_is_explicit: 'true' + name: Molecular INTeraction database + prefix: MINT + uri_format: https://mint.bio.uniroma2.it/cgi-bin/protein.py?id=$1 +mipmod: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIPMOD + uri_format: http://identifiers.org/mipmod/$1 + mappings: + biocontext: MIPMOD + miriam: mipmod + n2t: mipmod + prefixcommons: mipmod + miriam: + deprecated: false + description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. + homepage: http://bioinfo.iitk.ac.in/MIPModDB + id: '00000256' + name: MIPModDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: mipmod + sampleId: HOSAPI0399 + uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 + n2t: + description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. + example: HOSAPI0399 + homepage: http://bioinfo.iitk.ac.in/MIPModDB + name: MIPModDB at Indian Institute of Technology Kanpur + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: mipmod + uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 + prefixcommons: + description: MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. + example: HOSAPI0399 + homepage: http://bioinfo.iitk.ac.in/MIPModDB + keywords: + - protein + - structure + name: MIPModDB + pattern: ^\w+$ + prefix: mipmod + pubmed_ids: + - '22080560' + uri_format: http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1 +mir: + banana: MIR + biocontext: + is_identifiers: true + is_obo: false + prefix: MIR + uri_format: http://identifiers.org/mir/$1 + mappings: + biocontext: MIR + miriam: mir + n2t: mir + miriam: + deprecated: false + description: The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources. + homepage: https://registry.identifiers.org/registry + id: '00000599' + name: Identifiers.org Registry + namespaceEmbeddedInLui: true + pattern: ^MIR:\d{8}$ + prefix: mir + sampleId: '00100037' + uri_format: https://registry.identifiers.org/registry?query="MIR:$1" + n2t: + description: The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources. + example: '00100037' + homepage: https://identifiers.org/registry + name: Identifiers.org Registry through EBI + namespaceEmbeddedInLui: true + pattern: ^MIR:\d{8}$ + prefix: mir + uri_format: https://identifiers.org/registry?query="MIR:$1" + pattern: ^\d{8}$ +mirbase: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIRBASE + uri_format: http://identifiers.org/mirbase/$1 + biolink: + is_identifiers: true + is_obo: false + prefix: mirbase + uri_format: http://identifiers.org/mirbase$1 + example: MI0026471 + fairsharing: + abbreviation: miRBase + description: The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. + id: '2100' + name: miRBase + prefix: FAIRsharing.hmgte8 + subjects: + - Biology + homepage: http://www.mirbase.org/ + mappings: + biocontext: MIRBASE + biolink: mirbase + fairsharing: FAIRsharing.hmgte8 + miriam: mirbase + n2t: mirbase + ncbi: miRBase + prefixcommons: mirbase + wikidata: P2870 + miriam: + deprecated: false + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). + homepage: http://www.mirbase.org/ + id: '00000078' + name: miRBase Sequence + namespaceEmbeddedInLui: false + pattern: MI\d{7} + prefix: mirbase + sampleId: MI0000001 + uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 + n2t: + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). + example: MI0000001 + homepage: http://www.mirbase.org/ + name: miRBase Sequence Database + namespaceEmbeddedInLui: false + pattern: MI\d{7} + prefix: mirbase + uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 + name: miRBase pre-miRNA + ncbi: + example: MI0000681 + homepage: http://www.mirbase.org/ + name: miRNA Database + prefix: miRBase + prefixcommons: + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results. The miRBase Targets database is a new resource of predicted miRNA targets in animals + example: MI0000001 + homepage: http://www.mirbase.org/ + keywords: + - RNA + - gene + name: miRBase Sequence Database + pattern: ^MI\d{7}$ + prefix: mirbase + pubmed_ids: + - '14681370' + uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 + uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 + wikidata: + database: Q6826947 + database.homepage: http://www.mirbase.org/ + database.label: miRBase + homepage: http://www.mirbase.org/ + name: miRBase pre-miRNA ID + pattern: MI\d{7} + prefix: P2870 + uri_format: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1 +mirbase.family: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. + example: MIPF0000002 + homepage: http://www.mirbase.org/ + name: miRBase Families + synonyms: + - MIRBASE_FAMILY + uri_format: http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1 + wikidata: + database: Q6826947 +mirbase.mature: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIRBASE.MATURE + uri_format: http://identifiers.org/mirbase.mature/$1 + example: MIMAT0046872 + homepage: http://www.mirbase.org/ + mappings: + biocontext: MIRBASE.MATURE + miriam: mirbase.mature + n2t: mirbase.mature + prefixcommons: mirbase.mature + wikidata: P2871 + miriam: + deprecated: false + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. + homepage: http://www.mirbase.org/ + id: '00000235' + name: miRBase mature sequence + namespaceEmbeddedInLui: false + pattern: MIMAT\d{7} + prefix: mirbase.mature + sampleId: MIMAT0000001 + uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1 + n2t: + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. + example: MIMAT0000001 + homepage: http://www.mirbase.org/ + name: miRBase + namespaceEmbeddedInLui: false + pattern: MIMAT\d{7} + prefix: mirbase.mature + uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1 + name: miRBase mature miRNA + prefixcommons: + description: The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. + example: MIMAT0000001 + keywords: + - nucleotide + - sequence + name: miRBase mature sequence + pattern: ^MIMAT\d{7}$ + prefix: mirbase.mature + uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1 + synonyms: + - MIRBASEM + uri_format: http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1 + wikidata: + database: Q6826947 + database.homepage: http://www.mirbase.org/ + database.label: miRBase + homepage: http://www.mirbase.org/ + name: miRBase mature miRNA ID + pattern: MIMAT\d{7} + prefix: P2871 + uri_format: http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$1 +mirex: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIREX + uri_format: http://identifiers.org/mirex/$1 + fairsharing: + abbreviation: mirEX + description: mirEX2 is a comprehensive platform for comparative analysis of primary microRNA expression data. RT–qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. + id: '1611' + name: mirEX + prefix: FAIRsharing.q3b39v + subjects: + - Life Science + mappings: + biocontext: MIREX + fairsharing: FAIRsharing.q3b39v + miriam: mirex + n2t: mirex + miriam: + deprecated: false + description: mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. + homepage: http://comgen.pl/mirex/?page=home + id: '00000329' + name: mirEX + namespaceEmbeddedInLui: false + pattern: ^\d+(\w+)?$ + prefix: mirex + sampleId: 165a + uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes + n2t: + description: mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. + example: 165a + homepage: http://comgen.pl/mirex/?page=home + name: mirEX at Adam Mickiewicz University + namespaceEmbeddedInLui: false + pattern: ^\d+(\w+)?$ + prefix: mirex + uri_format: http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes +miriam: + fairsharing: + abbreviation: MIRIAM + description: The Minimal Information Required In the Annotation of Models (MIRIAM), initiated by the BioModels.net effort, is a set of guidelines for the consistent annotation and curation of computational models in biology. It is suitable for use with any structured format for computational models. + id: '988' + name: Minimal Information Required In the Annotation of Models + prefix: FAIRsharing.ap169a + subjects: + - Biochemistry + - Life Science + - Biomedical Science + mappings: + fairsharing: FAIRsharing.ap169a + miriam: identifiers.namespace + miriam: + deprecated: false + description: Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. + homepage: https://www.ebi.ac.uk + id: '00000859' + name: Identifiers.org namespace + namespaceEmbeddedInLui: false + pattern: ^[a-z_\.]+$ + prefix: identifiers.namespace + sampleId: pubmed + uri_format: https://registry.identifiers.org/registry/$1 + synonyms: + - identifiers.namespace +miriam.collection: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIRIAM.COLLECTION + uri_format: http://identifiers.org/miriam.collection/$1 + mappings: + biocontext: MIRIAM.COLLECTION + miriam: miriam.collection + n2t: miriam.collection + miriam: + deprecated: true + description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. + id: '00000008' + name: MIRIAM Registry collection + namespaceEmbeddedInLui: false + pattern: ^MIR:000\d{5}$ + prefix: miriam.collection + sampleId: MIR:00000008 + n2t: + description: MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. + example: MIR:00000008 + homepage: https://www.ebi.ac.uk/miriam/ + name: MIRIAM Resources (data collection) + namespaceEmbeddedInLui: false + pattern: ^MIR:000\d{5}$ + prefix: miriam.collection + uri_format: https://www.ebi.ac.uk/miriam/main/$1 +miriam.resource: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIRIAM.RESOURCE + uri_format: http://identifiers.org/miriam.resource/$1 + comment: yo dawg i heard you like registries... + mappings: + biocontext: MIRIAM.RESOURCE + miriam: miriam.resource + n2t: miriam.resource + prefixcommons: miriam.resource + miriam: + deprecated: false + description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. + homepage: https://www.ebi.ac.uk/miriam/ + id: '00000188' + name: MIRIAM Registry resource + namespaceEmbeddedInLui: false + pattern: ^MIR:001\d{5}$ + prefix: miriam.resource + sampleId: MIR:00100005 + uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1 + n2t: + description: MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. + example: MIR:00100005 + homepage: https://www.ebi.ac.uk/miriam/ + name: MIRIAM Registry (resources) + namespaceEmbeddedInLui: false + pattern: ^MIR:001\d{5}$ + prefix: miriam.resource + uri_format: https://www.ebi.ac.uk/miriam/main/resources/$1 + prefixcommons: + description: MIRIAM Resources is an online resource created to catalogue the data-types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding physical URLs, whether these are controlled vocabularies or databases. + example: MIR:00100245 + homepage: http://www.ebi.ac.uk/miriam/ + keywords: + - registry + name: MIRIAM Resources + pattern: ^MIR:001\d{5}$ + prefix: miriam.resource + pubmed_ids: + - '18078503' + uri_format: http://www.ebi.ac.uk/miriam/main/resources/$1 +mirnao: + biocontext: + is_identifiers: false + is_obo: true + prefix: MIRNAO + uri_format: http://purl.obolibrary.org/obo/MIRNAO_$1 + bioportal: + name: MicroRNA Ontology + prefix: MIRNAO + mappings: + biocontext: MIRNAO + bioportal: MIRNAO + obofoundry: mirnao + ontobee: miRNAO + obofoundry: + contact: topalis@imbb.forth.gr + contact.label: Pantelis Topalis + deprecated: true + description: An application ontology for use with miRNA databases. + download.owl: http://purl.obolibrary.org/obo/mirnao.owl + homepage: http://code.google.com/p/mirna-ontology/ + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: microRNA Ontology + prefix: mirnao + ontobee: + library: Library + name: microRNA Ontology + prefix: miRNAO +mirnest: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIRNEST + uri_format: http://identifiers.org/mirnest/$1 + fairsharing: + abbreviation: miRNEST + description: miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mirtrons, miRNA gene structures) as well as from other databases and publications. + id: '1667' + name: miRNEST + prefix: FAIRsharing.5pfx4r + subjects: + - Genomics + - Life Science + mappings: + biocontext: MIRNEST + fairsharing: FAIRsharing.5pfx4r + miriam: mirnest + n2t: mirnest + prefixcommons: mirnest + miriam: + deprecated: false + description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. + homepage: http://rhesus.amu.edu.pl/mirnest/copy/ + id: '00000246' + name: miRNEST + namespaceEmbeddedInLui: false + pattern: ^MNEST\d+$ + prefix: mirnest + sampleId: MNEST029358 + uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 + n2t: + description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. + example: MNEST029358 + homepage: http://rhesus.amu.edu.pl/mirnest/copy/ + name: miRNEST at Adam Mickiewicz University + namespaceEmbeddedInLui: false + pattern: ^MNEST\d+$ + prefix: mirnest + uri_format: http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 + prefixcommons: + description: miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. + example: MNEST029358 + homepage: http://lemur.amu.edu.pl/share/php/mirnest/ + keywords: + - expression + - prediction + name: miRNEST + pattern: ^MNEST\d+$ + prefix: mirnest + pubmed_ids: + - '22135287' + uri_format: http://lemur.amu.edu.pl/share/php/mirnest/search.php?search_term=$1 +miro: + biocontext: + is_identifiers: false + is_obo: true + prefix: MIRO + uri_format: http://purl.obolibrary.org/obo/MIRO_$1 + bioportal: + name: Mosquito Insecticide Resistance + prefix: MIRO + download_obo: http://purl.obolibrary.org/obo/miro.obo + example: '40000617' + fairsharing: + abbreviation: MIRO + description: Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more efficiently when assisted by IT (Information Technology) tools, ranging from modern integrated databases to GIS (Geographic Information System). MIRO is an application ontology that can be used for the purpose of controlling mosquitoes and, thus, the diseases that they transmit. + id: '720' + name: Mosquito Insecticide Resistance Ontology + prefix: FAIRsharing.sjf113 + subjects: + - Life Science + mappings: + biocontext: MIRO + bioportal: MIRO + fairsharing: FAIRsharing.sjf113 + obofoundry: miro + ols: miro + ontobee: MIRO + obofoundry: + contact: louis@imbb.forth.gr + contact.label: Christos (Kitsos) Louis + deprecated: true + description: Application ontology for entities related to insecticide resistance in mosquitos + download.obo: http://purl.obolibrary.org/obo/miro.obo + download.owl: http://purl.obolibrary.org/obo/miro.owl + homepage: https://github.com/VEuPathDB-ontology/MIRO + name: Mosquito insecticide resistance + prefix: miro + repository: https://github.com/VEuPathDB-ontology/MIRO + ols: + description: Application ontology for entities related to insecticide resistance in mosquitos + download: http://purl.obolibrary.org/obo/miro.owl + name: Mosquito insecticide resistance + prefix: miro + version: 2014-05-14 + version.iri: http://purl.obolibrary.org/obo/miro/releases/2014-05-14/miro.owl + ontobee: + library: Library + name: Mosquito insecticide resistance + prefix: MIRO + pattern: ^\d{8}$ +mirtarbase: + biocontext: + is_identifiers: true + is_obo: false + prefix: MIRTARBASE + uri_format: http://identifiers.org/mirtarbase/$1 + fairsharing: + abbreviation: miRTarBase + description: As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases. + id: '2143' + name: miRTarBase + prefix: FAIRsharing.f0bxfg + subjects: + - Life Science + mappings: + biocontext: MIRTARBASE + fairsharing: FAIRsharing.f0bxfg + miriam: mirtarbase + n2t: mirtarbase + miriam: + deprecated: false + description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. + homepage: http://mirtarbase.mbc.nctu.edu.tw/ + id: '00000562' + name: miRTarBase + namespaceEmbeddedInLui: false + pattern: ^MIRT\d{6}$ + prefix: mirtarbase + sampleId: MIRT000002 + uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1 + n2t: + description: miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. + example: MIRT000002 + homepage: http://mirtarbase.mbc.nctu.edu.tw/ + name: miRTarBase at National Chiao Tung University + namespaceEmbeddedInLui: false + pattern: ^MIRT\d{6}$ + prefix: mirtarbase + uri_format: http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1 +mirte: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs + example: miR-1 + homepage: http://www.russelllab.org/miRNAs/ + name: miRNA Target Prediction at EMBL +mlc: + mappings: + miriam: mlc + miriam: + deprecated: false + description: MLCommons Association artifacts, including benchmark results, datasets, and saved models. + homepage: https://mlcommons.org/en/ + id: '00000828' + name: MLCommons Association + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z\.\-\_]+$ + prefix: mlc + sampleId: 0.7-123 + uri_format: https://www.mlcommons.org/mlc-id/$1 +mmdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: MMDB + uri_format: http://identifiers.org/mmdb/$1 + mappings: + biocontext: MMDB + miriam: mmdb + n2t: mmdb + prefixcommons: mmdb + miriam: + deprecated: false + description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. + homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure + id: '00000121' + name: Molecular Modeling Database + namespaceEmbeddedInLui: false + pattern: ^\d{1,5}$ + prefix: mmdb + sampleId: '50885' + uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 + n2t: + description: The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. + example: '50885' + homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure + name: MMDB at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d{1,5}$ + prefix: mmdb + uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 + prefixcommons: + description: The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. + example: '50885' + homepage: http://www.ncbi.nlm.nih.gov/Structure/ + keywords: + - structure + - protein + - DNA + - small molecule + - interaction + name: Molecular Modeling Database + pattern: ^\d{1,5}$ + prefix: mmdb + pubmed_ids: + - '17135201' + uri_format: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 +mmmp.biomaps: + biocontext: + is_identifiers: true + is_obo: false + prefix: MMMP:BIOMAPS + uri_format: http://identifiers.org/mmmp:biomaps/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: mmmp.biomaps + uri_format: https://bioregistry.io/mmmp.biomaps:$1 + mappings: + biocontext: MMMP:BIOMAPS + biolink: mmmp.biomaps + miriam: mmmp:biomaps + n2t: biomaps + miriam: + deprecated: false + description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. + homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp + id: '00000075' + name: Melanoma Molecular Map Project Biomaps + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mmmp:biomaps + sampleId: '37' + uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 + n2t: + description: A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. + example: '37' + homepage: http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp + name: main webpage + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: biomaps + uri_format: http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 + synonyms: + - mmmp:biomaps +mmo: + biocontext: + is_identifiers: false + is_obo: true + prefix: MMO + uri_format: http://purl.obolibrary.org/obo/MMO_$1 + bioportal: + name: Measurement Method Ontology + prefix: MMO + example: '0000574' + fairsharing: + abbreviation: MMO + description: The Measurement Method Ontology is designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. + id: '1030' + name: Measurement Method Ontology + prefix: FAIRsharing.bgkyd7 + subjects: + - Life Science + - Biomedical Science + - Preclinical Studies + mappings: + biocontext: MMO + bioportal: MMO + fairsharing: FAIRsharing.bgkyd7 + obofoundry: mmo + ols: mmo + ontobee: MMO + obofoundry: + contact: jrsmith@mcw.edu + contact.github: jrsjrs + contact.label: Jennifer Smith + contact.orcid: 0000-0002-6443-9376 + deprecated: false + description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' + download.obo: http://purl.obolibrary.org/obo/mmo.obo + download.owl: http://purl.obolibrary.org/obo/mmo.owl + homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Measurement method ontology + preferredPrefix: MMO + prefix: mmo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 + title: Three ontologies to define phenotype measurement data. + - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 + title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' + repository: https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology + ols: + description: 'A representation of the variety of methods used to make clinical and phenotype measurements. ' + download: http://purl.obolibrary.org/obo/mmo.owl + homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 + name: Measurement method ontology + prefix: mmo + version: 2019-03-27 + version.iri: http://purl.obolibrary.org/obo/mmo/2.39/mmo.owl + ontobee: + library: Library + name: Measurement method ontology + prefix: MMO + pattern: ^\d{7}$ +mmp.cat: + biocontext: + is_identifiers: true + is_obo: false + prefix: MMP.CAT + uri_format: http://identifiers.org/mmp.cat/$1 + mappings: + biocontext: MMP.CAT + miriam: mmp.cat + n2t: mmp.cat + miriam: + deprecated: false + description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. + homepage: https://mmp.sfb.uit.no/databases/marcat/ + id: '00000615' + name: MarCat + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.cat + sampleId: MMP743597.11 + uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1 + n2t: + description: MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. + example: MMP743597.11 + homepage: https://mmp.sfb.uit.no/databases/marcat/ + name: MarCat through SfB + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.cat + uri_format: https://mmp.sfb.uit.no/databases/marcat/#/records/$1 +mmp.db: + biocontext: + is_identifiers: true + is_obo: false + prefix: MMP.DB + uri_format: http://identifiers.org/mmp.db/$1 + mappings: + biocontext: MMP.DB + miriam: mmp.db + n2t: mmp.db + miriam: + deprecated: false + description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness. + homepage: https://mmp.sfb.uit.no/databases/mardb/ + id: '00000614' + name: MarDB + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.db + sampleId: MMP02954345.1 + uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1 + n2t: + description: MarDB includes all sequenced marine microbial genomes regardless of level of completeness. + example: MMP02954345.1 + homepage: https://mmp.sfb.uit.no/databases/mardb/ + name: MarDB through SfB + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.db + uri_format: https://mmp.sfb.uit.no/databases/mardb/#/records/$1 +mmp.fun: + mappings: + miriam: mmp.fun + miriam: + deprecated: false + description: MarFun is manually curated database for marine fungi which is a part of the MAR databases. + homepage: https://mmp.sfb.uit.no/databases/marfun + id: '00000729' + name: MarFun + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.fun + sampleId: MMP3888430 + uri_format: https://mmp.sfb.uit.no/databases/marfun/#/records/$1 +mmp.ref: + biocontext: + is_identifiers: true + is_obo: false + prefix: MMP.REF + uri_format: http://identifiers.org/mmp.ref/$1 + mappings: + biocontext: MMP.REF + miriam: mmp.ref + n2t: mmp.ref + miriam: + deprecated: false + description: MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. + homepage: https://mmp.sfb.uit.no/databases/marref/ + id: '00000613' + name: MarRef + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.ref + sampleId: MMP3312982.2 + uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1 + n2t: + description: MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. + example: MMP3312982.2 + homepage: https://mmp.sfb.uit.no/databases/marref/ + name: MarRef through SfB + namespaceEmbeddedInLui: false + pattern: ^MMP\d+.\d+$ + prefix: mmp.ref + uri_format: https://mmp.sfb.uit.no/databases/marref/#/records/$1 +mmrrc: + biocontext: + is_identifiers: false + is_obo: false + prefix: MMRRC + uri_format: https://www.mmrrc.org/catalog/sds.php?mmrrc_id=$1 + cellosaurus: + category: Cell line collections + homepage: https://www.mmrrc.org/ + name: Mutant Mouse Resource & Research Centers + prefix: MMRRC + uri_format: https://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 + fairsharing: + abbreviation: MMRRC + description: The MMRRC distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community. The Catalog provides information on the strains available from the MMRRC. + id: '2068' + name: Mutant Mouse Resource and Research Centers + prefix: FAIRsharing.9dpd18 + subjects: + - Biology + homepage: https://www.mmrrc.org + mappings: + biocontext: MMRRC + cellosaurus: MMRRC + fairsharing: FAIRsharing.9dpd18 + miriam: mmrrc + n2t: mmrrc + miriam: + deprecated: false + description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. + homepage: http://www.mmrrc.org/ + id: '00000324' + name: MMRRC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mmrrc + sampleId: '70' + uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 + n2t: + description: The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. + example: '70' + homepage: http://www.mmrrc.org/ + name: MMRRC at University of North Carolina + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mmrrc + uri_format: http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 + name: Mutant Mouse Resource and Research Centers +mmsl: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included. + example: '3355' + homepage: https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html + name: Multum MediSource Lexicon + pattern: ^\d+$ + synonyms: + - MMSL_CODE +mmusdv: + biocontext: + is_identifiers: false + is_obo: true + prefix: MMUSDV + uri_format: http://purl.obolibrary.org/obo/MMUSDV_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: MmusDv + uri_format: http://purl.obolibrary.org/obo/MMUSDV_$1 + bioportal: + name: Mouse Developmental Stages + prefix: MMUSDV + example: '0000066' + fairsharing: + abbreviation: MMUSDV + description: Life cycle stages for Mus Musculus. MmusDv was developed by the Bgee group with assistance from the core Uberon developers and the Mouse anatomy ontology developers. Currently it includes both embryonic stages and adult stages. + id: '556' + name: Mouse Developmental Stages + prefix: FAIRsharing.zchb68 + subjects: [] + mappings: + biocontext: MMUSDV + biolink: MmusDv + bioportal: MMUSDV + fairsharing: FAIRsharing.zchb68 + obofoundry: mmusdv + ols: mmusdv + ontobee: MMUSDV + obofoundry: + contact: frederic.bastian@unil.ch + contact.github: fbastian + contact.label: Frédéric Bastian + contact.orcid: 0000-0002-9415-5104 + deprecated: false + description: Life cycle stages for Mus Musculus + download.obo: http://purl.obolibrary.org/obo/mmusdv.obo + download.owl: http://purl.obolibrary.org/obo/mmusdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Mouse Developmental Stages + preferredPrefix: MmusDv + prefix: mmusdv + repository: https://github.com/obophenotype/developmental-stage-ontologies + ols: + description: Life cycle stages for Mus Musculus + download: http://purl.obolibrary.org/obo/mmusdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv + name: Mouse Developmental Stages + prefix: mmusdv + version: 2020-03-10 + version.iri: http://purl.obolibrary.org/obo/mmusdv/releases/2020-03-10/mmusdv.owl + ontobee: + library: Library + name: Mouse Developmental Stages + prefix: MMUSDV + pattern: ^\d{7}$ + synonyms: + - MmusDv +mo: + biocontext: + is_identifiers: false + is_obo: true + prefix: MO + uri_format: http://purl.obolibrary.org/obo/MO_$1 + bioportal: + name: Microarray and Gene Expression Data Ontology + prefix: MO + mappings: + biocontext: MO + bioportal: MO + miriam: mo + n2t: mo + obofoundry: mo + miriam: + deprecated: false + description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. + homepage: http://bioportal.bioontology.org/ + id: '00000303' + name: MGED Ontology + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: mo + providers: + - code: ebi + description: MGED Ontology at SourceForge + homepage: https://mged.sourceforge.net/ontologies/MGEDontology.php + name: MGED Ontology at SourceForge + uri_format: https://mged.sourceforge.net/ontologies/MGEDontology.php#$1 + sampleId: ArrayGroup + uri_format: http://purl.bioontology.org/ontology/MO/$1 + n2t: + description: The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. + example: ArrayGroup + homepage: http://bioportal.bioontology.org/ + name: MGED Ontology at BioPortal + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: mo + uri_format: http://purl.bioontology.org/ontology/MO/$1 + obofoundry: + contact: stoeckrt@pcbi.upenn.edu + contact.label: Chris Stoeckert + contact.orcid: 0000-0002-5714-991X + deprecated: true + description: A standardized description of a microarray experiment in support of MAGE v.1. + download.owl: http://purl.obolibrary.org/obo/mo.owl + homepage: http://mged.sourceforge.net/ontologies/MGEDontology.php + name: Microarray experimental conditions + prefix: mo +mobidb: + biocontext: + is_identifiers: true + is_obo: false + prefix: MOBIDB + uri_format: http://identifiers.org/mobidb/$1 + fairsharing: + abbreviation: MobiDB + description: 'MobiDB is a database of intrinsically disordered regions (IDRs) and related features from various sources and prediction tools. Different levels of reliability and different features are reported as different and independent annotations. The database features three levels of annotation: manually curated, indirect and predicted. MobiDB annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined.' + id: '2176' + name: MobiDB + prefix: FAIRsharing.jwra3e + subjects: + - Biology + homepage: http://mobidb.bio.unipd.it + mappings: + biocontext: MOBIDB + fairsharing: FAIRsharing.jwra3e + miriam: mobidb + n2t: mobidb + uniprot: MobiDB + miriam: + deprecated: false + description: MobiDB is a database of protein disorder and mobility annotations. + homepage: https://mobidb.org/ + id: '00000637' + name: MobiDB + namespaceEmbeddedInLui: false + pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ + prefix: mobidb + sampleId: P10636 + uri_format: https://mobidb.org/$1 + n2t: + description: MobiDB is a database of protein disorder and mobility annotations. + example: P10636 + homepage: http://mobidb.bio.unipd.it + name: MobiDB + namespaceEmbeddedInLui: false + pattern: ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ + prefix: mobidb + uri_format: http://mobidb.bio.unipd.it/$1 + provides: uniprot + uniprot: + category: Family and domain databases + identifier: '183' + name: 'MobiDB: a database of protein disorder and mobility annotations' + prefix: MobiDB + uri_format: https://mobidb.bio.unipd.it/entries/$1 +mod: + biocontext: + is_identifiers: false + is_obo: true + prefix: MOD + uri_format: http://purl.obolibrary.org/obo/MOD_$1 + bioportal: + name: Protein Modification Ontology + prefix: PSIMOD + example: '01467' + fairsharing: + abbreviation: PSI-MOD + description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified. + id: '1163' + name: Protein MODification + prefix: FAIRsharing.2m4ms9 + subjects: + - Life Science + go: + homepage: http://www.psidev.info/groups/protein-modifications + name: Proteomics Standards Initiative protein modification ontology + prefix: PSI-MOD + synonyms: + - MOD + mappings: + biocontext: MOD + bioportal: PSIMOD + fairsharing: FAIRsharing.2m4ms9 + go: PSI-MOD + miriam: mod + n2t: mod + obofoundry: mod + ols: mod + ontobee: MOD + prefixcommons: psi.mod + miriam: + deprecated: false + description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. + homepage: https://www.ebi.ac.uk/ols/ontologies/mod + id: '00000056' + name: Protein Modification Ontology + namespaceEmbeddedInLui: true + pattern: ^MOD:\d{5} + prefix: mod + sampleId: '00001' + uri_format: https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1 + n2t: + description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. + example: '00001' + homepage: http://bioportal.bioontology.org/ontologies/PSIMOD + name: Protein modifications ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^MOD:\d{5} + prefix: mod + uri_format: http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=MOD:$1 + obofoundry: + contact: pierre-alain.binz@chuv.ch + contact.github: pabinz + contact.label: Pierre-Alain Binz + contact.orcid: 0000-0002-0045-7698 + deprecated: false + description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications + download.obo: http://purl.obolibrary.org/obo/mod.obo + download.owl: http://purl.obolibrary.org/obo/mod.owl + homepage: http://www.psidev.info/MOD + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Protein modification + preferredPrefix: MOD + prefix: mod + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/18688235 + title: The PSI-MOD community standard for representation of protein modification data + repository: https://github.com/HUPO-PSI/psi-mod-CV + ols: + description: PSI-MOD is an ontology consisting of terms that describe protein chemical modifications + download: http://purl.obolibrary.org/obo/mod.owl + homepage: http://www.psidev.info/MOD + name: Protein modification + prefix: mod + version.iri: http://purl.obolibrary.org/obo/mod/1.031.4/mod.owl + ontobee: + library: Library + name: Protein modification + prefix: MOD + pattern: ^\d{5}$ + prefixcommons: + bioportal: '1041' + description: The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. + example: MOD:00001 + homepage: http://psidev.sourceforge.net/mod/ + keywords: + - ontology + - protein + - molecule + - structure + name: Protein Modification ontology + pattern: ^MOD:\d{5}$ + prefix: psi.mod + synonyms: + - PSI-MOD +modeldb: + biocontext: + is_identifiers: true + is_obo: false + prefix: MODELDB + uri_format: http://identifiers.org/modeldb/$1 + fairsharing: + abbreviation: ModelDB + description: ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. A ModelDB entry contains a model's source code, concise description, and a citation of the article that published it. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. + id: '1641' + name: ModelDB + prefix: FAIRsharing.5rb3fk + subjects: + - Neurobiology + - Computational Biology + - Life Science + mappings: + biocontext: MODELDB + fairsharing: FAIRsharing.5rb3fk + miriam: modeldb + n2t: modeldb + prefixcommons: modeldb + miriam: + deprecated: false + description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. + homepage: http://senselab.med.yale.edu/ModelDB/ + id: '00000131' + name: ModelDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: modeldb + sampleId: '45539' + uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 + n2t: + description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. + example: '45539' + homepage: http://senselab.med.yale.edu/ModelDB/ + name: ModelDB at SenseLab + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: modeldb + uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 + prefixcommons: + description: ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. + example: '45539' + homepage: http://senselab.med.yale.edu/ModelDB/ + name: ModelDB + pattern: ^\d+$ + prefix: modeldb + pubmed_ids: + - '15055399' + uri_format: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 +molbase: + biocontext: + is_identifiers: true + is_obo: false + prefix: MOLBASE + uri_format: http://identifiers.org/molbase/$1 + mappings: + biocontext: MOLBASE + miriam: molbase + n2t: molbase + miriam: + deprecated: false + description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. + homepage: http://www.molbase.com/ + id: '00000458' + name: Molbase + namespaceEmbeddedInLui: false + pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ + prefix: molbase + sampleId: 128796-39-4 + uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1 + n2t: + description: Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. + example: 128796-39-4 + homepage: http://www.molbase.com/ + name: Molbase at Chinese Academy of Sciences + namespaceEmbeddedInLui: false + pattern: ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ + prefix: molbase + uri_format: http://www.molbase.com/en/index.php?app=search&search_keyword=$1 +molbase.sheffield: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + description: An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students. + example: '1868' + homepage: https://winter.group.shef.ac.uk/molbase/ + name: MolBase + pattern: ^\d+$ +molmedb: + fairsharing: + abbreviation: MolMeDB + description: MolMeDB is an open chemistry database concerning the interaction of molecules with membranes. + id: '2782' + name: 'MolMeDB: Molecules on Membranes Database' + prefix: FAIRsharing.CWzk3C + subjects: + - Molecular biology + - Cheminformatics + - Biochemistry + - Molecular Chemistry + - Chemistry + - Molecular Physical Chemistry + - Molecular Dynamics + - Computational Chemistry + mappings: + fairsharing: FAIRsharing.CWzk3C + miriam: molmedb + miriam: + deprecated: false + description: 'MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ' + homepage: http://www.upol.cz/en/ + id: '00000768' + name: MolMeDB + namespaceEmbeddedInLui: false + pattern: ^[m,M]{2}[0-9]{5}[0-9]*$ + prefix: molmedb + sampleId: MM00040 + uri_format: https://molmedb.upol.cz/mol/$1 +mondo: + biocontext: + is_identifiers: false + is_obo: true + prefix: MONDO + uri_format: http://purl.obolibrary.org/obo/MONDO_$1 + bioportal: + name: Mondo Disease Ontology + prefix: MONDO + download_obo: http://purl.obolibrary.org/obo/mondo.obo + example: '0000001' + fairsharing: + abbreviation: MONDO + description: MonDO (Monarch Disease Ontology) is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. + id: '667' + name: Monarch Disease Ontology + prefix: FAIRsharing.b2979t + subjects: [] + mappings: + biocontext: MONDO + bioportal: MONDO + fairsharing: FAIRsharing.b2979t + obofoundry: mondo + ols: mondo + ontobee: MONDO + name: Monarch Disease Ontology + obofoundry: + contact: nicole@tislab.org + contact.github: nicolevasilevsky + contact.label: Nicole Vasilevsky + contact.orcid: 0000-0001-5208-3432 + deprecated: false + description: A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. + download.json: http://purl.obolibrary.org/obo/mondo.json + download.obo: http://purl.obolibrary.org/obo/mondo.obo + download.owl: http://purl.obolibrary.org/obo/mondo.owl + homepage: https://monarch-initiative.github.io/mondo + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Mondo Disease Ontology + preferredPrefix: MONDO + prefix: mondo + publications: + - id: https://www.medrxiv.org/content/10.1101/2022.04.13.22273750 + title: 'Mondo: Unifying diseases for the world, by the world' + repository: https://github.com/monarch-initiative/mondo + ols: + description: A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. + download: http://purl.obolibrary.org/obo/mondo.owl + homepage: http://obofoundry.org/ontology/mondo.html + name: Mondo Disease Ontology + prefix: mondo + version: 2022-05-02 + version.iri: http://purl.obolibrary.org/obo/mondo/releases/2022-05-02/mondo.owl + ontobee: + library: Library + name: Mondo Disease Ontology + prefix: MONDO + pattern: ^\d{7}$ + twitter: MonarchInit + wikidata: + prefix: P5270 +mop: + biocontext: + is_identifiers: false + is_obo: true + prefix: MOP + uri_format: http://purl.obolibrary.org/obo/MOP_$1 + bioportal: + name: Molecular Process Ontology + prefix: MOP + download_obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo + example: '0000079' + fairsharing: + abbreviation: MOP + description: The Molecular Process Ontology (MOP) was created to work together with the Name Reaction Ontology (RXNO). MOP describes underlying molecular processes in organic reactions such as cyclization, methylation and demethylation. + id: '577' + name: Molecular Process Ontology + prefix: FAIRsharing.mct09a + subjects: + - Molecular Chemistry + mappings: + biocontext: MOP + bioportal: MOP + fairsharing: FAIRsharing.mct09a + obofoundry: mop + ols: mop + ontobee: MOP + name: Molecular Process Ontology + obofoundry: + contact: batchelorc@rsc.org + contact.github: batchelorc + contact.label: Colin Batchelor + contact.orcid: 0000-0001-5985-7429 + deprecated: false + description: Processes at the molecular level + download.owl: http://purl.obolibrary.org/obo/mop.owl + homepage: https://github.com/rsc-ontologies/rxno + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Molecular Process Ontology + preferredPrefix: MOP + prefix: mop + repository: https://github.com/rsc-ontologies/rxno + ols: + contact: chemistry-ontologies@googlegroups.com + description: MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. + download: http://purl.obolibrary.org/obo/mop.owl + homepage: https://github.com/rsc-ontologies/rxno + name: MOP + prefix: mop + version: 2022-02-01 + version.iri: http://purl.obolibrary.org/obo/mop/releases/2022-02-01/mop.owl + ontobee: + library: Library + name: Molecular Process Ontology + prefix: MOP + pattern: ^\d{7}$ +morpheus: + mappings: + miriam: morpheus + miriam: + deprecated: false + description: > + The Morpheus model repository is an open-access data resource to store, + search and retrieve unpublished and published computational models of + spatio-temporal and multicellular biological systems, encoded in the + MorpheusML language and readily executable with the Morpheus software. + homepage: https://morpheus.gitlab.io/ + id: '00000725' + name: Morpheus model repository + namespaceEmbeddedInLui: false + pattern: ^M[0-9]{4,}$ + prefix: morpheus + sampleId: M0001 + uri_format: https://morpheus.gitlab.io/models/$1 +mp: + biocontext: + is_identifiers: false + is_obo: true + prefix: MP + uri_format: http://purl.obolibrary.org/obo/MP_$1 + bioportal: + name: Mammalian Phenotype Ontology + prefix: MP + fairsharing: + abbreviation: MP + description: The observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan. + id: '75' + name: Mammalian Phenotype Ontology + prefix: FAIRsharing.kg1x4z + subjects: + - Developmental Biology + - Life Science + - Physiology + mappings: + biocontext: MP + bioportal: MP + fairsharing: FAIRsharing.kg1x4z + miriam: mp + n2t: mp + obofoundry: mp + ols: mp + ontobee: MP + prefixcommons: mp + miriam: + deprecated: false + description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. + homepage: http://www.informatics.jax.org/ + id: '00000580' + name: Mammalian Phenotype Ontology + namespaceEmbeddedInLui: true + pattern: ^MP:\d{7}$ + prefix: mp + sampleId: '0005452' + uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1 + n2t: + description: The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. + example: '0005452' + homepage: https://bioportal.bioontology.org/ontologies/MP + name: Mammalian Phenotype Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^MP:\d{7}$ + prefix: mp + uri_format: https://bioportal.bioontology.org/ontologies/MP/MP:$1 + obofoundry: + appears_in: + - chiro + - scdo + contact: drsbello@gmail.com + contact.github: sbello + contact.label: Sue Bello + contact.orcid: 0000-0003-4606-0597 + deprecated: false + description: Standard terms for annotating mammalian phenotypic data. + download.json: http://purl.obolibrary.org/obo/mp.json + download.obo: http://purl.obolibrary.org/obo/mp.obo + download.owl: http://purl.obolibrary.org/obo/mp.owl + homepage: http://www.informatics.jax.org/searches/MP_form.shtml + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Mammalian Phenotype Ontology + preferredPrefix: MP + prefix: mp + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22961259 + title: The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data + repository: https://github.com/mgijax/mammalian-phenotype-ontology + ols: + description: The Mammalian Phenotype Ontology is being developed by Cynthia L. Smith, Susan M. Bello, Anna, Anagnostopoulos, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Questions, comments and suggestions are welcome, and should be directed to pheno@jax.org, Susan.Bello@jax.org or to GitHub tracker (https://github.com/mgijax/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330. + download: http://purl.obolibrary.org/obo/mp.owl + homepage: http://www.informatics.jax.org/searches/MP_form.shtml + name: The Mammalian Phenotype Ontology + prefix: mp + version.iri: http://purl.obolibrary.org/obo/mp/releases/2022-04-21 + ontobee: + library: Library + name: Mammalian Phenotype Ontology + prefix: MP + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1025' + description: The Mammalian Phenotype Ontology is under development as a community effort to provide standard terms for annotating mammalian phenotypic data. + example: MP:0000001 + homepage: http://www.informatics.jax.org/searches/MP_form.shtml + keywords: + - obo + - phenotype + - mammalian + name: Mammalian phenotype + pattern: ^MP:\d+$ + prefix: mp + uri_format: http://www.informatics.jax.org/searches/Phat.cgi?id=$1 +mpath: + biocontext: + is_identifiers: false + is_obo: true + prefix: MPATH + uri_format: http://purl.obolibrary.org/obo/MPATH_$1 + bioportal: + name: Mouse Pathology Ontology + prefix: MPATH + download_obo: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo + example: '728' + fairsharing: + abbreviation: MPATH + description: Mouse PATHology (MPATH) ontology is a structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes. This resource was developed by the Pathology Consortium of Pathbase (www.pathbase.net). + id: '56' + name: Mouse PATHology + prefix: FAIRsharing.3wbgm0 + subjects: + - Anatomy + - Biomedical Science + mappings: + biocontext: MPATH + bioportal: MPATH + fairsharing: FAIRsharing.3wbgm0 + obofoundry: mpath + ols: mpath + ontobee: MPATH + prefixcommons: mpath + obofoundry: + contact: pns12@hermes.cam.ac.uk + contact.github: PaulNSchofield + contact.label: Paul Schofield + contact.orcid: 0000-0002-5111-7263 + deprecated: false + description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes + download.owl: http://purl.obolibrary.org/obo/mpath.owl + homepage: http://www.pathbase.net + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Mouse pathology ontology + preferredPrefix: MPATH + prefix: mpath + repository: https://github.com/PaulNSchofield/mpath + ols: + description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes + download: http://purl.obolibrary.org/obo/mpath.owl + homepage: http://www.pathbase.net + name: Mouse pathology ontology + prefix: mpath + version: 2020-05-19 + version.iri: http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl + ontobee: + library: Not Specified/No + name: Mouse pathology + prefix: MPATH + pattern: ^\d+$ + prefixcommons: + bioportal: '1031' + description: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes + example: MPATH_606 + homepage: http://www.pathbase.net + keywords: + - obo + - phenotype + - mouse + name: Mouse pathology + pattern: ^MPATH_\d+$ + prefix: mpath + synonyms: + - MPATH +mpid: + biocontext: + is_identifiers: true + is_obo: false + prefix: MPID + uri_format: http://identifiers.org/mpid/$1 + fairsharing: + abbreviation: MPIDB + description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about this resource. + id: '1937' + name: Microbial Protein Interaction Database + prefix: FAIRsharing.eyjkws + subjects: + - Life Science + mappings: + biocontext: MPID + fairsharing: FAIRsharing.eyjkws + miriam: mpid + n2t: mpid + miriam: + deprecated: false + description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. + homepage: http://www.jcvi.org/mpidb/about.php + id: '00000124' + name: Microbial Protein Interaction Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mpid + providers: + - code: ebi + description: Microbial Protein Interaction Database subset through IntAct + homepage: https://www.ebi.ac.uk/intact/ + name: Microbial Protein Interaction Database subset through IntAct + uri_format: https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1 + sampleId: '172' + uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 + n2t: + description: The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. + example: '172' + homepage: http://www.jcvi.org/mpidb/about.php + name: Microbial Protein Interaction Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mpid + uri_format: http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 + synonyms: + - mpidb +mpio: + biocontext: + is_identifiers: false + is_obo: true + prefix: MPIO + uri_format: http://purl.obolibrary.org/obo/MPIO_$1 + bioportal: + name: Minimum PDDI Information Ontology + prefix: MPIO + example: '0000004' + mappings: + biocontext: MPIO + bioportal: MPIO + obofoundry: mpio + ols: mpio + ontobee: MPIO + obofoundry: + contact: mbrochhausen@uams.edu + contact.github: mbrochhausen + contact.label: Mathias Brochhausen + contact.orcid: 0000-0003-1834-3856 + deprecated: false + description: An ontology of minimum information regarding potential drug-drug interaction information. + download.owl: http://purl.obolibrary.org/obo/mpio.owl + homepage: https://github.com/MPIO-Developers/MPIO + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Minimum PDDI Information Ontology + preferredPrefix: MPIO + prefix: mpio + repository: https://github.com/MPIO-Developers/MPIO + ols: + description: An ontology of minimum information regarding potential drug-drug interaction information. + download: http://purl.obolibrary.org/obo/mpio.owl + homepage: https://github.com/MPIO-Developers/MPIO + name: Minimum PDDI Information Ontology + prefix: mpio + version: 2019-01-30 + version.iri: http://purl.obolibrary.org/obo/mpio/release/2019-01-30/mpio.owl + ontobee: + library: Library + name: Minimum PDDI Information Ontology + prefix: MPIO + pattern: ^\d{7}$ +mro: + biocontext: + is_identifiers: false + is_obo: true + prefix: MRO + uri_format: http://purl.obolibrary.org/obo/MRO_$1 + bioportal: + name: Defen + prefix: MRO + example: '0000634' + fairsharing: + abbreviation: MRO + description: MHC molecules form a highly diverse family of proteins that play a key role in cellular immune recognition. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology (MaHCO) and created MRO to represent MHC molecules as they relate to immunological experiments. MRO models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multichain proteins, and establishes evidence codes for MHC restriction. + id: '849' + name: MHC Restriction Ontology + prefix: FAIRsharing.k893xa + subjects: + - Immunology + mappings: + biocontext: MRO + bioportal: MRO + fairsharing: FAIRsharing.k893xa + obofoundry: mro + ols: mro + ontobee: MRO + obofoundry: + contact: bpeters@lji.org + contact.github: bpeters42 + contact.label: Bjoern Peters + contact.orcid: 0000-0002-8457-6693 + deprecated: false + description: An ontology for Major Histocompatibility Complex (MHC) restriction in experiments + download.owl: http://purl.obolibrary.org/obo/mro.owl + homepage: https://github.com/IEDB/MRO + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: MHC Restriction Ontology + preferredPrefix: MRO + prefix: mro + repository: https://github.com/IEDB/MRO + ols: + description: The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. + download: http://purl.obolibrary.org/obo/mro.owl + homepage: https://github.com/IEDB/MRO + name: MHC Restriction Ontology + prefix: mro + version: 2022-03-14 + version.iri: http://purl.obolibrary.org/obo/mro/2022-03-14/mro.owl + ontobee: + library: Library + name: MHC Restriction Ontology + prefix: MRO + pattern: ^\d{7}$ +ms: + biocontext: + is_identifiers: false + is_obo: true + prefix: MS + uri_format: http://purl.obolibrary.org/obo/MS_$1 + bioportal: + name: Mass Spectrometry Ontology + prefix: MS + example: '1000560' + mappings: + biocontext: MS + bioportal: MS + miriam: ms + n2t: ms + obofoundry: ms + ols: ms + ontobee: MS + miriam: + deprecated: false + description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. + homepage: https://www.ebi.ac.uk/ols/ontologies/ms + id: '00000590' + name: Mass Spectrometry Controlled Vocabulary + namespaceEmbeddedInLui: true + pattern: ^MS:\d{7}$ + prefix: ms + sampleId: '1000001' + uri_format: https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1 + n2t: + description: The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. + example: '1000001' + homepage: https://bioportal.bioontology.org/ontologies/MS + name: Mass Spectrometry Controlled Vocabulary through BioPortal + namespaceEmbeddedInLui: true + pattern: ^MS:\d{7}$ + prefix: ms + uri_format: http://purl.bioontology.org/ontology/MS/MS:$1 + obofoundry: + contact: gerhard.mayer@rub.de + contact.github: germa + contact.label: Gerhard Mayer + contact.orcid: 0000-0002-1767-2343 + depends_on: + - pato + - uo + deprecated: false + description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. + download.obo: http://purl.obolibrary.org/obo/ms.obo + download.owl: http://purl.obolibrary.org/obo/ms.owl + homepage: http://www.psidev.info/groups/controlled-vocabularies + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Mass spectrometry ontology + preferredPrefix: MS + prefix: ms + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/23482073 + title: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. + repository: https://github.com/HUPO-PSI/psi-ms-CV + ols: + contact: psidev-ms-vocab@lists.sourceforge.net + description: A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry. + download: http://purl.obolibrary.org/obo/ms.owl + homepage: http://www.psidev.info/groups/controlled-vocabularies + name: Mass spectrometry ontology + prefix: ms + version.iri: http://purl.obolibrary.org/obo/ms/4.1.86/ms.owl + ontobee: + library: Library + name: Mass spectrometry ontology + prefix: MS + pattern: ^\d{7}$ +msigdb: + biolink: + is_identifiers: false + is_obo: false + prefix: MSigDB + uri_format: https://www.gsea-msigdb.org/gsea/msigdb/$1 + description: The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can + example: NADELLA_PRKAR1A_TARGETS_DN + homepage: https://www.gsea-msigdb.org + mappings: + biolink: MSigDB + name: Molecular Signatures Database + synonyms: + - msig + wikidata: + paper: Q34509167 +msio: + example: '0000111' + mappings: + ols: msio + name: Metabolomics Standards Initiative Ontology + ols: + description: an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. + download: https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl + homepage: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO + name: Metabolomics Standards Initiative Ontology (MSIO) + prefix: msio + version: 1.0.1 + pattern: ^\d{7}$ + repository: https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO +multicellds: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. + example: MCDS_S_0000000001 + fairsharing: + abbreviation: MultiCellDS + description: 'MultiCellDS (Multicellular data specification), an outgrowth of the earlier MultiCellXML project, aims to create a data standard for sharing multicellular experimental, simulation, and clinical data. Our ultimate goal is to foster a community that develops user-friendly tools that can read, write, and recombine data into better simulations and analyses for multicellular biology and predictive medicine. As part of this effort, we are developing MultiCellDB: a repository for a curated library of digital cell lines and peer-reviewed simulation and experimental data. A novel part of MultiCellDS is the digital cell line: a digital analogue of experimental cell lines that will help to collect biophysical cell line measurements coming from many research groups and make them readily accessible to an ecosystem of compatible computational models. You can learn more about digital cell lines and other core ideas on this page. We are currently preparing a draft of the upcoming MultiCellDS 1.0 specification. After a multiple rounds of comment and review by a multidisciplinary review panel and the general public, we target an October 2016 release of the data specification and software support tools.' + id: '1542' + name: MultiCellular Data Standard + prefix: FAIRsharing.pqzyd5 + subjects: + - Life Science + homepage: http://multicellds.org/MultiCellDB.php + mappings: + fairsharing: FAIRsharing.pqzyd5 + name: MultiCellDS + uri_format: http://multicellds.org/MultiCellDB/$1 +multicellds.cell_line: + biocontext: + is_identifiers: true + is_obo: false + prefix: MULTICELLDS.CELL_LINE + uri_format: http://identifiers.org/multicellds.cell_line/$1 + mappings: + biocontext: MULTICELLDS.CELL_LINE + miriam: multicellds.cell_line + n2t: multicellds.cell_line + miriam: + deprecated: false + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. + homepage: http://multicellds.org/MultiCellDB.php + id: '00000584' + name: MultiCellDS Digital Cell Line + namespaceEmbeddedInLui: false + pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.cell_line + sampleId: MCDS_L_0000000001 + uri_format: http://multicellds.org/MultiCellDB/$1 + n2t: + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. + example: MCDS_L_0000000001 + homepage: http://multicellds.org/MultiCellDB.php + name: MultiCellDS Digital Cell Line at Keck School of Medicine + namespaceEmbeddedInLui: false + pattern: ^MCDS_L_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.cell_line + uri_format: http://multicellds.org/MultiCellDB/$1 + part_of: multicellds +multicellds.collection: + biocontext: + is_identifiers: true + is_obo: false + prefix: MULTICELLDS.COLLECTION + uri_format: http://identifiers.org/multicellds.collection/$1 + mappings: + biocontext: MULTICELLDS.COLLECTION + miriam: multicellds.collection + n2t: multicellds.collection + miriam: + deprecated: false + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). + homepage: http://multicellds.org/MultiCellDB.php + id: '00000582' + name: MultiCellDS collection + namespaceEmbeddedInLui: false + pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.collection + sampleId: MCDS_C_0000000001 + uri_format: http://multicellds.org/MultiCellDB/$1 + n2t: + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). + example: MCDS_C_0000000001 + homepage: http://multicellds.org/MultiCellDB.php + name: MultiCellDScollection at Keck School of Medicine + namespaceEmbeddedInLui: false + pattern: ^MCDS_C_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.collection + uri_format: http://multicellds.org/MultiCellDB/$1 + part_of: multicellds +multicellds.snapshot: + biocontext: + is_identifiers: true + is_obo: false + prefix: MULTICELLDS.SNAPSHOT + uri_format: http://identifiers.org/multicellds.snapshot/$1 + mappings: + biocontext: MULTICELLDS.SNAPSHOT + miriam: multicellds.snapshot + n2t: multicellds.snapshot + miriam: + deprecated: false + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. + homepage: http://multicellds.org/MultiCellDB.php + id: '00000583' + name: MultiCellDS Digital snapshot + namespaceEmbeddedInLui: false + pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.snapshot + sampleId: MCDS_S_0000000001 + uri_format: http://multicellds.org/MultiCellDB/$1 + n2t: + description: MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. + example: MCDS_S_0000000001 + homepage: http://multicellds.org/MultiCellDB.php + name: MultiCellDS snapshot at Keck School of Medicine + namespaceEmbeddedInLui: false + pattern: ^MCDS_S_[a-zA-Z0-9]{1,10}$ + prefix: multicellds.snapshot + uri_format: http://multicellds.org/MultiCellDB/$1 + part_of: multicellds +mw.project: + biocontext: + is_identifiers: true + is_obo: false + prefix: MW.PROJECT + uri_format: http://identifiers.org/mw.project/$1 + mappings: + biocontext: MW.PROJECT + miriam: mw.project + n2t: mw.project + miriam: + deprecated: false + description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). + homepage: http://www.metabolomicsworkbench.org/ + id: '00000647' + name: Metabolomics Workbench Project + namespaceEmbeddedInLui: false + pattern: ^PR[0-9]{6}$ + prefix: mw.project + sampleId: PR000001 + uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1 + n2t: + description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). + example: PR000001 + homepage: http://www.metabolomicsworkbench.org/ + name: Metabolomics Workbench Project + namespaceEmbeddedInLui: false + pattern: ^PR[0-9]{6}$ + prefix: mw.project + uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1 +mw.study: + biocontext: + is_identifiers: true + is_obo: false + prefix: MW.STUDY + uri_format: http://identifiers.org/mw.study/$1 + mappings: + biocontext: MW.STUDY + miriam: mw.study + n2t: mw.study + miriam: + deprecated: false + description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). + homepage: http://www.metabolomicsworkbench.org/ + id: '00000646' + name: Metabolomics Workbench Study + namespaceEmbeddedInLui: false + pattern: ^ST[0-9]{6}$ + prefix: mw.study + providers: + - code: omicsdi + description: Metabolomics Workbench Study through OmicsDI + homepage: https://www.omicsdi.org/ + name: Metabolomics Workbench Study through OmicsDI + uri_format: https://www.omicsdi.org/dataset/metabolomics_workbench/$1 + sampleId: ST000900 + uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1 + n2t: + description: Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). + example: ST000900 + homepage: http://www.metabolomicsworkbench.org/ + name: Metabolomics Workbench Study + namespaceEmbeddedInLui: false + pattern: ^ST[0-9]{6}$ + prefix: mw.study + uri_format: http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1 +myco.lepra: + biocontext: + is_identifiers: true + is_obo: false + prefix: MYCO.LEPRA + uri_format: http://identifiers.org/myco.lepra/$1 + mappings: + biocontext: MYCO.LEPRA + miriam: myco.lepra + n2t: myco.lepra + prefixcommons: myco.lepra + miriam: + deprecated: false + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. + homepage: http://mycobrowser.epfl.ch/leprosy.html + id: '00000217' + name: MycoBrowser leprae + namespaceEmbeddedInLui: false + pattern: ^ML\w+$ + prefix: myco.lepra + sampleId: ML0224 + uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 + n2t: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. + example: ML0224 + homepage: http://mycobrowser.epfl.ch/leprosy.html + name: MycoBrowser leprae at Global Health Institute + namespaceEmbeddedInLui: false + pattern: ^ML\w+$ + prefix: myco.lepra + uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 + prefixcommons: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. + example: ML0224 + homepage: http://mycobrowser.epfl.ch/leprosy.html + keywords: + - genome + - sequence + name: MycoBrowser leprae + pattern: ^ML\w+$ + prefix: myco.lepra + uri_format: http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1 +myco.marinum: + biocontext: + is_identifiers: true + is_obo: false + prefix: MYCO.MARINUM + uri_format: http://identifiers.org/myco.marinum/$1 + mappings: + biocontext: MYCO.MARINUM + miriam: myco.marinum + n2t: myco.marinum + prefixcommons: myco.marinum + miriam: + deprecated: false + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. + homepage: http://mycobrowser.epfl.ch/marinolist.html + id: '00000218' + name: MycoBrowser marinum + namespaceEmbeddedInLui: false + pattern: ^MMAR\_\d+$ + prefix: myco.marinum + sampleId: MMAR_2462 + uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 + n2t: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. + example: MMAR_2462 + homepage: http://mycobrowser.epfl.ch/marinolist.html + name: MycoBrowser marinum at Global Health Institute + namespaceEmbeddedInLui: false + pattern: ^MMAR\_\d+$ + prefix: myco.marinum + uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 + prefixcommons: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. + example: MMAR_2462 + homepage: http://mycobrowser.epfl.ch/marinolist.html + keywords: + - genome + - sequence + name: MycoBrowser marinum + pattern: ^MMAR\_\d+$ + prefix: myco.marinum + uri_format: http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1 +myco.smeg: + biocontext: + is_identifiers: true + is_obo: false + prefix: MYCO.SMEG + uri_format: http://identifiers.org/myco.smeg/$1 + mappings: + biocontext: MYCO.SMEG + miriam: myco.smeg + n2t: myco.smeg + prefixcommons: myco.smeg + miriam: + deprecated: false + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. + homepage: http://mycobrowser.epfl.ch/smegmalist.html + id: '00000219' + name: MycoBrowser smegmatis + namespaceEmbeddedInLui: false + pattern: ^MSMEG\w+$ + prefix: myco.smeg + sampleId: MSMEG_3769 + uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 + n2t: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. + example: MSMEG_3769 + homepage: http://mycobrowser.epfl.ch/smegmalist.html + name: MycoBrowser smegmatis at Global Health Institute + namespaceEmbeddedInLui: false + pattern: ^MSMEG\w+$ + prefix: myco.smeg + uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 + prefixcommons: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. + example: MSMEG_3769 + homepage: http://mycobrowser.epfl.ch/smegmalist.html + keywords: + - genome + - sequence + name: MycoBrowser smegmatis + pattern: ^MSMEG\w+$ + prefix: myco.smeg + uri_format: http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1 +myco.tuber: + biocontext: + is_identifiers: true + is_obo: false + prefix: MYCO.TUBER + uri_format: http://identifiers.org/myco.tuber/$1 + mappings: + biocontext: MYCO.TUBER + miriam: myco.tuber + n2t: myco.tuber + ncbi: TubercuList + prefixcommons: tuberculist + uniprot: TubercuList + miriam: + deprecated: false + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. + homepage: http://tuberculist.epfl.ch/ + id: '00000216' + name: MycoBrowser tuberculosis + namespaceEmbeddedInLui: false + pattern: ^Rv\d{4}(A|B|c)?$ + prefix: myco.tuber + sampleId: Rv1908c + uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 + n2t: + description: Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. + example: Rv1908c + homepage: http://tuberculist.epfl.ch/ + name: MycoBrowser tuberculosis at Global Health Institute + namespaceEmbeddedInLui: false + pattern: ^Rv\d{4}(A|B|c)?$ + prefix: myco.tuber + uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 + ncbi: + example: Rv3322c + homepage: http://tuberculist.epfl.ch/ + name: TubercuList knowledge base + prefix: TubercuList + prefixcommons: + description: The TubercuList knowledge base integrates genome details, protein information, drug and transcriptome data, mutant and operon annotation, bibliography; structural views and comparative genomics, in a structured manner required for the rational development of new diagnostic, therapeutic and prophylactic measures against tuberculosis. + example: Rv0115 + homepage: http://tuberculist.epfl.ch + keywords: + - genome + - protein + - DNA + name: Mycobacterium tuberculosis strain H37Rv genome database + pattern: ^Rv[0-9,a-z]+$ + prefix: tuberculist + uri_format: http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1 + synonyms: + - TubercuList + uniprot: + category: Organism-specific databases + identifier: '106' + link_is_explicit: 'true' + name: Mycobacterium tuberculosis strain H37Rv genome database + prefix: TubercuList + uri_format: https://mycobrowser.epfl.ch/genes/$1 +mycobank: + biocontext: + is_identifiers: true + is_obo: false + prefix: MYCOBANK + uri_format: http://identifiers.org/mycobank/$1 + fairsharing: + abbreviation: MycoBank + description: MycoBank was created for the mycological community (as well as scientific community more generally) to document new mycological names, combinations and associated data (such as descriptions and illustrations). Pairwise sequence alignments and polyphasic identifications of fungi and yeasts against curated references databases are available. Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural error. Deposited names can remain confidential until after publication as required. Once public, the names are accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute. + id: '1932' + name: MycoBank + prefix: FAIRsharing.v8se8r + subjects: + - Taxonomy + - Biology + mappings: + biocontext: MYCOBANK + fairsharing: FAIRsharing.v8se8r + miriam: mycobank + n2t: mycobank + ncbi: MycoBank + prefixcommons: mycobank + miriam: + deprecated: false + description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. + homepage: http://www.mycobank.org/ + id: '00000178' + name: MycoBank + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mycobank + sampleId: '349124' + uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1 + n2t: + description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. + example: '349124' + homepage: http://www.mycobank.org/ + name: MycoBank at Fungal Biodiversity Centre + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: mycobank + uri_format: http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1 + ncbi: + example: '8284' + homepage: http://www.mycobank.org + name: Fungal Nomenclature and Species Bank + prefix: MycoBank + prefixcommons: + description: MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. + example: '349124' + homepage: http://www.mycobank.org + keywords: + - classification + name: Fungal Nomenclature and Species Bank + pattern: ^\d+$ + prefix: mycobank + uri_format: http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=$1 +mzspec: + banana: mzspec + biocontext: + is_identifiers: true + is_obo: false + prefix: MZSPEC + uri_format: http://identifiers.org/mzspec/$1 + mappings: + biocontext: MZSPEC + miriam: mzspec + n2t: mzspec + miriam: + deprecated: false + description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. + homepage: http://proteomecentral.proteomexchange.org/ + id: '00000625' + name: Universal Spectrum Identifier + namespaceEmbeddedInLui: true + pattern: ^mzspec:.+$ + prefix: mzspec + providers: + - code: CURATOR_REVIEW + description: Universal Spectrum Identifier through Peptide Atlas + homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum + name: Universal Spectrum Identifier through Peptide Atlas + uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1 + sampleId: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 + uri_format: http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1 + n2t: + description: The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. + example: PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 + homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum + name: Universal Spectrum Identifier through Peptide Atlas + namespaceEmbeddedInLui: true + pattern: ^mzspec:.+$ + prefix: mzspec + uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1 + pattern: ^.+$ +n2t: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: An ARK resolver as well as resolver built with common prefixes as in Identifiers.org + example: chebi + homepage: https://n2t.net + name: Name-to-Thing + uri_format: 'https://n2t.net/$1:' +namerxn: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO). + example: 4.2.78 + homepage: https://www.nextmovesoftware.com/namerxn.html + name: NameRXN + proprietary: true + references: + - https://www.nextmovesoftware.com/products/HazELNutPoster.pdf + - https://twitter.com/cthoyt/status/1443929184745758723 + - https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b00153 + - https://www.nature.com/articles/s42256-020-00284-w +napdi: + biocontext: + is_identifiers: true + is_obo: false + prefix: NAPDI + uri_format: http://identifiers.org/napdi/$1 + fairsharing: + abbreviation: NaPDI + description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). The repository is funded by the United States National Center for Complementary and Integrative Health. + id: '2535' + name: Natural Product-Drug Interaction Research Data Repository + prefix: FAIRsharing.y9x8wk + subjects: + - Pharmacology + - Biomedical Science + mappings: + biocontext: NAPDI + fairsharing: FAIRsharing.y9x8wk + miriam: napdi + n2t: napdi + miriam: + deprecated: false + description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). + homepage: https://repo.napdi.org/ + id: '00000620' + name: Natural Product-Drug Interaction Research Data Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: napdi + sampleId: '28' + uri_format: https://repo.napdi.org/study/$1 + n2t: + description: The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). + example: '28' + homepage: https://repo.napdi.org/ + name: Natural Product-Drug Interaction Research Data Repository + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: napdi + uri_format: https://repo.napdi.org/study/$1 +napp: + biocontext: + is_identifiers: true + is_obo: false + prefix: NAPP + uri_format: http://identifiers.org/napp/$1 + fairsharing: + abbreviation: NAPP + description: NAPP (Nucleic Acids Phylogenetic Profile) enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can be contiged into larger elements and retrieved at once as a CSV or GFF file for use in a genome browser or comparison with other predictions/RNA-seq experiments. + id: '1617' + name: Nucleic Acid Phylogenetic Profile + prefix: FAIRsharing.vr52p3 + subjects: + - Genomics + mappings: + biocontext: NAPP + fairsharing: FAIRsharing.vr52p3 + miriam: napp + n2t: napp + prefixcommons: napp + miriam: + deprecated: false + description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. + homepage: http://napp.u-psud.fr/ + id: '00000247' + name: NAPP + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: napp + sampleId: '351' + uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1 + n2t: + description: NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. + example: '351' + homepage: http://napp.u-psud.fr/ + name: NAPP at CNRS + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: napp + uri_format: http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1 + name: Nucleic Acids Phylogenetic Profiling + prefixcommons: + description: NAPP (Nucleic Acids Phylogenetic Profiling) is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. + example: '351' + homepage: http://napp.u-psud.fr/ + keywords: + - clustering + - nucleotide + name: 'NAPP: Nucleic Acids Phylogenetic Profiling' + pattern: ^\d+$ + prefix: napp + uri_format: http://napp.u-psud.fr/Niveau2.php?specie=$1 +narcis: + biocontext: + is_identifiers: true + is_obo: false + prefix: NARCIS + uri_format: http://identifiers.org/narcis/$1 + fairsharing: + abbreviation: NARCIS + description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. + id: '2041' + name: NARCIS + prefix: FAIRsharing.f63h4k + subjects: + - Subject Agnostic + homepage: http://www.narcis.nl + mappings: + biocontext: NARCIS + fairsharing: FAIRsharing.f63h4k + miriam: narcis + n2t: narcis + miriam: + deprecated: false + description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. + homepage: http://www.narcis.nl/?Language=en + id: '00000240' + name: NARCIS + namespaceEmbeddedInLui: false + pattern: ^oai\:cwi\.nl\:\d+$ + prefix: narcis + sampleId: oai:cwi.nl:4725 + uri_format: http://www.narcis.nl/publication/RecordID/$1 + n2t: + description: NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. + example: oai:cwi.nl:4725 + homepage: http://www.narcis.nl/?Language=en + name: NARCIS at The Hague + namespaceEmbeddedInLui: false + pattern: ^oai\:cwi\.nl\:\d+$ + prefix: narcis + uri_format: http://www.narcis.nl/publication/RecordID/$1 + name: National Academic Research and Collaborations Information System +nasc: + biocontext: + is_identifiers: true + is_obo: false + prefix: NASC + uri_format: http://identifiers.org/nasc/$1 + fairsharing: + abbreviation: NASC + description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. + id: '1740' + name: Nottingham Arabidopsis Stock Centre Seeds Database + prefix: FAIRsharing.2sqcxs + subjects: + - Life Science + mappings: + biocontext: NASC + fairsharing: FAIRsharing.2sqcxs + miriam: nasc + n2t: nasc + prefixcommons: nasc + miriam: + deprecated: false + description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. + homepage: http://arabidopsis.info/ + id: '00000304' + name: NASC code + namespaceEmbeddedInLui: false + pattern: ^(\w+)?\d+$ + prefix: nasc + sampleId: N1899 + uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1 + n2t: + description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. + example: N1899 + homepage: http://arabidopsis.info/ + name: NASC at University of Nottingham + namespaceEmbeddedInLui: false + pattern: ^(\w+)?\d+$ + prefix: nasc + uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1 + prefixcommons: + description: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. + example: '57961' + homepage: http://arabidopsis.info + keywords: + - genome + name: Nottingham Arabidopsis Stock Centre Seeds Database + pattern: ^\d+$ + prefix: nasc + uri_format: http://arabidopsis.info/StockInfo?NASC_id=$1 +nbn: + biocontext: + is_identifiers: true + is_obo: false + prefix: NBN + uri_format: http://identifiers.org/nbn/$1 + mappings: + biocontext: NBN + miriam: nbn + n2t: nbn + miriam: + deprecated: false + description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. + homepage: http://nbn-resolving.org/resolve_urn.htm + id: '00000381' + name: National Bibliography Number + namespaceEmbeddedInLui: false + pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ + prefix: nbn + sampleId: urn:nbn:fi:tkk-004781 + uri_format: http://nbn-resolving.org/resolver?identifier=$1&verb=redirect + n2t: + description: The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. + example: urn:nbn:fi:tkk-004781 + homepage: http://nbn-resolving.org/resolve_urn.htm + name: NBN through URN Resolver at German National Library + namespaceEmbeddedInLui: false + pattern: ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ + prefix: nbn + uri_format: http://nbn-resolving.org/resolver?identifier=urn:nbn:$1&verb=redirect +nbo: + biocontext: + is_identifiers: false + is_obo: true + prefix: NBO + uri_format: http://purl.obolibrary.org/obo/NBO_$1 + bioportal: + name: Neuro Behavior Ontology + prefix: NBO + download_obo: https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo + example: '0000564' + fairsharing: + abbreviation: NBO + description: The Neurobehavior Ontology (NBO) consists of two main components, an ontology of behavioral processes and an ontology of behavioral phenotypes. The behavioral process branch of NBO contains a classification of behavior processes complementing and extending GO’s process ontology. The behavior phenotype branch of NBO consists of a classification of both normal and abnormal behavioral characteristics of organisms . + id: '1470' + name: Neuro Behavior Ontology + prefix: FAIRsharing.pktgc6 + subjects: + - Social and Behavioural Science + - Systemic Neuroscience + mappings: + biocontext: NBO + bioportal: NBO + fairsharing: FAIRsharing.pktgc6 + obofoundry: nbo + ols: nbo + ontobee: NBO + obofoundry: + appears_in: + - ecto + - pcl + - scdo + contact: g.gkoutos@bham.ac.uk + contact.github: gkoutos + contact.label: George Gkoutos + contact.orcid: 0000-0002-2061-091X + deprecated: false + description: An ontology of human and animal behaviours and behavioural phenotypes + download.owl: http://purl.obolibrary.org/obo/nbo.owl + homepage: https://github.com/obo-behavior/behavior-ontology/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Neuro Behavior Ontology + preferredPrefix: NBO + prefix: nbo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/24177753 + title: Analyzing gene expression data in mice with the Neuro Behavior Ontology + repository: https://github.com/obo-behavior/behavior-ontology + ols: + description: An ontology of human and animal behaviours and behavioural phenotypes + download: http://purl.obolibrary.org/obo/nbo.owl + homepage: https://github.com/obo-behavior/behavior-ontology/ + name: Neuro Behavior Ontology + prefix: nbo + version: 2021-02-15 + version.iri: http://purl.obolibrary.org/obo/nbo/releases/2021-02-15/nbo.owl + ontobee: + library: Library + name: Neuro Behavior Ontology + prefix: NBO + pattern: ^\d{7}$ +nbrc: + biocontext: + is_identifiers: true + is_obo: false + prefix: NBRC + uri_format: http://identifiers.org/nbrc/$1 + fairsharing: + abbreviation: NBRC + description: To provide attractive biological resources with useful information attached, the NITE Biological Resource Center (NBRC) actively collects potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic researches as well as industrial applications. + id: '2001' + name: NITE Biological Research Center Catalogue + prefix: FAIRsharing.ftamrc + subjects: [] + mappings: + biocontext: NBRC + fairsharing: FAIRsharing.ftamrc + miriam: nbrc + n2t: nbrc + ncbi: NBRC + prefixcommons: nbrc + miriam: + deprecated: false + description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. + homepage: http://www.nbrc.nite.go.jp/e/index.html + id: '00000179' + name: NITE Biological Research Center Catalogue + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: nbrc + sampleId: '00001234' + uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 + n2t: + description: NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. + example: '00001234' + homepage: http://www.nbrc.nite.go.jp/e/index.html + name: NBRC Catalogue at National Institute of Technology Evaluation + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: nbrc + uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 + ncbi: + example: '3189' + homepage: http://www.nbrc.nite.go.jp/e/catalog-e.html + name: NITE Biological Resource Center + prefix: NBRC + prefixcommons: + description: To provide attractive biological resources with useful information attached, the NITE Biological Resource Center (NBRC) actively collects potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic researches as well as industrial applications. + example: '00001234' + homepage: http://www.nbrc.nite.go.jp/e/index.html + keywords: + - microbial + - taxonomy + name: NITE Biological Research Center Catalogue + pattern: ^\d+$ + prefix: nbrc + uri_format: http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 +ncats.drug: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + contributor_extras: + - email: cjmungall@lbl.gov + github: cmungall + name: Chris Mungall + orcid: 0000-0002-6601-2165 + - github: vdancik + name: Vlado Dancik + orcid: 0000-0002-5970-6660 + description: 'The [National Center for Advancing Translational Sciences (NCATS)](https://ncats.nih.gov/) has developed Inxight: Drugs as a comprehensive portal for drug development information. NCATS Inxight: Drugs contains information on ingredients in medicinal products, including:' + example: '44259' + example_extras: + - 1IJV77EI07 + homepage: https://drugs.ncats.io/ + name: NCATS Drugs + synonyms: + - inxight + - inxight-drugs + uri_format: https://drugs.ncats.io/drug/$1 +ncbi.assembly: + biocontext: + is_identifiers: false + is_obo: false + prefix: NCBIAssembly + uri_format: http://www.ncbi.nlm.nih.gov/assembly/$1 + mappings: + biocontext: NCBIAssembly + miriam: assembly + miriam: + deprecated: false + description: A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. + homepage: https://www.ncbi.nlm.nih.gov/ + id: '00000884' + name: Assembly + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9_\.]+$ + prefix: assembly + sampleId: GCF_000005845.2 + uri_format: https://www.ncbi.nlm.nih.gov/assembly/$1 +ncbi.genome: + biocontext: + is_identifiers: false + is_obo: false + prefix: NCBIGenome + uri_format: http://www.ncbi.nlm.nih.gov/genome/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. + example: '51' + homepage: https://www.ncbi.nlm.nih.gov/genome + mappings: + biocontext: NCBIGenome + name: NCBI Genome + pattern: ^\d+$ + uri_format: https://www.ncbi.nlm.nih.gov/genome/$1 +ncbi.resource: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources + example: ECOCYC + homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ + name: NCBI Registry + uri_format: https://bioregistry.io/metaregistry/ncbi/$1 +ncbibook: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ' + example: NBK331 + homepage: https://www.ncbi.nlm.nih.gov/books + name: NCBI Bookshelf + pattern: ^NBK\d+$ + uri_format: https://www.ncbi.nlm.nih.gov/books/$1 +ncbigene: + biocontext: + is_identifiers: false + is_obo: false + prefix: NCBIGene + uri_format: http://www.ncbi.nlm.nih.gov/gene/$1 + biolink: + is_identifiers: true + is_obo: false + prefix: NCBIGene + uri_format: http://identifiers.org/ncbigene/$1 + fairsharing: + abbreviation: NCBI Gene + description: Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems. Gene comprises sequences from thousands of distinct taxonomic identifiers, ranging from viruses to bacteria to eukaryotes. It represents chromosomes, organelles, plasmids, viruses, transcripts, and millions of proteins. + id: '1983' + name: NCBI Gene + prefix: FAIRsharing.5h3maw + subjects: + - Genomics + - Genetics + go: + homepage: http://www.ncbi.nlm.nih.gov/ + name: NCBI Gene + prefix: NCBIGene + synonyms: + - GeneID + - LocusID + - NCBI_Gene + uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 + mappings: + biocontext: NCBIGene + biolink: NCBIGene + fairsharing: FAIRsharing.5h3maw + go: NCBIGene + miriam: ncbigene + n2t: ncbigene + ncbi: GeneID + prefixcommons: ncbigene + scholia: ncbi-gene + wikidata: P351 + miriam: + deprecated: false + description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. + homepage: https://www.ncbi.nlm.nih.gov/gene + id: '00000069' + name: NCBI Gene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ncbigene + providers: + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: http://ncbigene.bio2rdf.org/fct + name: Bio2RDF + uri_format: http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$1 + sampleId: '100010' + uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 + n2t: + description: Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. + example: '100010' + homepage: https://www.ncbi.nlm.nih.gov/gene + name: Entrez Gene (NCBI) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ncbigene + uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 + name: Entrez Gene + ncbi: + example: '3054987' + homepage: https://www.ncbi.nlm.nih.gov/gene + name: Entrez Gene Database (replaces NCBI Locus Link) + prefix: GeneID + preferred_prefix: NCBIGene + prefixcommons: + description: NCBI Gene provides information for genes from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide. + example: '1' + homepage: http://www.ncbi.nlm.nih.gov/gene + keywords: + - genome + - gene + - DNA + name: NCBI Gene + pattern: ^\d+$ + prefix: ncbigene + pubmed_ids: + - '15608257' + uri_format: http://www.ncbi.nlm.nih.gov/gene/$1 + providers: + - code: marrvel + description: Helps browse potential orthologs in model organisms for a given gene + homepage: http://marrvel.org + name: Model organism Aggregated Resources for Rare Variant ExpLoration + uri_format: http://marrvel.org/model/gene/$1 + synonyms: + - EGID + - EntrezGene + - NCBIGene + - entrez + - entrez gene/locuslink + wikidata: + database: Q1345229 + database.homepage: http://www.ncbi.nlm.nih.gov/gquery/ + database.label: Entrez + format.rdf: http://purl.uniprot.org/geneid/$1 + name: Entrez Gene ID + pattern: '[1-9]\d{0,8}' + prefix: P351 + uri_format: https://www.ncbi.nlm.nih.gov/gene/$1 +ncbiprotein: + biocontext: + is_identifiers: false + is_obo: false + prefix: NCBIProtein + uri_format: http://www.ncbi.nlm.nih.gov/protein/$1 + go: + homepage: https://www.ncbi.nlm.nih.gov/protein + name: NCBI Protein + prefix: NCBI_NP + mappings: + biocontext: NCBIProtein + go: NCBI_NP + miriam: ncbiprotein + n2t: ncbiprotein + prefixcommons: ncbi.protein + miriam: + deprecated: false + description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. + homepage: https://www.ncbi.nlm.nih.gov/protein + id: '00000344' + name: NCBI Protein + namespaceEmbeddedInLui: false + pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$ + prefix: ncbiprotein + sampleId: CAA71118.1 + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 + n2t: + description: The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. + example: CAA71118.1 + homepage: https://www.ncbi.nlm.nih.gov/protein + name: NCBI Protein at NCBI + namespaceEmbeddedInLui: false + pattern: ^(\w+\d+(\.\d+)?)|(NP_\d+)$ + prefix: ncbiprotein + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 + preferred_prefix: NCBIProtein + prefixcommons: + description: The Entrez Protein search and retrieval system contains protein entries that have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq. + example: CAA71118.1 + homepage: http://www.ncbi.nlm.nih.gov/protein + keywords: + - protein + name: NCBI Protein + pattern: ^\w+\d+(\.\d+)?$ + prefix: ncbi.protein + uri_format: http://www.ncbi.nlm.nih.gov/protein/$1 +ncbitaxon: + biocontext: + is_identifiers: false + is_obo: true + prefix: NCBITaxon + uri_format: http://purl.obolibrary.org/obo/NCBITaxon_$1 + bioportal: + name: National Center for Biotechnology Information (NCBI) Organismal Classification + prefix: NCBITAXON + cellosaurus: + category: Taxonomy + homepage: https://www.ncbi.nlm.nih.gov/taxonomy + name: NCBI taxonomy database + prefix: NCBI_TaxID + uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1&lvl=3 + download_obo: http://purl.obolibrary.org/obo/ncbitaxon.obo + example: '2170610' + fairsharing: + abbreviation: NCBITAXON + description: The NCBI Taxonomy is a database of taxonomic information. It does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. + id: '1220' + name: NCBI Taxonomy + prefix: FAIRsharing.fj07xj + subjects: + - Taxonomy + - Phylogenetics + - Life Science + go: + homepage: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ + name: NCBI Taxonomy + prefix: taxon + synonyms: + - NCBITaxon + - ncbi_taxid + uri_format: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1 + mappings: + biocontext: NCBITaxon + bioportal: NCBITAXON + cellosaurus: NCBI_TaxID + fairsharing: FAIRsharing.fj07xj + go: taxon + miriam: taxonomy + n2t: taxonomy + ncbi: taxon + obofoundry: ncbitaxon + ols: ncbitaxon + ontobee: NCBITaxon + prefixcommons: taxonomy + scholia: ncbi-taxon + wikidata: P685 + miriam: + deprecated: false + description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. + homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/ + id: '00000006' + name: Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: taxonomy + providers: + - code: CURATOR_REVIEW + description: Taxonomy through UniProt PURL + homepage: https://www.uniprot.org/taxonomy/ + name: Taxonomy through UniProt PURL + uri_format: https://purl.uniprot.org/taxonomy/$1 + - code: ebi + description: European Nucleotide Archive (ENA) + homepage: https://www.ebi.ac.uk/ena/ + name: European Nucleotide Archive (ENA) + uri_format: https://www.ebi.ac.uk/ena/data/view/Taxon:$1 + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: https://bio2rdf.org/ + name: Bio2RDF + uri_format: https://bio2rdf.org/taxonomy:$1 + sampleId: '9606' + uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 + n2t: + description: The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. + example: '9606' + homepage: https://www.ncbi.nlm.nih.gov/Taxonomy/ + name: NCBI Taxonomy + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: taxonomy + uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 + name: NCBI Taxonomy + namespace_in_lui: false + ncbi: + example: '4932' + homepage: https://www.ncbi.nlm.nih.gov/taxonomy + name: NCBI's taxonomic identifier + prefix: taxon + obofoundry: + appears_in: + - go + - agro + - chiro + - cl + - clo + - ecto + - envo + - foodon + - genepio + - hso + - mco + - ons + - pcl + - pco + contact: frederic.bastian@unil.ch + contact.github: fbastian + contact.label: Frederic Bastian + contact.orcid: 0000-0002-9415-5104 + deprecated: false + description: An ontology representation of the NCBI organismal taxonomy + download.json: http://purl.obolibrary.org/obo/ncbitaxon.json + download.obo: http://purl.obolibrary.org/obo/ncbitaxon.obo + download.owl: http://purl.obolibrary.org/obo/ncbitaxon.owl + homepage: https://github.com/obophenotype/ncbitaxon + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: NCBI organismal classification + preferredPrefix: NCBITaxon + prefix: ncbitaxon + repository: https://github.com/obophenotype/ncbitaxon + ols: + download: http://purl.obolibrary.org/obo/ncbitaxon.owl + name: ncbitaxon + prefix: ncbitaxon + version: 2021-12-14 + version.iri: http://purl.obolibrary.org/obo/ncbitaxon/2021-12-14/ncbitaxon.owl + ontobee: + library: Library + name: NCBI organismal classification + prefix: NCBITaxon + pattern: ^\d+$ + prefixcommons: + bioportal: '1132' + description: The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence. + example: '9606' + homepage: http://www.ncbi.nlm.nih.gov/taxonomy + keywords: + - DNA + - protein + - structure + - classification + name: NCBI Taxonomy + pattern: ^\d+$ + prefix: taxonomy + uri_format: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=$1 + synonyms: + - NCBITaxon + - NCBI_Taxon_ID + - NCBI_taxid + - TAX + - TaxonomyID + - taxid + - taxon + - taxonomy + wikidata: + database: Q13711410 + database.homepage: https://www.ncbi.nlm.nih.gov/taxonomy + database.label: Taxonomy database of the U.S. National Center for Biotechnology Information + format.rdf: http://purl.uniprot.org/taxonomy/$1 + homepage: http://www.ncbi.nlm.nih.gov/taxonomy + name: NCBI taxonomy ID + pattern: '[1-9][0-9]{0,6}' + prefix: P685 + uri_format: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 +ncim: + biocontext: + is_identifiers: true + is_obo: false + prefix: NCIM + uri_format: http://identifiers.org/ncim/$1 + mappings: + biocontext: NCIM + miriam: ncim + n2t: ncim + miriam: + deprecated: false + description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. + homepage: http://ncim.nci.nih.gov/ + id: '00000353' + name: NCIm + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: ncim + sampleId: C0026339 + uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1 + n2t: + description: NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. + example: C0026339 + homepage: http://ncim.nci.nih.gov/ + name: NCIm at National Cancer Institue + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: ncim + uri_format: http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1 + name: NCI Metathesaurus +ncit: + biocontext: + is_identifiers: false + is_obo: true + prefix: NCIT + uri_format: http://purl.obolibrary.org/obo/NCIT_$1 + bioportal: + name: National Cancer Institute Thesaurus + prefix: NCIT + cellosaurus: + category: Medical resources + homepage: https://ncit.nci.nih.gov/ncitbrowser + name: NCI thesaurus + prefix: NCIt + uri_format: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=$1 + download_obo: http://purl.obolibrary.org/obo/ncit.obo + example: C138986 + fairsharing: + abbreviation: NCIt + description: 'NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. NCIt features: stable, unique codes for biomedical concepts; preferred terms, synonyms, research codes, external source codes, and other information; over 100,000 textual definitions; links to NCI Metathesaurus and other information sources; and over 400,000 cross-links between concepts, providing formal logic-based definition of many concepts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).' + id: '1337' + name: NCI Thesaurus + prefix: FAIRsharing.4cvwxa + subjects: + - Biomedical Science + - Translational Medicine + - Preclinical Studies + mappings: + biocontext: NCIT + bioportal: NCIT + cellosaurus: NCIt + fairsharing: FAIRsharing.4cvwxa + miriam: ncit + n2t: ncit + obofoundry: ncit + ols: ncit + ontobee: NCIT + prefixcommons: ncit + miriam: + deprecated: false + description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. + homepage: http://ncit.nci.nih.gov/ + id: '00000139' + name: NCIt + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: ncit + sampleId: C80519 + uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 + n2t: + description: NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. + example: C80519 + homepage: http://ncit.nci.nih.gov/ + name: NCIt at National Cancer Institute + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: ncit + uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 + name: NCI Thesaurus + namespace_in_lui: false + obofoundry: + appears_in: + - ecto + - mco + - ontoavida + - scdo + contact: haendel@ohsu.edu + contact.github: mellybelly + contact.label: Melissa Haendel + contact.orcid: 0000-0001-9114-8737 + deprecated: false + description: NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental. + download.obo: http://purl.obolibrary.org/obo/ncit.obo + download.owl: http://purl.obolibrary.org/obo/ncit.owl + homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: NCI Thesaurus OBO Edition + preferredPrefix: NCIT + prefix: ncit + repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition + ols: + description: NCI Thesaurus (NCIt)is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. The NCIt OBO Edition aims to increase integration of the NCIt with OBO Library ontologies. NCIt OBO Edition releases should be considered experimental. + download: http://purl.obolibrary.org/obo/ncit.owl + homepage: https://github.com/NCI-Thesaurus/thesaurus-obo-edition + name: NCI Thesaurus OBO Edition + prefix: ncit + version: 22.03d + version.iri: http://purl.obolibrary.org/obo/ncit/releases/2022-04-14/ncit.owl + ontobee: + library: Library + name: NCI Thesaurus OBO Edition + prefix: NCIT + prefixcommons: + bioportal: '1032' + description: A vocabulary for clinical care, translational and basic research, and public information and administrative activities. + example: C80519 + homepage: https://cabig.nci.nih.gov/community/concepts/EVS/ + keywords: + - thesaurus + name: NCI Thesaurus + pattern: ^C\d+$ + prefix: ncit + pubmed_ids: + - '19789731' + uri_format: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 + synonyms: + - NCI + - NCI2004_11_17 + - NCIT + - NCIT_Thesaurus + - NCITm + - NCITt + - NCI_Thesaurus + - NCIt + - ncithesaurus + wikidata: + database: Q19404626 + prefix: P1748 +ncro: + biocontext: + is_identifiers: false + is_obo: true + prefix: NCRO + uri_format: http://purl.obolibrary.org/obo/NCRO_$1 + bioportal: + name: Non-coding RNA Ontology + prefix: NCRO + download_obo: https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo + download_owl: http://purl.obolibrary.org/obo/ncro.owl + example: '0002927' + fairsharing: + abbreviation: NCRO + description: The NCRO is a reference ontology in the non-coding RNA (ncRNA) field, aiming to provide a common set of terms and relations that will facilitate the curation, analysis, exchange, sharing, and management of ncRNA structural, functional, and sequence data. + id: '535' + name: Non-coding RNA Ontology + prefix: FAIRsharing.vppyga + subjects: [] + mappings: + biocontext: NCRO + bioportal: NCRO + fairsharing: FAIRsharing.vppyga + obofoundry: ncro + ols: ncro + ontobee: NCRO + obofoundry: + contact: huang@southalabama.edu + contact.github: Huang-OMIT + contact.label: Jingshan Huang + contact.orcid: 0000-0003-2408-2883 + deprecated: false + description: An ontology for non-coding RNA, both of biological origin, and engineered. + homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Non-Coding RNA Ontology + preferredPrefix: NCRO + prefix: ncro + repository: https://github.com/OmniSearch/ncro + ols: + contact: ncro-devel@googlegroups.com + description: An ontology for non-coding RNA, both of biological origin, and engineered. + download: http://purl.obolibrary.org/obo/ncro.owl + homepage: http://omnisearch.soc.southalabama.edu/w/index.php/Ontology + name: Non-Coding RNA Ontology + prefix: ncro + version: 2015-12-10 + version.iri: http://purl.obolibrary.org/obo/ncro/2015-12-10/ncro-combined.owl + ontobee: + library: Library + name: Non-Coding RNA Ontology + prefix: NCRO + pattern: ^\d{7}$ +ndc: + biocontext: + is_identifiers: true + is_obo: false + prefix: NDC + uri_format: http://identifiers.org/ndc/$1 + mappings: + biocontext: NDC + miriam: ndc + n2t: ndc + miriam: + deprecated: false + description: The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. + homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/ + id: '00000431' + name: National Drug Code + namespaceEmbeddedInLui: false + pattern: ^\d+\-\d+\-\d+ + prefix: ndc + providers: + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: http://ndc.bio2rdf.org/fct + name: Bio2RDF + uri_format: http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:$1 + sampleId: 0002-1975-61 + uri_format: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1 + n2t: + description: The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. + example: 0002-1975-61 + homepage: http://www.accessdata.fda.gov/scripts/cder/ndc/ + name: National Drug Code at Food and Drug Administration + namespaceEmbeddedInLui: false + pattern: ^\d+\-\d+\-\d+ + prefix: ndc + uri_format: http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1 +nddf: + biolink: + is_identifiers: false + is_obo: false + prefix: NDDF + uri_format: http://purl.bioontology.org/ontology/NDDF/$1 + bioportal: + name: National Drug Data File + prefix: NDDF + description: FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements. + example: '002678' + fairsharing: + abbreviation: NDDF + description: The National Drug Data File vocabulary supports clinical research and patient care. Please note that we have been unable to confirm the current status of NDDF and its relationship with FDB MedKnowledge. Until that time, the FAIRsharing team has marked this resource as having an Uncertain status. Please get in touch if you have any information. + id: '1073' + name: National Drug Data File + prefix: FAIRsharing.8qcbs0 + subjects: + - Biomedical Science + - Medicinal Chemistry + homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF + mappings: + biolink: NDDF + bioportal: NDDF + fairsharing: FAIRsharing.8qcbs0 + name: National Drug Data File + pattern: ^\d{6}$ +ndex: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge. + example: aa78a43f-9c4d-11eb-9e72-0ac135e8bacf + fairsharing: + abbreviation: NDEx + description: NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytoscape as well as programmatic access using a variety of languages including Python and Java and R. NDEx users can easily create accounts or sign in using their Google credentials thanks to the supported open authentication (OAUTH2) method and mint DOIs for their networks to use in publications or include in other resources for long term access. + id: '2533' + name: The Network Data Exchange + prefix: FAIRsharing.8nq9t6 + subjects: + - Life Science + - Microbiology + - Epidemiology + homepage: https://www.ndexbio.org + mappings: + fairsharing: FAIRsharing.8nq9t6 + name: Network Data Exchange + uri_format: https://www.ndexbio.org/viewer/networks/$1 +ndfrt: + bioportal: + name: National Drug File - Reference Terminology + prefix: NDFRT + description: 'NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction].' + example: N0000001662 + fairsharing: + abbreviation: NDFRT + description: The National Drug File Reference Terminology contains a novel reference hierarchy to describe physiologic effects (PE) of drugs. + id: '155' + name: National Drug File + prefix: FAIRsharing.901nkj + subjects: + - Medicine + - Health Science + - Physiology + - Biomedical Science + homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT + mappings: + bioportal: NDFRT + fairsharing: FAIRsharing.901nkj + ontobee: NDF-RT + prefixcommons: ndfrt + name: National Drug File - Reference Terminology + ontobee: + library: Not Specified/No + name: National Drug File Reference Terminology + prefix: NDF-RT + prefixcommons: + bioportal: '1352' + description: National Drug File - Reference Terminology Public Inferred Edition, 2008_03_11 + example: N0000175600 + homepage: http://www.va.gov + name: National Drug File + pattern: ^N\d+$ + prefix: ndfrt + synonyms: + - NUI + - ndf-rt + wikidata: + database: Q21008030 + prefix: P2115 +nemo: + bioportal: + name: Neural ElectroMagnetic Ontology + prefix: NEMO + fairsharing: + abbreviation: NEMO + description: Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource. + id: '30' + name: Neural ElectroMagnetic Ontologies + prefix: FAIRsharing.n66krd + subjects: + - Neurobiology + - Cognitive Neuroscience + - Life Science + mappings: + bioportal: NEMO + fairsharing: FAIRsharing.n66krd + miriam: nemo + miriam: + deprecated: false + description: This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects. + homepage: https://www.nemoarchive.org + id: '00000744' + name: Neuroscience Multi-Omic BRAIN Initiative Data + namespaceEmbeddedInLui: false + pattern: '[a-z]{3}-[a-km-z0-9]{7}' + prefix: nemo + sampleId: smp-m3w9hbe + uri_format: https://assets.nemoarchive.org/$1 +neurolex: + biocontext: + is_identifiers: true + is_obo: false + prefix: NEUROLEX + uri_format: http://identifiers.org/neurolex/$1 + mappings: + biocontext: NEUROLEX + miriam: neurolex + n2t: neurolex + prefixcommons: neurolex + miriam: + deprecated: false + description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). + homepage: http://www.neurolex.org/wiki/Main_Page + id: '00000126' + name: NeuroLex + namespaceEmbeddedInLui: false + pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$ + prefix: neurolex + sampleId: Birnlex_721 + uri_format: http://www.neurolex.org/wiki/$1 + n2t: + description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). + example: Birnlex_721 + homepage: http://www.neurolex.org/wiki/Main_Page + name: NeuroLex Neuroscience Lexicon + namespaceEmbeddedInLui: false + pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$ + prefix: neurolex + uri_format: http://www.neurolex.org/wiki/$1 + prefixcommons: + description: The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). + example: Birnlex_721 + homepage: http://www.neurolex.org/wiki/Main_Page + keywords: + - classification + - neuroscience + - ontology + name: NeuroLex + pattern: ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO)\d+$ + prefix: neurolex + pubmed_ids: + - '18975148' + uri_format: http://www.neurolex.org/wiki/$1 +neuromorpho: + biocontext: + is_identifiers: true + is_obo: false + prefix: NEUROMORPHO + uri_format: http://identifiers.org/neuromorpho/$1 + mappings: + biocontext: NEUROMORPHO + miriam: neuromorpho + n2t: neuromorpho + prefixcommons: neuromorpho + miriam: + deprecated: false + description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. + homepage: http://neuromorpho.org/index.jsp + id: '00000095' + name: NeuroMorpho + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: neuromorpho + sampleId: Rosa2 + uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1 + n2t: + description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. + example: Rosa2 + homepage: http://neuromorpho.org/index.jsp + name: NeuroMorpho + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: neuromorpho + uri_format: http://neuromorpho.org/neuron_info.jsp?neuron_name=$1 + prefixcommons: + description: NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. + example: Rosa2 + homepage: http://neuromorpho.org/neuroMorpho/index.jsp + keywords: + - anatomy + - structure + name: NeuroMorpho + pattern: ^\w+$ + prefix: neuromorpho + pubmed_ids: + - '16552417' + uri_format: http://neuromorpho.org/neuroMorpho/neuron_info.jsp?neuron_name=$1 +neuronames: + description: BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it. + example: '268' + homepage: http://braininfo.rprc.washington.edu/ + mappings: + wikidata: P4394 + name: NeuroNames + pattern: ^\d+$ + references: + - https://en.wikipedia.org/wiki/NeuroNames + synonyms: + - neuroname + uri_format: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1 + wikidata: + prefix: P4394 +neurondb: + biocontext: + is_identifiers: true + is_obo: false + prefix: NEURONDB + uri_format: http://identifiers.org/neurondb/$1 + fairsharing: + abbreviation: NeuronDB + description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' + id: '3281' + name: NeuronDB + prefix: FAIRsharing.45a10e + subjects: + - Cellular Neuroscience + - Neurophysiology + - Neurobiology + - Computational Neuroscience + - Molecular Neuroscience + - Comparative Neurobiology + mappings: + biocontext: NEURONDB + fairsharing: FAIRsharing.45a10e + miriam: neurondb + n2t: neurondb + prefixcommons: neurondb + miriam: + deprecated: false + description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' + homepage: http://senselab.med.yale.edu/NeuronDB/ + id: '00000094' + name: NeuronDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: neurondb + sampleId: '265' + uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1 + n2t: + description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' + example: '265' + homepage: http://senselab.med.yale.edu/NeuronDB/ + name: NeuronDB at SenseLab + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: neurondb + uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1 + prefixcommons: + description: 'NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.' + example: '265' + homepage: http://senselab.med.yale.edu/NeuronDB/ + keywords: + - anatomy + - structure + name: NeuronDB + pattern: ^\d+$ + prefix: neurondb + uri_format: http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1 +neurovault.collection: + biocontext: + is_identifiers: true + is_obo: false + prefix: NEUROVAULT.COLLECTION + uri_format: http://identifiers.org/neurovault.collection/$1 + mappings: + biocontext: NEUROVAULT.COLLECTION + miriam: neurovault.collection + n2t: neurovault.collection + miriam: + deprecated: false + description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images. + homepage: http://neurovault.org + id: '00000635' + name: NeuroVault Collection + namespaceEmbeddedInLui: false + pattern: ^[1-9][0-9]*$ + prefix: neurovault.collection + sampleId: '3304' + uri_format: https://neurovault.org/collections/$1 + n2t: + description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images. + example: '3304' + homepage: http://neurovault.org + name: NeuroVault Collection + namespaceEmbeddedInLui: false + pattern: ^[1-9][0-9]*$ + prefix: neurovault.collection + uri_format: https://neurovault.org/collections/$1 +neurovault.image: + biocontext: + is_identifiers: true + is_obo: false + prefix: NEUROVAULT.IMAGE + uri_format: http://identifiers.org/neurovault.image/$1 + mappings: + biocontext: NEUROVAULT.IMAGE + miriam: neurovault.image + n2t: neurovault.image + miriam: + deprecated: false + description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images. + homepage: http://neurovault.org + id: '00000638' + name: NeuroVault Image + namespaceEmbeddedInLui: false + pattern: ^[1-9][0-9]*$ + prefix: neurovault.image + sampleId: '58788' + uri_format: https://neurovault.org/images/$1 + n2t: + description: Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images. + example: '58788' + homepage: http://neurovault.org + name: NeuroVault + namespaceEmbeddedInLui: false + pattern: ^[1-9][0-9]*$ + prefix: neurovault.image + uri_format: https://neurovault.org/images/$1 +nextdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: NEXTDB + uri_format: http://identifiers.org/nextdb/$1 + fairsharing: + abbreviation: NextDB + description: The Kohara lab has been constructing an expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from the expression pattern project. + id: '2000' + name: Nematode Expression Pattern DataBase + prefix: FAIRsharing.xz5m1a + subjects: + - Life Science + mappings: + biocontext: NEXTDB + fairsharing: FAIRsharing.xz5m1a + miriam: nextdb + n2t: nextdb + ncbi: NextDB + prefixcommons: nextdb + miriam: + deprecated: false + description: NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. + homepage: http://nematode.lab.nig.ac.jp/ + id: '00000289' + name: NEXTDB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: nextdb + sampleId: 6b1 + uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1 + n2t: + description: NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. + example: 6b1 + homepage: http://nematode.lab.nig.ac.jp/ + name: NEXTDB at Shizuoka + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: nextdb + uri_format: http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1 + ncbi: + example: CELK01662 + homepage: http://nematode.lab.nig.ac.jp/ + name: Nematode Expression Pattern DataBase + prefix: NextDB + prefixcommons: + description: The Kohara lab has been constructing an expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from the expression pattern project. + example: C24A3 + homepage: http://nematode.lab.nig.ac.jp/ + keywords: + - gene expression + - genome + - DNA + name: Nematode Expression Pattern DataBase + pattern: ^[A-Z]\d+$ + prefix: nextdb + uri_format: http://nematode.lab.nig.ac.jp/cgi-bin/dbest/SrchByCosmid.sh?csmd=$1 +nextprot: + biocontext: + is_identifiers: true + is_obo: false + prefix: NEXTPROT + uri_format: http://identifiers.org/nextprot/$1 + fairsharing: + abbreviation: neXtProt + description: neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. + id: '1681' + name: neXtProt + prefix: FAIRsharing.62evqh + subjects: + - Proteomics + - Life Science + mappings: + biocontext: NEXTPROT + fairsharing: FAIRsharing.62evqh + miriam: nextprot + n2t: nextprot + uniprot: neXtProt + miriam: + deprecated: false + description: neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. + homepage: https://www.nextprot.org/ + id: '00000236' + name: nextProt + namespaceEmbeddedInLui: false + pattern: ^NX_\w+ + prefix: nextprot + sampleId: NX_O00165 + uri_format: https://www.nextprot.org/db/entry/$1 + n2t: + description: neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. + example: NX_O00165 + homepage: https://www.nextprot.org/ + name: nextProt at Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^NX_\w+ + prefix: nextprot + uri_format: https://www.nextprot.org/db/entry/$1 + synonyms: + - NXP + twitter: neXtProt_news + uniprot: + category: Organism-specific databases + identifier: '161' + link_is_explicit: 'true' + name: neXtProt; the human protein knowledge platform + prefix: neXtProt + uri_format: https://www.nextprot.org/entry/$1 + wikidata: + database: Q6983890 +nextprot.family: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: >- + NeXtProt is a comprehensive human-centric discovery platform, offering its + users a seamless integration of and navigation through protein-related + data. + + (Developed by the SIB Swiss Institute of Bioinformatics) + example: '01406' + homepage: https://www.nextprot.org/ + name: neXtProt family + pattern: ^\d+$ + synonyms: + - NXPFA + twitter: neXtProt_news + uri_format: https://www.nextprot.org/term/FA-$1 +ngl: + biocontext: + is_identifiers: true + is_obo: false + prefix: NGL + uri_format: http://identifiers.org/ngl/$1 + mappings: + biocontext: NGL + miriam: ngl + n2t: ngl + miriam: + deprecated: false + description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. + homepage: https://genelab-data.ndc.nasa.gov/genelab/ + id: '00000618' + name: NASA GeneLab + namespaceEmbeddedInLui: false + pattern: ^GLDS-\d+$ + prefix: ngl + sampleId: GLDS-141 + uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1 + n2t: + description: NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. + example: GLDS-141 + homepage: https://genelab-data.ndc.nasa.gov/genelab/ + name: NASA GeneLab + namespaceEmbeddedInLui: false + pattern: ^GLDS-\d+$ + prefix: ngl + uri_format: https://genelab-data.ndc.nasa.gov/genelab/accession/$1 +nhcdr: + cellosaurus: + category: Cell line collections + homepage: https://stemcells.nindsgenetics.org + name: NINDS Human Cell and Data Repository + prefix: NHCDR + uri_format: https://stemcells.nindsgenetics.org?line=$1 + example: ND50028 + mappings: + cellosaurus: NHCDR +niaest: + biocontext: + is_identifiers: true + is_obo: false + prefix: NIAEST + uri_format: http://identifiers.org/niaest/$1 + fairsharing: + abbreviation: niaEST + description: A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells was assembled. The cDNA libraries are freely distributed to the research community, providing a standard platform for expression studies using microarrays. + id: '2002' + name: NIA Mouse cDNA Project + prefix: FAIRsharing.xwqg9h + subjects: + - Life Science + mappings: + biocontext: NIAEST + fairsharing: FAIRsharing.xwqg9h + miriam: niaest + n2t: niaest + ncbi: niaEST + prefixcommons: niaest + miriam: + deprecated: false + description: A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. + homepage: http://lgsun.grc.nia.nih.gov/cDNA/ + id: '00000305' + name: NIAEST + namespaceEmbeddedInLui: false + pattern: ^\w\d{4}\w\d{2}(\-[35])?$ + prefix: niaest + sampleId: J0705A10 + uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1 + n2t: + description: A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. + example: J0705A10 + homepage: http://lgsun.grc.nia.nih.gov/cDNA/ + name: NIAEST at National Institute on Aging + namespaceEmbeddedInLui: false + pattern: ^\w\d{4}\w\d{2}(\-[35])?$ + prefix: niaest + uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1 + ncbi: + example: L0304H12-3 + homepage: http://esbank.nia.nih.gov/ + name: NIA Mouse cDNA Project + prefix: niaEST + prefixcommons: + description: A searchable mouse cDNA library. + example: J0705A10-3 + homepage: http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html + keywords: + - DNA + name: NIA Mouse cDNA Project + pattern: ^[A-Z,0-9]+$ + prefix: niaest + uri_format: http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1 +nif_cell: + biocontext: + is_identifiers: false + is_obo: true + prefix: NIF_CELL + uri_format: http://purl.obolibrary.org/obo/NIF_CELL_$1 + bioportal: + name: Neuroscience Information Framework (NIF) Cell Ontology + prefix: NIFCELL + mappings: + biocontext: NIF_CELL + bioportal: NIFCELL + obofoundry: nif_cell + obofoundry: + contact: smtifahim@gmail.com + contact.label: Fahim Imam + deprecated: true + description: Neuronal cell types + homepage: http://neuinfo.org/ + name: NIF Cell + prefix: nif_cell +nif_dysfunction: + biocontext: + is_identifiers: false + is_obo: true + prefix: NIF_DYSFUNCTION + uri_format: http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 + mappings: + biocontext: NIF_DYSFUNCTION + obofoundry: nif_dysfunction + obofoundry: + contact: smtifahim@gmail.com + contact.label: Fahim Imam + deprecated: true + homepage: http://neuinfo.org/ + name: NIF Dysfunction + prefix: nif_dysfunction +nif_grossanatomy: + biocontext: + is_identifiers: false + is_obo: true + prefix: NIF_GROSSANATOMY + uri_format: http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 + mappings: + biocontext: NIF_GROSSANATOMY + obofoundry: nif_grossanatomy + obofoundry: + contact: smtifahim@gmail.com + contact.label: Fahim Imam + deprecated: true + homepage: http://neuinfo.org/ + name: NIF Gross Anatomy + prefix: nif_grossanatomy +nihreporter.project: + contributor: + email: benjamin_gyori@hms.harvard.edu + github: bgyori + name: Benjamin Gyori + orcid: 0000-0001-9439-5346 + description: RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding. + example: '10343835' + homepage: https://reporter.nih.gov/ + name: NIH RePORTER + pattern: ^\d+$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: https://reporter.nih.gov/project-details/$1 +nist: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species. + homepage: https://webbook.nist.gov/chemistry/ + name: NIST Chemistry WebBook + no_own_terms: true + synonyms: + - NIST + - NIST Chemistry WebBook +nlm: + biolink: + is_identifiers: false + is_obo: false + prefix: NLMID + uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=$1 + description: Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings. + example: '101775319' + homepage: https://www.ncbi.nlm.nih.gov/nlmcatalog + mappings: + biolink: NLMID + name: National Library of Medicine Catalog + pattern: ^\d+$ + uri_format: https://www.ncbi.nlm.nih.gov/nlmcatalog/$1 +nlxanat: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. + example: '090201' + homepage: https://scicrunch.org/scicrunch/interlex/dashboard + name: NeuroLex Anatomy + part_of: neurolex + pattern: ^\d{6}$ + uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1 +nlxdys: + appears_in: + - mondo + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. + example: '20090303' + homepage: https://scicrunch.org/scicrunch/interlex/dashboard + name: NeuroLex Dysfunction + part_of: neurolex + pattern: ^\d+$ + uri_format: http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1 +nmdc: + contact: + email: donny@polyneme.xyz + github: dwinston + name: Donny Winston + orcid: 0000-0002-8424-0604 + contributor: + email: donny@polyneme.xyz + github: dwinston + name: Donny Winston + orcid: 0000-0002-8424-0604 + description: An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem. + example: y3ax-8bq3-60 + homepage: https://microbiomedata.org/ + mappings: + miriam: nmdc + miriam: + deprecated: false + description: The National Microbiome Data Collaborative (NMDC) is an initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem. + homepage: https://ror.org/02jbv0t02 + id: '00000837' + name: National Microbiome Data Collaborative + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9._~\-\:]+$ + prefix: nmdc + sampleId: 6m4e-1vbv-03 + uri_format: https://drs.microbiomedata.org/objects/$1 + name: National Microbiome Data Collaborative + pattern: ^[\w\-.]{3,}$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: https://drs.microbiomedata.org/objects/$1 + wikidata: + database: Q107698738 +nmr: + biocontext: + is_identifiers: false + is_obo: true + prefix: NMR + uri_format: http://purl.obolibrary.org/obo/NMR_$1 + bioportal: + name: NMR-Controlled Vocabulary + prefix: NMR + download_owl: https://nmrml.org/cv/stable/nmrCV.owl + mappings: + biocontext: NMR + bioportal: NMR + miriam: nmr + n2t: nmr + obofoundry: nmr + ols: nmrcv + prefixcommons: nmr + miriam: + deprecated: false + description: nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. + homepage: https://www.ebi.ac.uk/ols/ontologies/nmrcv + id: '00000639' + name: Nuclear Magnetic Resonance Controlled Vocabulary + namespaceEmbeddedInLui: true + pattern: ^NMR:\d+$ + prefix: nmr + sampleId: '1000003' + uri_format: https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1 + n2t: + description: nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. + example: '1000003' + homepage: https://www.ebi.ac.uk/ols/ontologies/nmrcv + name: NMR through OLS + namespaceEmbeddedInLui: true + pattern: ^NMR:\d+$ + prefix: nmr + uri_format: https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1 + obofoundry: + contact: schober@imbi.uni-freiburg.de + contact.label: Schober Daniel + deprecated: true + description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. + download.owl: http://purl.obolibrary.org/obo/nmr.owl + homepage: http://msi-ontology.sourceforge.net/ + name: NMR-instrument specific component of metabolomics investigations + prefix: nmr + ols: + description: 'This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.' + download: http://nmrml.org/cv/stable/nmrCV.owl + homepage: http://nmrml.org/cv/ + name: nuclear magnetic resonance CV + prefix: nmrcv + version: 1.1.0 + pattern: ^\d+$ + prefixcommons: + bioportal: '1033' + description: Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. + example: NMR_400113 + homepage: http://msi-ontology.sourceforge.net/ + keywords: + - owl + - nmr + name: NMR-instrument specific component of metabolomics investigations + pattern: ^NMR_\d+$ + prefix: nmr + synonyms: + - nmrcv +nmrshiftdb2: + fairsharing: + abbreviation: nmrshiftdb2 + description: nmrshiftdb2 is an NMR database for organic structures and their nuclear magnetic resonance (NMR) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. It also features peer-reviewed submission of datasets by its users. The nmrshiftdb2 software is open source, the data is published under an open content license. + id: '2783' + name: nmrshiftdb2 + prefix: FAIRsharing.nYaZ1N + subjects: + - Analytical Chemistry + mappings: + fairsharing: FAIRsharing.nYaZ1N + miriam: nmrshiftdb2 + miriam: + deprecated: false + description: NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. + homepage: https://nmrshiftdb.nmr.uni-koeln.de + id: '00000748' + name: NMR Shift Database + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: nmrshiftdb2 + sampleId: '234' + uri_format: https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1 +nomen: + bioportal: + name: NOMEN - A nomenclatural ontology for biological names + prefix: NOMEN + example: '0000295' + mappings: + bioportal: NOMEN + obofoundry: nomen + ols: nomen + ontobee: NOMEN + name: A nomenclatural ontology for biological names + obofoundry: + contact: diapriid@gmail.com + contact.github: mjy + contact.label: Matt Yoder + contact.orcid: 0000-0002-5640-5491 + deprecated: false + description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. + download.owl: http://purl.obolibrary.org/obo/nomen.owl + homepage: https://github.com/SpeciesFileGroup/nomen + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: NOMEN - A nomenclatural ontology for biological names + preferredPrefix: NOMEN + prefix: nomen + repository: https://github.com/SpeciesFileGroup/nomen + ols: + description: NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. + download: http://purl.obolibrary.org/obo/nomen.owl + homepage: https://github.com/SpeciesFileGroup/nomen + name: NOMEN - A nomenclatural ontology for biological names + prefix: nomen + version: 2019-04-17 + ontobee: + library: Library + name: NOMEN - A nomenclatural ontology for biological names + prefix: NOMEN + pattern: ^\d{7}$ +noncodev3: + biocontext: + is_identifiers: true + is_obo: false + prefix: NONCODEV3 + uri_format: http://identifiers.org/noncodev3/$1 + mappings: + biocontext: NONCODEV3 + miriam: noncodev3 + n2t: noncodev3 + miriam: + deprecated: false + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. + homepage: http://www.noncode.org/ + id: '00000248' + name: NONCODE v3 + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: noncodev3 + sampleId: '377550' + uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1 + n2t: + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. + example: '377550' + homepage: http://www.noncode.org/ + name: NONCODE at Chinese Academy of Sciences + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: noncodev3 + uri_format: http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1 +noncodev4.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: NONCODEV4.GENE + uri_format: http://identifiers.org/noncodev4.gene/$1 + mappings: + biocontext: NONCODEV4.GENE + miriam: noncodev4.gene + n2t: noncodev4.gene + miriam: + deprecated: false + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. + homepage: http://www.bioinfo.org/NONCODEv4/ + id: '00000480' + name: NONCODE v4 Gene + namespaceEmbeddedInLui: false + pattern: ^NONHSAG\d{5}$ + prefix: noncodev4.gene + sampleId: NONHSAG00001 + uri_format: http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1 + n2t: + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. + example: NONHSAG00001 + homepage: http://www.bioinfo.org/NONCODEv4/ + name: NONCODE v4 Gene at Chinese Academy of Sciences + namespaceEmbeddedInLui: false + pattern: ^NONHSAG\d{5}$ + prefix: noncodev4.gene + uri_format: http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1 +noncodev4.rna: + biocontext: + is_identifiers: true + is_obo: false + prefix: NONCODEV4.RNA + uri_format: http://identifiers.org/noncodev4.rna/$1 + mappings: + biocontext: NONCODEV4.RNA + miriam: noncodev4.rna + n2t: noncodev4.rna + miriam: + deprecated: false + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts. + homepage: http://www.bioinfo.org/NONCODEv4/ + id: '00000481' + name: NONCODE v4 Transcript + namespaceEmbeddedInLui: false + pattern: ^NONHSAT\d{6}$ + prefix: noncodev4.rna + sampleId: NONHSAT000001 + uri_format: http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1 + n2t: + description: NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts. + example: NONHSAT000001 + homepage: http://www.bioinfo.org/NONCODEv4/ + name: NONCODE v4 Transcript at Chinese Academy of Sciences + namespaceEmbeddedInLui: false + pattern: ^NONHSAT\d{6}$ + prefix: noncodev4.rna + uri_format: http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1 +norine: + biocontext: + is_identifiers: true + is_obo: false + prefix: NORINE + uri_format: http://identifiers.org/norine/$1 + fairsharing: + abbreviation: NORINE + description: Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides. + id: '1774' + name: Non-Ribosomal Peptides Database + prefix: FAIRsharing.gf8yhy + subjects: + - Life Science + mappings: + biocontext: NORINE + fairsharing: FAIRsharing.gf8yhy + miriam: norine + n2t: norine + prefixcommons: norine + miriam: + deprecated: false + description: Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. + homepage: http://bioinfo.lifl.fr/norine/ + id: '00000498' + name: NORINE + namespaceEmbeddedInLui: false + pattern: ^NOR\d+$ + prefix: norine + sampleId: NOR00681 + uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1 + n2t: + description: Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. + example: NOR00681 + homepage: http://bioinfo.lifl.fr/norine/ + name: NORINE at Computer Science Laboratory of Lille + namespaceEmbeddedInLui: false + pattern: ^NOR\d+$ + prefix: norine + uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1 + name: Nonribosomal Peptides Database + prefixcommons: + description: Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides. + example: NOR00681 + homepage: http://bioinfo.lifl.fr/norine/ + keywords: + - protein + name: Non-Ribosomal Peptides Database + pattern: ^NOR\d+$ + prefix: norine + uri_format: http://bioinfo.lifl.fr/norine/result.jsp?ID=$1 +novus: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A vendor of antibodies and other biologics + example: nb100-56351 + homepage: https://www.novusbio.com + name: Novus Biologicals + uri_format: https://www.novusbio.com/products/$1 +npass: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: > + Database for integrating species source of natural products & connecting + natural products to biological targets via experimental-derived + quantitative activity data. + example: NPC139585 + homepage: http://bidd.group/NPASS/ + name: Natural Product Activity and Species Source Database + pattern: ^NPC\d+$ +npo: + bioportal: + name: NanoParticle Ontology + prefix: NPO + contact: + email: nathan.baker@pnl.gov + name: Nathan Baker + description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. + example: '1731' + fairsharing: + abbreviation: NPO + description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. + id: '319' + name: NanoParticle Ontology + prefix: FAIRsharing.vy0p71 + subjects: + - Life Science + homepage: https://bioportal.bioontology.org/ontologies/NPO + mappings: + bioportal: NPO + fairsharing: FAIRsharing.vy0p71 + name: NanoParticle Ontology + pattern: ^\d+$ +nuclearbd: + biocontext: + is_identifiers: true + is_obo: false + prefix: NUCLEARBD + uri_format: http://identifiers.org/nuclearbd/$1 + mappings: + biocontext: NUCLEARBD + miriam: nuclearbd + n2t: nuclearbd + miriam: + deprecated: false + description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. + homepage: http://www.receptors.org/nucleardb/ + id: '00000356' + name: NucleaRDB + namespaceEmbeddedInLui: false + pattern: ^\w+\_\w+$ + prefix: nuclearbd + sampleId: prgr_human + uri_format: http://www.receptors.org/nucleardb/proteins/$1 + n2t: + description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. + example: prgr_human + homepage: http://www.receptors.org/nucleardb/ + name: NucleaRDB at Radboud University Nijmegen Medical Centre + namespaceEmbeddedInLui: false + pattern: ^\w+\_\w+$ + prefix: nuclearbd + uri_format: http://www.receptors.org/nucleardb/proteins/$1 +nucleotide: + has_canonical: insdc + mappings: + miriam: nucleotide + miriam: + deprecated: false + description: The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. + homepage: https://www.ncbi.nlm.nih.gov/ + id: '00000882' + name: Nucleotide + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z0-9_\.]+$ + prefix: nucleotide + sampleId: '880798137' + uri_format: https://www.ncbi.nlm.nih.gov/nuccore/$1 +oa: + biocontext: + is_identifiers: false + is_obo: false + prefix: oa + uri_format: http://www.w3.org/ns/oa#$1 + bioportal: + name: Web Annotation Ontology + prefix: OA + description: The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture. + example: sourceDateStart + homepage: http://www.w3.org/ns/oa + mappings: + biocontext: oa + bioportal: OA + name: Web Annotation Ontology + uri_format: http://www.w3.org/ns/oa#$1 +oae: + biocontext: + is_identifiers: false + is_obo: true + prefix: OAE + uri_format: http://purl.obolibrary.org/obo/OAE_$1 + bioportal: + name: Ontology of Adverse Events + prefix: OAE + example: '0002959' + fairsharing: + abbreviation: OAE + description: The Ontology of Adverse Events (OAE) is a community-driven ontology that is developed to standardize and integrate data on biomedical adverse events (e.g., vaccine and drug adverse events) and support computer-assisted reasoning. As a result of a medical intervention, events may occur which lie outside the intended consequences of the intervention. Some of these events are adverse events, in the sense that they are pathological bodily processes. For many such adverse events it is unclear whether they are causal consequences of the medical intervention which preceded them, since adverse events may also occur due to other reasons (for example a natural viral infection). OAE was created to represent the whole process from initial medical intervention to subsequent outcomes. + id: '763' + name: Ontology of Adverse Events + prefix: FAIRsharing.tw4q8x + subjects: + - Biomedical Science + mappings: + biocontext: OAE + bioportal: OAE + fairsharing: FAIRsharing.tw4q8x + obofoundry: oae + ols: oae + ontobee: OAE + obofoundry: + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqunh He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: A biomedical ontology in the domain of adverse events + download.owl: http://purl.obolibrary.org/obo/oae.owl + homepage: https://github.com/OAE-ontology/OAE/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Ontology of Adverse Events + preferredPrefix: OAE + prefix: oae + repository: https://github.com/OAE-ontology/OAE + ols: + description: The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. + download: http://purl.obolibrary.org/obo/oae.owl + homepage: https://github.com/OAE-ontology/OAE/ + name: 'OAE: Ontology of Adverse Events' + prefix: oae + version: 1.2.44 + ontobee: + library: Library + name: Ontology of Adverse Events + prefix: OAE + pattern: ^\d{7}$ +oarcs: + biocontext: + is_identifiers: false + is_obo: true + prefix: OARCS + uri_format: http://purl.obolibrary.org/obo/OARCS_$1 + bioportal: + name: Ontology of Arthropod Circulatory Systems + prefix: OARCS + example: '0000029' + fairsharing: + abbreviation: OArCS + description: OArCS is a structural model for the description of anatomical features (morphemes) using ontologies. Its domain is the Arthropod ciruclatory system. This ontology has not been updated recently, and therefore has been marked as uncertain. Please get in touch with us if you have any information. + id: '579' + name: Ontology of Arthropod Circulatory Systems + prefix: FAIRsharing.yqn857 + subjects: + - Anatomy + - Angiology + mappings: + biocontext: OARCS + bioportal: OARCS + fairsharing: FAIRsharing.yqn857 + obofoundry: oarcs + ols: oarcs + ontobee: OARCS + obofoundry: + contact: mjyoder@illinois.edu + contact.github: mjy + contact.label: Matt Yoder + contact.orcid: 0000-0002-5640-5491 + deprecated: false + description: OArCS is an ontology describing the Arthropod ciruclatory system. + download.owl: http://purl.obolibrary.org/obo/oarcs.owl + homepage: https://github.com/aszool/oarcs + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Ontology of Arthropod Circulatory Systems + preferredPrefix: OARCS + prefix: oarcs + repository: https://github.com/aszool/oarcs + ols: + description: OArCS is an ontology describing the Arthropod ciruclatory system. + download: http://purl.obolibrary.org/obo/oarcs.owl + homepage: https://github.com/aszool/oarcs + name: Ontology of Arthropod Circulatory Systems + prefix: oarcs + version: 2019-04-18 + version.iri: http://purl.obolibrary.org/obo/hao/2019-04-18/hao.owl + ontobee: + library: Library + name: Ontology of Arthropod Circulatory Systems + prefix: OARCS + pattern: ^\d{7}$ +oba: + biocontext: + is_identifiers: false + is_obo: true + prefix: OBA + uri_format: http://purl.obolibrary.org/obo/OBA_$1 + bioportal: + name: Ontology of Biological Attributes + prefix: OBA + example: '0000001' + fairsharing: + abbreviation: OBA + description: A collection of biological attributes / traits covering all kingdoms of life. It is interoperable with a number of other community ontologies. + id: '634' + name: Ontology of Biological Attributes + prefix: FAIRsharing.mp0rwf + subjects: + - Biology + mappings: + biocontext: OBA + bioportal: OBA + fairsharing: FAIRsharing.mp0rwf + obofoundry: oba + ols: oba + ontobee: OBA + obofoundry: + appears_in: + - fovt + contact: cjmungall@lbl.gov + contact.github: cmungall + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + deprecated: false + description: A collection of biological attributes (traits) covering all kingdoms of life. + download.obo: http://purl.obolibrary.org/obo/oba.obo + download.owl: http://purl.obolibrary.org/obo/oba.owl + homepage: https://github.com/obophenotype/bio-attribute-ontology + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Ontology of Biological Attributes + preferredPrefix: OBA + prefix: oba + repository: https://github.com/obophenotype/bio-attribute-ontology + ols: + description: A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. + download: http://purl.obolibrary.org/obo/oba.owl + homepage: https://github.com/obophenotype/bio-attribute-ontology + name: Ontology of Biological Attributes (OBA) + prefix: oba + version: 2021-12-03 + version.iri: http://purl.obolibrary.org/obo/oba/releases/2021-12-03/oba.owl + ontobee: + library: Library + name: Ontology of Biological Attributes + prefix: OBA + pattern: ^\d{7}$ +obcs: + biocontext: + is_identifiers: false + is_obo: true + prefix: OBCS + uri_format: http://purl.obolibrary.org/obo/OBCS_$1 + bioportal: + name: Ontology of Biological and Clinical Statistics + prefix: OBCS + example: '0000121' + fairsharing: + abbreviation: OBCS + description: The Ontology of Biological and Clinical Statistics (OBCS) is a biomedical ontology in the domain of biological and clinical statistics. OBCS is primarily targeted for statistical representation in the fields in biological, biomedical, and clinical domains. OBCS uses the Basic Formal Ontology (BFO) as the upper level ontology. OBCS imports all biostatistics related terms in the Ontology for Biomedical Investigations (OBI) including all logical axioms. + id: '1185' + name: Ontology of Biological and Clinical Statistics + prefix: FAIRsharing.5p12xh + subjects: + - Medicine + - Statistics + - Biomedical Science + - Biology + - Medical Informatics + mappings: + biocontext: OBCS + bioportal: OBCS + fairsharing: FAIRsharing.5p12xh + obofoundry: obcs + ols: obcs + ontobee: OBCS + obofoundry: + contact: jiezheng@pennmedicine.upenn.edu + contact.github: zhengj2007 + contact.label: Jie Zheng + contact.orcid: 0000-0002-2999-0103 + deprecated: false + description: A biomedical ontology in the domain of biological and clinical statistics. + download.owl: http://purl.obolibrary.org/obo/obcs.owl + homepage: https://github.com/obcs/obcs + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Ontology of Biological and Clinical Statistics + preferredPrefix: OBCS + prefix: obcs + repository: https://github.com/obcs/obcs + ols: + description: 'OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ' + download: http://purl.obolibrary.org/obo/obcs.owl + homepage: https://github.com/obcs/obcs + name: Ontology of Biological and Clinical Statistics + prefix: obcs + version: '101' + version.iri: http://purl.obolibrary.org/obo/obcs/2018-02-22/obcs.owl + ontobee: + library: Library + name: Ontology of Biological and Clinical Statistics + prefix: OBCS + pattern: ^\d{7}$ +obi: + biocontext: + is_identifiers: false + is_obo: true + prefix: OBI + uri_format: http://purl.obolibrary.org/obo/OBI_$1 + bioportal: + name: Ontology for Biomedical Investigations + prefix: OBI + download_obo: https://github.com/obi-ontology/obi/raw/master/views/obi.obo + example: '0400109' + fairsharing: + abbreviation: OBI + description: The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI fosters clear communication about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more. + id: '1488' + name: Ontology for Biomedical Investigations + prefix: FAIRsharing.284e1z + subjects: + - Functional Genomics + - Life Science + - Biomedical Science + go: + homepage: http://obi-ontology.org/ + name: Ontology for Biomedical Investigations + prefix: OBI + mappings: + biocontext: OBI + bioportal: OBI + fairsharing: FAIRsharing.284e1z + go: OBI + miriam: obi + n2t: obi + obofoundry: obi + ols: obi + ontobee: OBI + prefixcommons: obi + miriam: + deprecated: false + description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). + homepage: http://www.ontobee.org/ + id: '00000127' + name: Ontology for Biomedical Investigations + namespaceEmbeddedInLui: false + pattern: (^OBI:\d{7}$)|(^OBI_\d{7}$) + prefix: obi + sampleId: OBI_0000070 + uri_format: http://purl.obolibrary.org/obo/$1 + n2t: + description: The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). + example: OBI_0000070 + homepage: http://www.ontobee.org/ + name: OBI through Ontobee + namespaceEmbeddedInLui: false + pattern: (^OBI:\d{7}$)|(^OBI_\d{7}$) + prefix: obi + uri_format: http://purl.obolibrary.org/obo/$1 + obofoundry: + appears_in: + - agro + - foodon + - hso + - labo + - mco + - one + - ons + - rbo + - scdo + contact: bpeters@lji.org + contact.github: bpeters42 + contact.label: Bjoern Peters + contact.orcid: 0000-0002-8457-6693 + deprecated: false + description: An integrated ontology for the description of life-science and clinical investigations + download.obo: http://purl.obolibrary.org/obo/obi.obo + download.owl: http://purl.obolibrary.org/obo/obi.owl + homepage: http://obi-ontology.org + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Ontology for Biomedical Investigations + preferredPrefix: OBI + prefix: obi + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/27128319 + title: The Ontology for Biomedical Investigations + repository: https://github.com/obi-ontology/obi + ols: + description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. + download: http://purl.obolibrary.org/obo/obi.owl + homepage: http://obi-ontology.org + name: Ontology for Biomedical Investigations + prefix: obi + version: 2022-01-03 + version.iri: http://purl.obolibrary.org/obo/obi/2022-01-03/obi.owl + ontobee: + library: Foundry + name: Ontology for Biomedical Investigations + prefix: OBI + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1123' + description: The Ontology for Biomedical Investigations (OBI) an ontology of investigations, the protocols and instrumentation used, the material used, the data generated and the types of analysis performed on it. + example: OBI_0000011 + homepage: http://purl.obolibrary.org/obo/obi + keywords: + - ontology + name: Ontology for Biomedical Investigations + pattern: ^OBI_\d{7}$ + prefix: obi + uri_format: http://purl.obolibrary.org/obo/$1 + uri_format: http://purl.obolibrary.org/obo/OBI_$1 +obib: + biocontext: + is_identifiers: false + is_obo: true + prefix: OBIB + uri_format: http://purl.obolibrary.org/obo/OBIB_$1 + bioportal: + name: Ontology for Biobanking + prefix: OBIB + example: '0000389' + fairsharing: + abbreviation: OBIB + description: The ontology for Biobanking (OBIB) is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigations (OBI) using Basic Formal Ontology (BFO) as top ontology and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology. + id: '1455' + name: Ontology for Biobanking + prefix: FAIRsharing.bxc508 + subjects: + - Health Science + mappings: + biocontext: OBIB + bioportal: OBIB + fairsharing: FAIRsharing.bxc508 + obofoundry: obib + ols: obib + ontobee: OBIB + obofoundry: + contact: jiezheng@pennmedicine.upenn.edu + contact.github: zhengj2007 + contact.label: Jie Zheng + contact.orcid: 0000-0002-2999-0103 + deprecated: false + description: An ontology built for annotation and modeling of biobank repository and biobanking administration + download.owl: http://purl.obolibrary.org/obo/obib.owl + homepage: https://github.com/biobanking/biobanking + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Ontology for Biobanking + preferredPrefix: OBIB + prefix: obib + repository: https://github.com/biobanking/biobanking + ols: + description: The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. + download: http://purl.obolibrary.org/obo/obib.owl + homepage: https://github.com/biobanking/biobanking + name: Ontology for BIoBanking (OBIB) + prefix: obib + version: 2021-11-12 + version.iri: http://purl.obolibrary.org/obo/obib/2021-11-12/obib.owl + ontobee: + library: Library + name: Ontology for Biobanking + prefix: OBIB + pattern: ^\d{7}$ +obo: + biocontext: + is_identifiers: false + is_obo: true + prefix: OBO + uri_format: http://purl.obolibrary.org/obo/$1 + description: Community development of interoperable ontologies for the biological sciences + fairsharing: + abbreviation: OBO + description: The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups. + id: '2600' + name: OBO Foundry + prefix: FAIRsharing.847069 + subjects: + - Ontology and Terminology + homepage: http://www.obofoundry.org/ + mappings: + biocontext: OBO + fairsharing: FAIRsharing.847069 + name: Internal OBO and PyOBO Relations +oboformat: + biolink: + is_identifiers: false + is_obo: false + prefix: oboformat + uri_format: http://www.geneontology.org/formats/oboInOwl#$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Related to the OBO in OWL meta-model + example: alt_id + fairsharing: + abbreviation: OBO Format + description: The first part of this specification describes the syntax and structure of OBO Format using BNF. This states how strings of characters in OBOF Files are parsed into abstract OBO documents, and describes constraints on the structure of these documents. The second part of this specification describes the semantics of an OBO document via a mapping to OWL2-DL and community metadata vocabularies. + id: '344' + name: OBO Format Syntax and Semantics + prefix: FAIRsharing.aa0eat + subjects: + - Life Science + homepage: https://github.com/geneontology/go-ontology/tree/master/contrib + mappings: + biolink: oboformat + fairsharing: FAIRsharing.aa0eat + name: OBO Format + preferred_prefix: oboFormat + repository: https://github.com/geneontology/go-ontology +oboinowl: + biocontext: + is_identifiers: false + is_obo: false + prefix: OIO + uri_format: http://www.geneontology.org/formats/oboInOwl#$1 + description: This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties + download_obo: https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo + example: hasDbXref + homepage: https://github.com/geneontology/go-ontology/tree/master/contrib + mappings: + biocontext: OIO + name: OBO in OWL + preferred_prefix: oboInOwl + repository: https://github.com/geneontology/go-ontology + synonyms: + - oio + uri_format: http://www.geneontology.org/formats/oboInOwl#$1 +occ: + mappings: + miriam: occ + n2t: occ + miriam: + deprecated: false + description: The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law. + homepage: https://w3id.org/oc/corpus + id: '00000693' + name: OpenCitations Corpus + namespaceEmbeddedInLui: false + pattern: ^[a-z][a-z]/[0-9]+$ + prefix: occ + sampleId: br/1 + uri_format: https://w3id.org/oc/corpus/$1 + n2t: + description: The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law. + example: br/1 + homepage: https://w3id.org/oc/corpus + name: OpenCitations Corpus + namespaceEmbeddedInLui: false + pattern: ^[a-z][a-z]/[0-9]+$ + prefix: occ + uri_format: https://w3id.org/oc/corpus/$1 +oci: + biocontext: + is_identifiers: true + is_obo: false + prefix: OCI + uri_format: http://identifiers.org/oci/$1 + mappings: + biocontext: OCI + miriam: oci + n2t: oci + miriam: + deprecated: false + description: "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings." + homepage: http://opencitations.net + id: '00000660' + name: OCI + namespaceEmbeddedInLui: false + pattern: ^[0-9]+-[0-9]+$ + prefix: oci + sampleId: 1-18 + uri_format: https://w3id.org/oc/oci/$1 + n2t: + description: 'Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information. OCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus. OCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312. OCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.' + example: 1-18 + homepage: http://opencitations.net + name: OpenCitations + namespaceEmbeddedInLui: false + pattern: ^[0-9]+-[0-9]+$ + prefix: oci + uri_format: https://w3id.org/oc/oci/$1 + name: Open Citation Identifier +ocid: + banana: ocid + mappings: + miriam: ocid + miriam: + deprecated: false + description: "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology." + homepage: https://ontochem.com/ + id: '00000738' + name: Ontology Concept Identifiers + namespaceEmbeddedInLui: true + pattern: ocid:[0-9]{12} + prefix: ocid + sampleId: '190000021540' + uri_format: https://ocid.ontochem.com/prefname?ocid=$1 + pattern: ^[0-9]{12}$ +oclc: + biocontext: + is_identifiers: true + is_obo: false + prefix: OCLC + uri_format: http://identifiers.org/oclc/$1 + mappings: + biocontext: OCLC + miriam: oclc + n2t: oclc + miriam: + deprecated: false + description: The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information. + homepage: https://www.oclc.org/en/about.html + id: '00000669' + name: Online Computer Library Center (OCLC) WorldCat + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: oclc + sampleId: '634515043' + uri_format: https://www.worldcat.org/oclc/$1 + n2t: + description: The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information. + example: '634515043' + homepage: https://www.oclc.org/en/about.html + name: Online Computer Library Center (OCLC) WorldCat + namespaceEmbeddedInLui: false + pattern: ^[0-9]+$ + prefix: oclc + uri_format: https://www.worldcat.org/oclc/$1 + name: Online Computer Library Center WorldCat +odam: + mappings: + miriam: odam + miriam: + deprecated: false + description: Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed. + homepage: https://metabolome.cgfb.u-bordeaux.fr/ + id: '00000722' + name: Open Data for Access and Mining + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: odam + sampleId: frim1 + uri_format: http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1 +odc.sci: + fairsharing: + abbreviation: ODC-SCI + description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. There are several challenges for scientific reproducibility and bench-to-bedside translation. For example, only research and data that are published actually get disseminated, a phenomenon known as publication bias. Published research reflects to only a small fraction of all data collected, and data that do not lead to publication are largely ignored, hidden away in filing cabinets and hard drives. This results in an abundance of inaccessible scientific data known as “dark data”. Even when research is disseminated, it is usually in the form of summary reports of aggregated data (e.g. averages across individual subjects) such as scientific articles. The fact that the individual subject-level data are inaccessible further contributes to dark data. The spinal cord injury (SCI) community created the ODC-SCI to mitigate dark data in SCI research. The ODC-SCI also aims to increase transparency with individual-level data, enhance collaboration, facilitate advanced analytics, and conform to increasing mandates by funders and publishers to make data accessible. Members of the ODC-SCI have access to a private digital lab space managed by the PI or multi-PIs for dataset storage and sharing. The PIs can share their labs’ datasets with the registered members of the ODC-SCI community and make their datasets public and citable. The ODC-SCI implements stewardship principles that scientific data be made FAIR (Findable, Accessible, Interoperable and Reusable) and has been widely adopted by the international SCI research community. + id: '3307' + name: Open Data Commons for Spinal Cord Injury + prefix: FAIRsharing.M6Ruz3 + subjects: + - Neurobiology + - Neurology + - Biomedical Science + - Neuroscience + mappings: + fairsharing: FAIRsharing.M6Ruz3 + miriam: odc.sci + miriam: + deprecated: false + description: The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. + homepage: https://odc-sci.org + id: '00000804' + name: Open Data Commons for Spinal Cord Injury + namespaceEmbeddedInLui: false + pattern: ^[0-9]*$ + prefix: odc.sci + sampleId: '602' + uri_format: https://odc-sci.org/data/$1 +odc.tbi: + mappings: + miriam: odc.tbi + miriam: + deprecated: false + description: The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data. + homepage: https://odc-tbi.org + id: '00000816' + name: Open Data Commons for Traumatic Brain Injury + namespaceEmbeddedInLui: false + pattern: ^[0-9]*$ + prefix: odc.tbi + sampleId: '408' + uri_format: https://odc-tbi.org/data/$1 +odor: + biocontext: + is_identifiers: true + is_obo: false + prefix: ODOR + uri_format: http://identifiers.org/odor/$1 + mappings: + biocontext: ODOR + miriam: odor + n2t: odor + miriam: + deprecated: false + description: OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors + homepage: http://senselab.med.yale.edu/OdorDB + id: '00000500' + name: Odor Molecules DataBase + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: odor + sampleId: '74' + uri_format: http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5 + n2t: + description: OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors + example: '74' + homepage: http://senselab.med.yale.edu/OdorDB + name: Odor Molecules DataBase at Yale University School of Medicine + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: odor + uri_format: http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5 +ogg: + biocontext: + is_identifiers: false + is_obo: true + prefix: OGG + uri_format: http://purl.obolibrary.org/obo/OGG_$1 + bioportal: + name: Ontology of Genes and Genomes + prefix: OGG + example: '3000887619' + fairsharing: + abbreviation: OGG + description: OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms. Each gene in OGG has over 10 annotation items, includes gene-associated Gene Ontology (GO) and PubMed article information. OGG has represented genes in human, two viruses, and four bacteria. Additionally, 7 OGG subsets are developed to represent genes and genomes of 7 model systems including mouse, fruit fly, zebrafish, yeast, A. thaliana, C. elegans, and P. falciparum. + id: '363' + name: Ontology of Genes and Genomes + prefix: FAIRsharing.zmx7nn + subjects: + - Life Science + - Biology + mappings: + biocontext: OGG + bioportal: OGG + fairsharing: FAIRsharing.zmx7nn + obofoundry: ogg + ols: ogg + ontobee: OGG + obofoundry: + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqun Oliver He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: A formal ontology of genes and genomes of biological organisms. + download.owl: http://purl.obolibrary.org/obo/ogg.owl + homepage: https://bitbucket.org/hegroup/ogg + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: The Ontology of Genes and Genomes + preferredPrefix: OGG + prefix: ogg + repository: https://bitbucket.org/hegroup/ogg + ols: + description: 'OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ' + download: http://purl.obolibrary.org/obo/ogg.owl + homepage: https://bitbucket.org/hegroup/ogg + name: 'OGG: Ontology of Genes and Genomes' + prefix: ogg + version: 1.0.59 + ontobee: + library: Library + name: The Ontology of Genes and Genomes + prefix: OGG + pattern: ^\d+$ +ogi: + biocontext: + is_identifiers: false + is_obo: true + prefix: OGI + uri_format: http://purl.obolibrary.org/obo/OGI_$1 + bioportal: + name: Ontology for Genetic Interval + prefix: OGI + deprecated: true + example: '0000019' + homepage: https://code.google.com/archive/p/ontology-for-genetic-interval/ + mappings: + biocontext: OGI + bioportal: OGI + obofoundry: ogi + ols: ogi + ontobee: OGI + obofoundry: + deprecated: true + description: An ontology that formalizes the genomic element by defining an upper class genetic interval + download.owl: http://purl.obolibrary.org/obo/ogi.owl + homepage: https://code.google.com/p/ontology-for-genetic-interval/ + name: Ontology for genetic interval + prefix: ogi + ols: + description: >+ + OGI formalized the genomic element by defining an upper class 'genetic + interval'. + + + The definition of 'genetic interval' is "the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture." + + + Related paper: + + + 1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology) + + Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf) + + Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF) + + + download: http://purl.obolibrary.org/obo/ogi.owl + homepage: https://code.google.com/p/ontology-for-genetic-interval/ + name: Ontology for genetic interval + prefix: ogi + version: '2.0' + ontobee: + library: Library + name: Ontology for genetic interval + prefix: OGI + pattern: ^\d{7}$ + synonyms: + - OGI.owl +ogms: + biocontext: + is_identifiers: false + is_obo: true + prefix: OGMS + uri_format: http://purl.obolibrary.org/obo/OGMS_$1 + bioportal: + name: Ontology for General Medical Science + prefix: OGMS + example: '0000031' + fairsharing: + abbreviation: OGMS + description: "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies." + id: '431' + name: Ontology for General Medical Science + prefix: FAIRsharing.rvz0m9 + subjects: + - Medicine + - Biomedical Science + mappings: + biocontext: OGMS + bioportal: OGMS + fairsharing: FAIRsharing.rvz0m9 + obofoundry: ogms + ols: ogms + ontobee: OGMS + obofoundry: + appears_in: + - labo + - scdo + contact: baeverma@jcvi.org + contact.github: BAevermann + contact.label: Brian Aevermann + contact.orcid: 0000-0003-1346-1327 + deprecated: false + description: An ontology for representing treatment of disease and diagnosis and on carcinomas and other pathological entities + download.owl: http://purl.obolibrary.org/obo/ogms.owl + homepage: https://github.com/OGMS/ogms + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Ontology for General Medical Science + preferredPrefix: OGMS + prefix: ogms + repository: https://github.com/OGMS/ogms + ols: + description: >- + The Ontology for General Medical Science (OGMS) is an ontology of entities + involved in a clinical encounter. OGMS includes very general terms that + are used across medical disciplines, including: 'disease', 'disorder', + 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS + uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope + of OGMS is restricted to humans, but many terms can be applied to a + variety of organisms. OGMS provides a formal theory of disease that can be + further elaborated by specific disease ontologies. This theory is + implemented using OWL-DL and OBO Relation Ontology relations and is + available in OWL and OBO formats. + + + OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + download: http://purl.obolibrary.org/obo/ogms.owl + homepage: https://github.com/OGMS/ogms + name: Ontology for General Medical Science + prefix: ogms + version: 2021-08-19 + version.iri: http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl + ontobee: + library: Library + name: Ontology for General Medical Science + prefix: OGMS + pattern: ^\d{7}$ + synonyms: + - ogms/OMRE + wikidata: + database: Q4866972 +ogsf: + biocontext: + is_identifiers: false + is_obo: true + prefix: OGSF + uri_format: http://purl.obolibrary.org/obo/OGSF_$1 + bioportal: + name: Ontology for Genetic Susceptibility Factor + prefix: OGSF + example: '0000025' + fairsharing: + abbreviation: OGSF + description: "Ontology for Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO 2.0's framework. The ontology is under the domain of genetic epidemiology. OGSF is built from a combination of three ontologies: the Ontology of Geographical Region (OGR), the Ontology of Glucose Metabolism (OGMD), and the Ontology of Genetic Disease Investigations (OGDI)." + id: '445' + name: Ontology for Genetic Susceptibility Factor + prefix: FAIRsharing.egv2cz + subjects: + - Genetics + - Biomedical Science + - Epidemiology + mappings: + biocontext: OGSF + bioportal: OGSF + fairsharing: FAIRsharing.egv2cz + obofoundry: ogsf + ols: ogsf + ontobee: OGSF + obofoundry: + contact: linikujp@gmail.com + contact.github: linikujp + contact.label: Asiyah Yu Lin + contact.orcid: 0000-0002-5379-5359 + deprecated: false + description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. + download.owl: http://purl.obolibrary.org/obo/ogsf.owl + homepage: https://github.com/linikujp/OGSF + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Ontology of Genetic Susceptibility Factor + preferredPrefix: OGSF + prefix: ogsf + repository: https://github.com/linikujp/OGSF + ols: + description: An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. + download: http://purl.obolibrary.org/obo/ogsf.owl + homepage: https://code.google.com/p/ogsf/ + name: Ontology of Genetic Susceptibility Factor + prefix: ogsf + version: '2.0' + ontobee: + library: Library + name: Ontology of Genetic Susceptibility Factor + prefix: OGSF + pattern: ^\d{7}$ +ohd: + biocontext: + is_identifiers: false + is_obo: true + prefix: OHD + uri_format: http://purl.obolibrary.org/obo/OHD_$1 + bioportal: + name: The Oral Health and Disease Ontology + prefix: OHD + example: '0000006' + fairsharing: + abbreviation: OHD + description: The Oral Health and Disease Ontology is intended as a BFO and OBO Foundry compliant ontology for the oral health domain. It is currently used to represent the content of dental practice health records and is intended to be further developed for use in translation medicine. It demonstrates a principled split between billing codes as information entities and what the codes are about, such as dental procedures, materials, and patients. OHD is structured using BFO uses terms from OGMS, OBI, IAO and FMA. In addition it uses terms from CARO, OMRSE, NCBITaxon, and a subset of terms from the Current Dental Terminology (CDT) OHD is in early development and subject to change without notice. + id: '1453' + name: The Oral Health and Disease Ontology + prefix: FAIRsharing.bg7bb6 + subjects: [] + mappings: + biocontext: OHD + bioportal: OHD + fairsharing: FAIRsharing.bg7bb6 + obofoundry: ohd + ols: ohd + ontobee: OHD + obofoundry: + contact: wdduncan@gmail.com + contact.github: wdduncan + contact.label: Bill Duncan + contact.orcid: 0000-0001-9625-1899 + deprecated: false + description: The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. + download.owl: http://purl.obolibrary.org/obo/ohd.owl + homepage: https://purl.obolibrary.org/obo/ohd/home + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Oral Health and Disease Ontology + preferredPrefix: OHD + prefix: ohd + repository: https://github.com/oral-health-and-disease-ontologies/ohd-ontology + ols: + description: The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. + download: http://purl.obolibrary.org/obo/ohd.owl + homepage: https://purl.obolibrary.org/obo/ohd/home + name: Oral Health and Disease Ontology + prefix: ohd + version: 2016-06-27 + version.iri: http://purl.obolibrary.org/obo/2016-06-27/ohd-inferred.owl + ontobee: + library: Library + name: The Oral Health and Disease Ontology + prefix: OHD + pattern: ^\d{7}$ +ohmi: + biocontext: + is_identifiers: false + is_obo: true + prefix: OHMI + uri_format: http://purl.obolibrary.org/obo/OHMI_$1 + bioportal: + name: Ontology of Host-Microbe Interactions + prefix: OHMI + example: '0000460' + fairsharing: + abbreviation: OHMI + description: OHMI is aimed to ontologically represent various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. + id: '166' + name: Ontology of Host-Microbe Interactions + prefix: FAIRsharing.cz9cnp + subjects: + - Life Science + mappings: + biocontext: OHMI + bioportal: OHMI + fairsharing: FAIRsharing.cz9cnp + obofoundry: ohmi + ols: ohmi + ontobee: OHMI + obofoundry: + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqun Oliver He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: The Ontology of Host-Microbiome Interactions aims to ontologically represent and standardize various entities and relations related to microbiomes, microbiome host organisms (e.g., human and mouse), and the interactions between the hosts and microbiomes at different conditions. + download.owl: http://purl.obolibrary.org/obo/ohmi.owl + homepage: https://github.com/ohmi-ontology/ohmi + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Ontology of Host-Microbiome Interactions + preferredPrefix: OHMI + prefix: ohmi + repository: https://github.com/ohmi-ontology/ohmi + ols: + description: OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. + download: http://purl.obolibrary.org/obo/ohmi.owl + homepage: https://github.com/ohmi-ontology/ohmi + name: 'OHMI: Ontology of Host-Microbiome Interactions' + prefix: ohmi + version: 2019-09-17 + version.iri: http://purl.obolibrary.org/obo/ohmi/2019-09-17/ohmi.owl + ontobee: + library: Library + name: Ontology of Host-Microbiome Interactions + prefix: OHMI + pattern: ^\d{7}$ +ohpi: + bioportal: + name: Ontology of Host-Pathogen Interactions + prefix: OHPI + example: '9001411' + fairsharing: + abbreviation: OHPI + description: OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is also developed to represent manually curated HPI knowledge available in the PHIDIAS resource. + id: '1295' + name: Ontology of Host-Pathogen Interactions + prefix: FAIRsharing.vxpUJ6 + subjects: + - Bioinformatics + - Biomedical Science + mappings: + bioportal: OHPI + fairsharing: FAIRsharing.vxpUJ6 + obofoundry: ohpi + ols: ohpi + ontobee: OHPI + obofoundry: + contact: edong@umich.edu + contact.github: e4ong1031 + contact.label: Edison Ong + contact.orcid: 0000-0002-5159-414X + deprecated: false + description: OHPI is a community-driven ontology of host-pathogen interactions (OHPI) and represents the virulence factors (VFs) and how the mutants of VFs in the Victors database become less virulence inside a host organism or host cells. It is developed to represent manually curated HPI knowledge available in the PHIDIAS resource. + download.owl: http://purl.obolibrary.org/obo/ohpi.owl + homepage: https://github.com/OHPI/ohpi + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Ontology of Host Pathogen Interactions + preferredPrefix: OHPI + prefix: ohpi + repository: https://github.com/OHPI/ohpi + ols: + description: OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). + download: http://purl.obolibrary.org/obo/ohpi.owl + homepage: https://github.com/OHPI/ohpi + name: 'OHPI: Ontology of Host-Pathogen Interactions' + prefix: ohpi + version: 2019-10-02 + version.iri: http://purl.obolibrary.org/obo/ohpi/releases/2019-09-30 + ontobee: + library: Library + name: Ontology of Host Pathogen Interactions + prefix: OHPI + pattern: ^\d+$ +oid: + mappings: + miriam: oid + n2t: oid + miriam: + deprecated: false + description: OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes. + homepage: http://www.oid-info.com/introduction.htm + id: '00000673' + name: OID Repository + namespaceEmbeddedInLui: false + pattern: ^[\d.]+$ + prefix: oid + sampleId: 2.16.840 + uri_format: http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display + n2t: + description: OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes. + example: 2.16.840 + homepage: http://www.oid-info.com/introduction.htm + name: OID Repository + namespaceEmbeddedInLui: false + pattern: ^[\d.]+$ + prefix: oid + uri_format: http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display +olatdv: + biocontext: + is_identifiers: false + is_obo: true + prefix: OLATDV + uri_format: http://purl.obolibrary.org/obo/OLATDV_$1 + bioportal: + name: Medaka Developmental Stages + prefix: OLATDV + example: '0000210' + fairsharing: + abbreviation: OlatDv + description: Life cycle stages for Medaka. OlatDv is based on the original medaka stage ontology MFO by Thorsten Henrich. Currently it includes only pre-adult stages. + id: '600' + name: Medaka Stage Ontology + prefix: FAIRsharing.c86z66 + subjects: + - Aquaculture + - Developmental Biology + - Life Science + mappings: + biocontext: OLATDV + bioportal: OLATDV + fairsharing: FAIRsharing.c86z66 + obofoundry: olatdv + ols: olatdv + ontobee: OLATDV + obofoundry: + contact: frederic.bastian@unil.ch + contact.github: fbastian + contact.label: Frédéric Bastian + contact.orcid: 0000-0002-9415-5104 + deprecated: false + description: Life cycle stages for Medaka + download.obo: http://purl.obolibrary.org/obo/olatdv.obo + download.owl: http://purl.obolibrary.org/obo/olatdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Medaka Developmental Stages + preferredPrefix: OlatDv + prefix: olatdv + repository: https://github.com/obophenotype/developmental-stage-ontologies + ols: + description: Life cycle stages for Medaka + download: http://purl.obolibrary.org/obo/olatdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv + name: Medaka Developmental Stages + prefix: olatdv + version: 2020-03-10 + version.iri: http://purl.obolibrary.org/obo/olatdv/releases/2020-03-10/olatdv.owl + ontobee: + library: Library + name: Medaka Developmental Stages + prefix: OLATDV + pattern: ^\d{7}$ +om: + bioportal: + name: Ontology of units of Measure + prefix: OM + example: Dimension + mappings: + bioportal: OM + ols: om + name: Ontology of units of Measure + ols: + contact: hajo.rijgersberg@wur.nl + description: 'The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging' + download: https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf + homepage: https://github.com/HajoRijgersberg/OM + name: Ontology of units of Measure (OM) + prefix: om + version: 2.0.35 + repository: https://github.com/HajoRijgersberg/OM +oma.grp: + biocontext: + is_identifiers: true + is_obo: false + prefix: OMA.GRP + uri_format: http://identifiers.org/oma.grp/$1 + mappings: + biocontext: OMA.GRP + miriam: oma.grp + n2t: oma.grp + miriam: + deprecated: false + description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. + homepage: https://omabrowser.org/cgi-bin/gateway.pl + id: '00000343' + name: OMA Group + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+$ + prefix: oma.grp + sampleId: LCSCCPN + uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1 + n2t: + description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. + example: LCSCCPN + homepage: https://omabrowser.org/cgi-bin/gateway.pl + name: OMA Group through OMA browser at ETH Zurich + namespaceEmbeddedInLui: false + pattern: ^[A-Z]+$ + prefix: oma.grp + uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1 +oma.hog: + banana: HOG + example: '0459895' + mappings: + miriam: oma.hog + miriam: + deprecated: false + description: 'Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ' + homepage: https://omabrowser.org + id: '00000785' + name: OMA HOGs + namespaceEmbeddedInLui: true + pattern: ^HOG:[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ + prefix: oma.hog + sampleId: HOG:0459895 + uri_format: https://omabrowser.org/oma/hog/resolve/HOG:$1/ + namespace_in_lui: false + pattern: ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ + uri_format: https://omabrowser.org/oma/hog/HOG:$1 +oma.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: OMA.PROTEIN + uri_format: http://identifiers.org/oma.protein/$1 + mappings: + biocontext: OMA.PROTEIN + miriam: oma.protein + n2t: oma.protein + miriam: + deprecated: false + description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. + homepage: https://omabrowser.org/cgi-bin/gateway.pl + id: '00000342' + name: OMA Protein + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]{5}\d+$ + prefix: oma.protein + sampleId: HUMAN16963 + uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1 + n2t: + description: OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. + example: HUMAN16963 + homepage: https://omabrowser.org/cgi-bin/gateway.pl + name: OMA Protein through OMA browser at ETH Zurich + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]{5}\d+$ + prefix: oma.protein + uri_format: https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1 +omia: + biocontext: + is_identifiers: false + is_obo: true + prefix: OMIA + uri_format: http://purl.obolibrary.org/obo/OMIA_$1 + comment: website is down as of 2021-10-04 + deprecated: true + mappings: + biocontext: OMIA + miriam: omia + n2t: omia + prefixcommons: omia + miriam: + deprecated: false + description: Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse). + homepage: http://omia.angis.org.au/ + id: '00000142' + name: OMIA + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: omia + sampleId: '1000' + uri_format: http://omia.angis.org.au/$1/ + n2t: + description: Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse). + example: '1000' + homepage: http://omia.angis.org.au/ + name: OMIA at University of Sydney + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: omia + uri_format: http://omia.angis.org.au/$1/ + name: Online Mendelian Inheritance in Animals + prefixcommons: + description: Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse). + example: '1000' + homepage: http://omia.angis.org.au/ + keywords: + - gene + - classification + name: Online Mendelian Inheritance in Animals + pattern: ^\d+$ + prefix: omia + uri_format: http://omia.angis.org.au/retrieve.shtml?pid=$1 +omiabis: + biocontext: + is_identifiers: false + is_obo: true + prefix: OMIABIS + uri_format: http://purl.obolibrary.org/obo/OMIABIS_$1 + bioportal: + name: Ontologized MIABIS + prefix: OMIABIS + example: '0001079' + mappings: + biocontext: OMIABIS + bioportal: OMIABIS + obofoundry: omiabis + ols: omiabis + ontobee: OMIABIS + obofoundry: + appears_in: + - labo + contact: mbrochhausen@gmail.com + contact.label: Mathias Brochhausen + contact.orcid: 0000-0003-1834-3856 + deprecated: true + description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) + download.owl: http://purl.obolibrary.org/obo/omiabis.owl + homepage: https://github.com/OMIABIS/omiabis-dev + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Ontologized MIABIS + prefix: omiabis + repository: https://github.com/OMIABIS/omiabis-dev + ols: + description: An ontological version of MIABIS (Minimum Information About BIobank data Sharing) + download: http://purl.obolibrary.org/obo/omiabis.owl + homepage: https://github.com/OMIABIS/omiabis-dev + name: Ontologized MIABIS + prefix: omiabis + version: 2014-05-28 + ontobee: + library: Library + name: Ontologized MIABIS + prefix: OMIABIS + pattern: ^\d{7}$ +omim: + biocontext: + is_identifiers: false + is_obo: true + prefix: OMIM + uri_format: http://purl.obolibrary.org/obo/OMIM_$1 + bioportal: + name: Online Mendelian Inheritance in Man + prefix: OMIM + contact: + email: ahamosh@jhmi.edu + github: ahamosh + name: Ada Hamosh + orcid: 0000-0002-1780-5230 + fairsharing: + abbreviation: MIM + description: First submission + id: '455' + name: Molecular Interaction Map + prefix: FAIRsharing.azq2t6 + subjects: [] + go: + homepage: https://omim.org/ + name: Mendelian Inheritance in Man + prefix: OMIM + synonyms: + - MIM + uri_format: https://omim.org/entry/$1 + mappings: + biocontext: OMIM + bioportal: OMIM + fairsharing: FAIRsharing.azq2t6 + go: OMIM + miriam: mim + n2t: mim + ncbi: MIM + prefixcommons: omim + uniprot: MIM + wikidata: P492 + miriam: + deprecated: false + description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. + homepage: https://omim.org/ + id: '00000016' + name: OMIM + namespaceEmbeddedInLui: false + pattern: ^[*#+%^]?\d{6}$ + prefix: mim + providers: + - code: CURATOR_REVIEW + description: OMIM mirror at John Hopkins + homepage: http://mirror.omim.org/ + name: OMIM mirror at John Hopkins + uri_format: http://mirror.omim.org/entry/$1 + sampleId: '603903' + uri_format: https://omim.org/entry/$1 + n2t: + description: Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. + example: '603903' + homepage: https://omim.org/ + name: OMIM at John Hopkins + namespaceEmbeddedInLui: false + pattern: ^[*#+%^]?\d{6}$ + prefix: mim + uri_format: https://omim.org/entry/$1 + name: Online Mendelian Inheritance in Man + ncbi: + example: '123456' + homepage: https://www.ncbi.nlm.nih.gov/omim + name: Mendelian Inheritance in Man numbers + prefix: MIM + pattern: ^\d+$ + prefixcommons: + description: OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. + example: '603903' + homepage: http://www.ncbi.nlm.nih.gov/omim/ + keywords: + - gene + - gene expression + name: Online Mendelian Inheritance in Man + pattern: ^[*#+%^]?\d{6}$ + prefix: omim + pubmed_ids: + - '15608251' + uri_format: http://www.ncbi.nlm.nih.gov/omim/$1 + synonyms: + - OMIM + - mim + uniprot: + category: Organism-specific databases + identifier: '62' + link_is_explicit: 'true' + name: Online Mendelian Inheritance in Man (OMIM) + prefix: MIM + uri_format: https://www.omim.org/entry/$1 + wikidata: + database: Q241953 + database.homepage: https://www.omim.org + database.label: Online Mendelian Inheritance in Man + name: OMIM ID + pattern: \d{6} + prefix: P492 + uri_format: https://omim.org/entry/$1 +omim.ps: + biolink: + is_identifiers: false + is_obo: false + prefix: OMIM.PS + uri_format: https://www.omim.org/phenotypicSeries/$1 + contact: + email: ahamosh@jhmi.edu + github: ahamosh + name: Ada Hamosh + orcid: 0000-0002-1780-5230 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + contributor_extras: + - github: sierra-moxon + name: Sierra Moxon + orcid: 0000-0002-8719-7760 + description: A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome. + example: PS214100 + homepage: https://www.omim.org/phenotypicSeriesTitles/all + mappings: + biolink: OMIM.PS + name: OMIM Phenotypic Series + part_of: mim + pattern: ^PS\d+$ + synonyms: + - MIMPS + - OMIMPS + - PS + - mim.ps + uri_format: https://omim.org/phenotypicSeries/$1 +omit: + biocontext: + is_identifiers: false + is_obo: true + prefix: OMIT + uri_format: http://purl.obolibrary.org/obo/OMIT_$1 + bioportal: + name: Ontology for MicroRNA Target + prefix: OMIT + download_obo: https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo + example: '0000069' + fairsharing: + abbreviation: OMIT + description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). + id: '762' + name: Ontology for MicroRNA Target + prefix: FAIRsharing.mf91p5 + subjects: + - Life Science + - Biology + mappings: + biocontext: OMIT + bioportal: OMIT + fairsharing: FAIRsharing.mf91p5 + miriam: omit + n2t: omit + obofoundry: omit + ols: omit + ontobee: OMIT + miriam: + deprecated: false + description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). + homepage: https://www.ebi.ac.uk/ols/ontologies/omit/ + id: '00000605' + name: OMIT + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: omit + sampleId: '0005506' + uri_format: https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1 + n2t: + description: The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). + example: '0005506' + homepage: https://www.ebi.ac.uk/ols/ontologies/omit/ + name: Ontology for miRNA Target (OMIT) through OLS + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: omit + uri_format: https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1 + name: Ontology for MicroRNA Target + obofoundry: + appears_in: + - mco + contact: huang@southalabama.edu + contact.github: Huang-OMIT + contact.label: Jingshan Huang + contact.orcid: 0000-0003-2408-2883 + deprecated: false + description: Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain + download.owl: http://purl.obolibrary.org/obo/omit.owl + homepage: http://omit.cis.usouthal.edu/ + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Ontology for MIRNA Target + preferredPrefix: OMIT + prefix: omit + repository: https://github.com/OmniSearch/omit + ols: + description: Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain + download: http://purl.obolibrary.org/obo/omit.owl + homepage: http://omit.cis.usouthal.edu/ + name: Ontology for MIRNA Target + prefix: omit + version: 2019-06-07 + version.iri: http://purl.obolibrary.org/obo/omit/dev/omit.owl + ontobee: + library: Library + name: Ontology for MIRNA Target + prefix: OMIT + synonyms: + - OMIT + wikidata: + database: Q55118529 +omo: + bioportal: + name: OBO Metadata Ontology + prefix: OMO + mappings: + bioportal: OMO + obofoundry: omo + ols: omo + ontobee: OMO + no_own_terms: true + obofoundry: + appears_in: + - pcl + contact: cjmungall@lbl.gov + contact.github: cmungall + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + deprecated: false + description: An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). + download.owl: http://purl.obolibrary.org/obo/omo.owl + homepage: https://github.com/information-artifact-ontology/ontology-metadata + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: OBO Metadata Ontology + preferredPrefix: OMO + prefix: omo + repository: https://github.com/information-artifact-ontology/ontology-metadata + ols: + description: An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). + download: http://purl.obolibrary.org/obo/omo.owl + homepage: https://github.com/information-artifact-ontology/ontology-metadata + name: OBO Metadata Ontology + prefix: omo + version: 2022-04-27 + version.iri: http://purl.obolibrary.org/obo/omo/releases/2022-04-27/omo.owl + ontobee: + library: Library + name: OBO Metadata Ontology + prefix: OMO +omop: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format. + homepage: https://www.ohdsi.org/data-standardization/the-common-data-model/ + name: Observational Medical Outcomes Partnership + no_own_terms: true + references: + - https://github.com/callahantiff/OMOP2OBO +omp: + biocontext: + is_identifiers: false + is_obo: true + prefix: OMP + uri_format: http://purl.obolibrary.org/obo/OMP_$1 + bioportal: + name: Ontology of Microbial Phenotypes + prefix: OMP + example: '0005067' + fairsharing: + abbreviation: OMP + description: The Ontology of Microbial Phenotypes (OMP) is a community ontology for annotating microbial phenotypes, including bacteria, archaea, protists, fungi, and viruses. It has been created to help with standardized capture of essential phenotypic information. OMP is designed to be compatible with other microbial phenotype ontologies, such as the Fission Yeast Phenotype Ontology (FYPO) and the Ascomycete Phenotype Ontology (APO), and aims to standardize the capture of phenotypic information to allow improved cross-species data mining and analysis. + id: '1190' + name: Ontology of Microbial Phenotypes + prefix: FAIRsharing.cc3f2x + subjects: + - Data Mining + - Microbiology + - Biology + mappings: + biocontext: OMP + bioportal: OMP + fairsharing: FAIRsharing.cc3f2x + obofoundry: omp + ols: omp + ontobee: OMP + obofoundry: + appears_in: + - mco + contact: jimhu@tamu.edu + contact.github: jimhu-tamu + contact.label: James C. Hu + contact.orcid: 0000-0001-9016-2684 + deprecated: false + description: An ontology of phenotypes covering microbes + download.obo: http://purl.obolibrary.org/obo/omp.obo + download.owl: http://purl.obolibrary.org/obo/omp.owl + homepage: http://microbialphenotypes.org + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Ontology of Microbial Phenotypes + preferredPrefix: OMP + prefix: omp + repository: https://github.com/microbialphenotypes/OMP-ontology + ols: + description: An ontology of phenotypes covering microbes + download: http://purl.obolibrary.org/obo/omp.owl + homepage: http://microbialphenotypes.org + name: Ontology of Microbial Phenotypes + prefix: omp + version: 2022-04-11 + version.iri: http://purl.obolibrary.org/obo/omp/releases/2022-04-11/omp.owl + ontobee: + library: Library + name: Ontology of Microbial Phenotypes + prefix: OMP + pattern: ^\d{7}$ + wikidata: + database: Q81661753 +omrse: + biocontext: + is_identifiers: false + is_obo: true + prefix: OMRSE + uri_format: http://purl.obolibrary.org/obo/OMRSE_$1 + bioportal: + name: Ontology of Medically Related Social Entities + prefix: OMRSE + download_obo: https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo + example: '00000022' + fairsharing: + abbreviation: OMRSE + description: This ontology covers the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital,etc.) + id: '643' + name: Ontology of Medically Related Social Entities + prefix: FAIRsharing.z0p37e + subjects: + - Demographics + - Social Science + - Health Science + - Biomedical Science + mappings: + biocontext: OMRSE + bioportal: OMRSE + fairsharing: FAIRsharing.z0p37e + obofoundry: omrse + ols: omrse + ontobee: OMRSE + obofoundry: + appears_in: + - labo + contact: hoganwr@gmail.com + contact.github: hoganwr + contact.label: Bill Hogan + contact.orcid: 0000-0002-9881-1017 + deprecated: false + description: This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. + download.owl: http://purl.obolibrary.org/obo/omrse.owl + homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Ontology of Medically Related Social Entities + preferredPrefix: OMRSE + prefix: omrse + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/27406187 + title: 'The ontology of medically related social entities: recent developments' + repository: https://github.com/ufbmi/OMRSE + ols: + description: This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. + download: http://purl.obolibrary.org/obo/omrse.owl + homepage: https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview + name: Ontology of Medically Related Social Entities + prefix: omrse + version: 2022-04-06 + version.iri: http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl + ontobee: + library: Library + name: Ontology of Medically Related Social Entities + prefix: OMRSE + pattern: ^\d{8}$ +oncotree: + appears_in: + - efo + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. + example: BLL + homepage: http://oncotree.mskcc.org + name: OncoTree + uri_format: http://oncotree.mskcc.org/api/tumorTypes/search/code/$1 +one: + bioportal: + name: Ontology for Nutritional Epidemiology + prefix: ONE + example: '0001021' + fairsharing: + abbreviation: ONE + description: The ontology for nutritional epidemiology (ONE) was developed to describe nutritional epidemiologic studies. + id: '1422' + name: Ontology for Nutritional epidemiology + prefix: FAIRsharing.USxx0K + subjects: + - Life Science + - Nutritional Science + - Epidemiology + mappings: + bioportal: ONE + fairsharing: FAIRsharing.USxx0K + obofoundry: one + ols: one + ontobee: ONE + obofoundry: + contact: chenyangnutrition@gmail.com + contact.github: cyang0128 + contact.label: Chen Yang + contact.orcid: 0000-0001-9202-5309 + depends_on: + - foodon + - obi + - ons + deprecated: false + description: An ontology to standardize research output of nutritional epidemiologic studies. + download.owl: http://purl.obolibrary.org/obo/one.owl + homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Ontology for Nutritional Epidemiology + preferredPrefix: ONE + prefix: one + repository: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies + ols: + description: An ontology to standardize research output of nutritional epidemiologic studies. + download: http://purl.obolibrary.org/obo/one.owl + homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies + name: Ontology for Nutritional Epidemiology + prefix: one + ontobee: + library: Library + name: Ontology for Nutritional Epidemiology + prefix: ONE + pattern: ^\d{7}$ +ons: + bioportal: + name: Ontology for Nutritional Studies + prefix: ONS + example: '0000060' + fairsharing: + abbreviation: ONS + description: Ontology For Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. It is the first systematic effort to provide a formal ontology framework for the description of nutritional studies. + id: '814' + name: Ontology for Nutritional Studies + prefix: FAIRsharing.rfec93 + subjects: + - Nutritional Science + - Biomedical Science + mappings: + bioportal: ONS + fairsharing: FAIRsharing.rfec93 + obofoundry: ons + ols: ons + ontobee: ONS + obofoundry: + appears_in: + - one + contact: francesco.vitali@ibba.cnr.it + contact.github: FrancescoVit + contact.label: Francesco Vitali + contact.orcid: 0000-0001-9125-4337 + depends_on: + - bfo + - chebi + - envo + - foodon + - ncbitaxon + - obi + - ro + - uberon + deprecated: false + description: An ontology for description of concepts in the nutritional studies domain. + download.owl: http://purl.obolibrary.org/obo/ons.owl + homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Ontology for Nutritional Studies + preferredPrefix: ONS + prefix: ons + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/29736190 + title: 'ONS: an ontology for a standardized description of interventions and observational studies in nutrition' + repository: https://github.com/enpadasi/Ontology-for-Nutritional-Studies + ols: + description: The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. + download: http://purl.obolibrary.org/obo/ons.owl + homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies + name: Ontology for Nutritional Studies + prefix: ons + version: June 2021 release + ontobee: + library: Library + name: Ontology for Nutritional Studies + prefix: ONS + pattern: ^\d{7}$ +ontoavida: + bioportal: + name: 'OntoAvida: ontology for Avida digital evolution platform' + prefix: ONTOAVIDA + example: '00000001' + mappings: + bioportal: ONTOAVIDA + obofoundry: ontoavida + ols: ontoavida + ontobee: ONTOAVIDA + name: Ontology for Avida digital evolution platform + obofoundry: + contact: fortuna@ebd.csic.es + contact.github: miguelfortuna + contact.label: Miguel A. Fortuna + contact.orcid: 0000-0002-8374-1941 + depends_on: + - fbcv + - gsso + - ncit + - ro + - stato + deprecated: false + description: OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). + download.obo: http://purl.obolibrary.org/obo/ontoavida.obo + download.owl: http://purl.obolibrary.org/obo/ontoavida.owl + homepage: https://gitlab.com/fortunalab/ontoavida + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: 'OntoAvida: ontology for Avida digital evolution platform' + preferredPrefix: ONTOAVIDA + prefix: ontoavida + repository: https://gitlab.com/fortunalab/ontoavida + ols: + description: >- + The Ontology for Avida (OntoAvida) project aims to develop an integrated + vocabulary for the description of the most widely used computational + approach for performing experimental evolution using digital organisms + (i.e., self-replicating computer programs that evolve within a + user-defined computational environment). + + + The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. + + + OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). + + + More information can be found at https://obofoundry.org/ontology/ontoavida.html + download: http://purl.obolibrary.org/obo/ontoavida.owl + homepage: https://gitlab.com/fortunalab/ontoavida + name: 'OntoAvida: ontology for Avida digital evolution platform.' + prefix: ontoavida + version: 2022-03-15 + version.iri: http://purl.obolibrary.org/obo/ontoavida/releases/2022-03-15/ontoavida.owl + ontobee: + library: Not Specified/No + name: 'OntoAvida: ontology for Avida digital evolution platform' + prefix: ONTOAVIDA + pattern: ^\d{8}$ +ontoneo: + biocontext: + is_identifiers: false + is_obo: true + prefix: ONTONEO + uri_format: http://purl.obolibrary.org/obo/ONTONEO_$1 + bioportal: + name: Obstetric and Neonatal Ontology + prefix: ONTONEO + example: '00000098' + fairsharing: + abbreviation: ONTONEO + description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. + id: '1458' + name: Obstetric and Neonatal Ontology + prefix: FAIRsharing.5a4y1y + subjects: [] + homepage: http://ontoneo.com + mappings: + biocontext: ONTONEO + bioportal: ONTONEO + fairsharing: FAIRsharing.5a4y1y + obofoundry: ontoneo + ols: ontoneo + ontobee: ONTONEO + obofoundry: + contact: fernanda.farinelli@gmail.com + contact.github: FernandaFarinelli + contact.label: Fernanda Farinelli + contact.orcid: 0000-0003-2338-8872 + deprecated: false + description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. + download.owl: http://purl.obolibrary.org/obo/ontoneo.owl + homepage: ontoneo.com + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Obstetric and Neonatal Ontology + preferredPrefix: ONTONEO + prefix: ontoneo + repository: https://github.com/ontoneo-project/Ontoneo + ols: + description: The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. + download: http://purl.obolibrary.org/obo/ontoneo.owl + homepage: https://ontoneo.com/ + name: Obstetric and Neonatal Ontology + prefix: ontoneo + version: v1.6 + version.iri: http://purl.obolibrary.org/obo/ontoneo/releases/2021-04-29/ontoneo.owl + ontobee: + library: Library + name: Obstetric and Neonatal Ontology + prefix: ONTONEO + pattern: ^\d{8}$ +oostt: + biocontext: + is_identifiers: false + is_obo: true + prefix: OOSTT + uri_format: http://purl.obolibrary.org/obo/OOSTT_$1 + bioportal: + name: Ontology of Organizational Structures of Trauma centers and Trauma systems + prefix: OOSTT + example: '00000099' + fairsharing: + abbreviation: OOSTT + description: The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). It is developed collaboratively by domain and ontology experts in the NIH-funded CAFE (Comparative Assessment Framework for Environments of trauma care) project (1R01GM111324-01A1). It will be used as the ontology backbone of a graphical user interface comparing graphical representations of organizational structures. + id: '759' + name: Ontology of Organizational Structures of Trauma centers and Trauma systems + prefix: FAIRsharing.b4sa0w + subjects: + - Traumatology + mappings: + biocontext: OOSTT + bioportal: OOSTT + fairsharing: FAIRsharing.b4sa0w + obofoundry: oostt + ols: oostt + ontobee: OOSTT + obofoundry: + contact: mbrochhausen@gmail.com + contact.github: mbrochhausen + contact.label: Mathias Brochhausen + contact.orcid: 0000-0003-1834-3856 + deprecated: false + description: An ontology built for representating the organizational components of trauma centers and trauma systems. + download.owl: http://purl.obolibrary.org/obo/oostt.owl + homepage: https://github.com/OOSTT/OOSTT + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Ontology of Organizational Structures of Trauma centers and Trauma systems + preferredPrefix: OOSTT + prefix: oostt + repository: https://github.com/OOSTT/OOSTT + ols: + description: An ontology built for representating the organizational components of trauma centers and trauma systems. + download: http://purl.obolibrary.org/obo/oostt.owl + homepage: https://github.com/OOSTT/OOSTT + name: Ontology of Organizational Structures of Trauma centers and Trauma Systems + prefix: oostt + version: 2021-01-11 + version.iri: http://purl.obolibrary.org/obo/oostt//2021-01-08/oostt.owl + ontobee: + library: Library + name: Ontology of Organizational Structures of Trauma centers and Trauma systems + prefix: OOSTT + pattern: ^\d{8}$ +opb: + biocontext: + is_identifiers: true + is_obo: false + prefix: OPB + uri_format: http://identifiers.org/opb/$1 + bioportal: + name: Ontology of Physics for Biology + prefix: OPB + example: '00573' + fairsharing: + abbreviation: OPB + description: The Ontology of Physics for Biology is a reference of classical physics as applied to the dynamics of biological systems. This resource provides a reference ontology of physical properties (e.g., pressure, chemical concentration) and principles (e.g., Ohm’s law, Ficke’s law) by which the physical meaning of biosimulation models may be annotated. + id: '177' + name: Ontology of Physics for Biology + prefix: FAIRsharing.qcceez + subjects: + - Life Science + - Physics + mappings: + biocontext: OPB + bioportal: OPB + fairsharing: FAIRsharing.qcceez + miriam: opb + n2t: opb + prefixcommons: opb + miriam: + deprecated: false + description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. + homepage: http://bioportal.bioontology.org/ontologies/OPB + id: '00000129' + name: Ontology of Physics for Biology + namespaceEmbeddedInLui: false + pattern: ^OPB_\d+$ + prefix: opb + sampleId: OPB_00573 + uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$1 + n2t: + description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. + example: OPB_00573 + homepage: http://bioportal.bioontology.org/ontologies/OPB + name: Ontology of Physics for Biology through Bioportal + namespaceEmbeddedInLui: false + pattern: ^OPB_\d+$ + prefix: opb + uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$1 + pattern: ^\d+$ + prefixcommons: + bioportal: '1141' + description: The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. + example: OPB_00573 + homepage: https://sites.google.com/site/semanticsofbiologicalprocesses/projects/the-ontology-of-physics-for-biology-opb + keywords: + - ontology + - structure + name: Ontology of Physics for Biology + pattern: ^OPB_\d+$ + prefix: opb + uri_format: http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1 +openalex: + contact: + email: hpiwowar@gmail.com + github: hpiwowar + name: Heather Piwowar + orcid: 0000-0003-1613-5981 + contributor: + github: dhimmel + name: Daniel Himmelstein + orcid: 0000-0002-3012-7446 + description: OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other. + example: W2741809807 + homepage: https://openalex.org/ + name: OpenAlex + pattern: ^[WAICV]\d{2,}$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: https://openalex.org/$1 +opl: + biocontext: + is_identifiers: false + is_obo: true + prefix: OPL + uri_format: http://purl.obolibrary.org/obo/OPL_$1 + bioportal: + name: Ontology for Parasite LifeCycle + prefix: OPL + example: '0000319' + fairsharing: + abbreviation: OPL + description: OPL models the life cycle stage details of T.cruzi and two related kinetoplastids, Trypanosoma brucei and Leishmania major. In addition, the ontology also models necessary contextual details such as host information, vector information, strain and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. + id: '165' + name: Ontology for Parasite LifeCycle + prefix: FAIRsharing.ez2nhb + subjects: + - Anatomy + - Developmental Biology + - Life Science + mappings: + biocontext: OPL + bioportal: OPL + fairsharing: FAIRsharing.ez2nhb + obofoundry: opl + ols: opl + ontobee: OPL + obofoundry: + contact: jiezheng@pennmedicine.upenn.edu + contact.github: zhengj2007 + contact.label: Jie Zheng + contact.orcid: 0000-0002-2999-0103 + deprecated: false + description: A reference ontology for parasite life cycle stages. + download.owl: http://purl.obolibrary.org/obo/opl.owl + homepage: https://github.com/OPL-ontology/OPL + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Ontology for Parasite LifeCycle + preferredPrefix: OPL + prefix: opl + repository: https://github.com/OPL-ontology/OPL + ols: + description: The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. + download: http://purl.obolibrary.org/obo/opl.owl + homepage: https://github.com/OPL-ontology/OPL + name: Ontology for Parasite Lifecycle + prefix: opl + version: 2021-01-28 + version.iri: http://purl.obolibrary.org/obo/opl/2021-01-28/opl.owl + ontobee: + library: Library + name: Ontology for Parasite LifeCycle + prefix: OPL + pattern: ^\d{7}$ +opm: + biocontext: + is_identifiers: true + is_obo: false + prefix: OPM + uri_format: http://identifiers.org/opm/$1 + fairsharing: + abbreviation: OPM + description: "The Open Provenance Model (OPM) is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any 'thing', whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation." + id: '1305' + name: Open Provenance Model + prefix: FAIRsharing.7c683b + subjects: + - Data Management + - Computer Science + mappings: + biocontext: OPM + fairsharing: FAIRsharing.7c683b + miriam: opm + n2t: opm + miriam: + deprecated: false + description: The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. + homepage: http://opm.phar.umich.edu/ + id: '00000333' + name: OPM + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: opm + sampleId: 1h68 + uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1 + n2t: + description: The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. + example: 1h68 + homepage: http://opm.phar.umich.edu/ + name: OPM at University of Michigan + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: opm + uri_format: http://opm.phar.umich.edu/protein.php?pdbid=$1 + name: Orientations of Proteins in Membranes Database +opmi: + bioportal: + name: Ontology of Precision Medicine and Investigation + prefix: OPMI + example: '0000101' + mappings: + bioportal: OPMI + obofoundry: opmi + ols: opmi + ontobee: OPMI + obofoundry: + appears_in: + - labo + - scdo + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqun Oliver He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: The Ontology of Precision Medicine and Investigation (OPMI) aims to ontologically represent and standardize various entities and relations associated with precision medicine and related investigations at different conditions. + download.owl: http://purl.obolibrary.org/obo/opmi.owl + homepage: https://github.com/OPMI/opmi + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Ontology of Precision Medicine and Investigation + preferredPrefix: OPMI + prefix: opmi + repository: https://github.com/OPMI/opmi + ols: + description: OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. + download: http://purl.obolibrary.org/obo/opmi.owl + homepage: https://github.com/OPMI/opmi + name: 'OPMI: Ontology of Precision Medicine and Investigation' + prefix: opmi + version: 1.0.152 + ontobee: + library: Library + name: Ontology of Precision Medicine and Investigation + prefix: OPMI + pattern: ^\d{7}$ +orcid: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORCID + uri_format: http://identifiers.org/orcid/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: ORCID + uri_format: https://orcid.org/$1 + mappings: + biocontext: ORCID + biolink: ORCID + miriam: orcid + n2t: orcid + scholia: orcid + miriam: + deprecated: false + description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. + homepage: https://orcid.org + id: '00000382' + name: ORCID + namespaceEmbeddedInLui: false + pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ + prefix: orcid + sampleId: 0000-0002-5355-2576 + uri_format: https://orcid.org/$1 + n2t: + description: ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. + example: 0000-0002-5355-2576 + homepage: https://orcid.org + name: ORCID at Bethesda + namespaceEmbeddedInLui: false + pattern: ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ + prefix: orcid + uri_format: https://orcid.org/$1 + name: Open Researcher and Contributor + synonyms: + - ORCID + - ORCiD + wikidata: + database: Q51044 + database.label: ORCID iD + homepage: https://orcid.org/ + name: ORCID iD + pattern: 0000-000(1-[5-9]|2-[0-9]|3-[0-4])\d{3}-\d{3}[\dX] + prefix: P496 + uri_format: https://orcid.org/$1 +ordb: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORDB + uri_format: http://identifiers.org/ordb/$1 + fairsharing: + abbreviation: ORDB + description: ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. + id: '2124' + name: Olfactory Receptor Database + prefix: FAIRsharing.6375zh + subjects: + - Life Science + mappings: + biocontext: ORDB + fairsharing: FAIRsharing.6375zh + miriam: ordb + n2t: ordb + prefixcommons: ordb + miriam: + deprecated: false + description: The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). + homepage: http://senselab.med.yale.edu/OrDB/ + id: '00000499' + name: Olfactory Receptor Database + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ordb + sampleId: '8497' + uri_format: http://senselab.med.yale.edu/ORDB/Data/$1 + n2t: + description: The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). + example: '8497' + homepage: http://senselab.med.yale.edu/OrDB/ + name: Olfactory Receptor Database at Yale University School of Medicine + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ordb + uri_format: http://senselab.med.yale.edu/ORDB/Data/$1 + prefixcommons: + description: ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. + example: '14673' + homepage: http://senselab.med.yale.edu/senselab/ordb/ + keywords: + - gene + - protein + name: Olfactory Receptor Database + pattern: ^\d+$ + prefix: ordb + uri_format: http://senselab.med.yale.edu/ordb/eavdata.asp?o=$1 +oridb.sacch: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORIDB.SACCH + uri_format: http://identifiers.org/oridb.sacch/$1 + mappings: + biocontext: ORIDB.SACCH + miriam: oridb.sacch + n2t: oridb.sacch + miriam: + deprecated: false + description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. + homepage: http://cerevisiae.oridb.org/index.php + id: '00000369' + name: OriDB Saccharomyces + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oridb.sacch + sampleId: '1' + uri_format: http://cerevisiae.oridb.org/details.php?id=$1 + n2t: + description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. + example: '1' + homepage: http://cerevisiae.oridb.org/index.php + name: OriDB Saccharomyces at University of Nottingham + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oridb.sacch + uri_format: http://cerevisiae.oridb.org/details.php?id=$1 +oridb.schizo: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORIDB.SCHIZO + uri_format: http://identifiers.org/oridb.schizo/$1 + mappings: + biocontext: ORIDB.SCHIZO + miriam: oridb.schizo + n2t: oridb.schizo + miriam: + deprecated: false + description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. + homepage: http://pombe.oridb.org/index.php + id: '00000368' + name: OriDB Schizosaccharomyces + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oridb.schizo + sampleId: '1' + uri_format: http://pombe.oridb.org/details.php?id=$1 + n2t: + description: OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. + example: '1' + homepage: http://pombe.oridb.org/index.php + name: OriDB Schizosaccharomyces at University of Nottingham + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oridb.schizo + uri_format: http://pombe.oridb.org/details.php?id=$1 +ornaseq: + bioportal: + name: Ontology of RNA Sequencing + prefix: ORNASEQ + example: '0000010' + mappings: + bioportal: ORNASEQ + obofoundry: ornaseq + ols: ornaseq + ontobee: ORNASEQ + obofoundry: + contact: safisher@upenn.edu + contact.github: safisher + contact.label: Stephen Fisher + contact.orcid: 0000-0001-8034-7685 + deprecated: false + description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. + download.owl: http://purl.obolibrary.org/obo/ornaseq.owl + homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Ontology of RNA Sequencing + preferredPrefix: ORNASEQ + prefix: ornaseq + repository: https://github.com/safisher/ornaseq + ols: + description: An application ontology designed to annotate next-generation sequencing experiments performed on RNA. + download: http://purl.obolibrary.org/obo/ornaseq.owl + homepage: http://kim.bio.upenn.edu/software/ornaseq.shtml + name: Ontology for RNA sequencing (ORNASEQ) + prefix: ornaseq + version: 2019-07-08 + version.iri: http://purl.obolibrary.org/obo/ornaseq/2019-07-08/ornaseq.owl + ontobee: + library: Library + name: Ontology of RNA Sequencing + prefix: ORNASEQ + pattern: ^\d{7}$ +orphanet: + biocontext: + is_identifiers: false + is_obo: false + prefix: Orphanet + uri_format: http://www.orpha.net/ORDO/Orphanet_$1 + fairsharing: + abbreviation: Orphanet + description: Orphanet is the reference resource for information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases. Orphanet maintains the Orphanet nomenclature, essential for interoperability, and the Orphanet Rare Disease Ontology (ORDO). + id: '2030' + name: Orphanet + prefix: FAIRsharing.6bd5k6 + subjects: + - Life Science + - Ontology and Terminology + mappings: + biocontext: Orphanet + fairsharing: FAIRsharing.6bd5k6 + miriam: orphanet + n2t: orphanet + prefixcommons: orphanet + uniprot: Orphanet + wikidata: P1550 + miriam: + deprecated: false + description: Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. + homepage: http://www.orpha.net/consor/ + id: '00000220' + name: Orphanet + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: orphanet + providers: + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: http://orphanet.bio2rdf.org/fct + name: Bio2RDF + uri_format: http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$1 + sampleId: '85163' + uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1 + n2t: + description: Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. + example: '85163' + homepage: http://www.orpha.net/consor/ + name: Orphanet at Inserm + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: orphanet + uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1 + name: Orphanet + prefixcommons: + description: Orphanet is a database of information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases. + example: '85163' + homepage: http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB + keywords: + - disease + - drug + - human + name: Orphanet; a database dedicated to information on rare diseases and orphan drugs + pattern: ^\d+$ + prefix: orphanet + pubmed_ids: + - '19058507' + uri_format: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=$1 + synonyms: + - ORPHA + uniprot: + category: Organism-specific databases + identifier: '68' + link_is_explicit: 'true' + name: Orphanet; a database dedicated to information on rare diseases and orphan drugs + prefix: Orphanet + uri_format: https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=$1 + wikidata: + database: Q1515833 + database.homepage: http://www.orpha.net/consor/cgi-bin/index.php + database.label: Orphanet + homepage: https://www.orpha.net + name: Orphanet ID + pattern: '[1-9]\d{0,5}' + prefix: P1550 + uri_format: https://www.orpha.net/consor/cgi-bin//OC_Exp.php?lng=EN&Expert=$1 +orphanet.ordo: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORPHANET.ORDO + uri_format: http://identifiers.org/orphanet.ordo/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: ORPHA + uri_format: http://www.orpha.net/ORDO/Orphanet_$1 + bioportal: + name: Orphanet Rare Disease Ontology + prefix: ORDO + cellosaurus: + category: Medical resources + homepage: https://www.ebi.ac.uk/ols/ontologies/ordo + name: Orphanet Rare Disease Ontology + prefix: ORDO + uri_format: https://www.ebi.ac.uk/ols/ontologies/ordo/terms?iri=http://www.orpha.net/ORDO/$1 + download_owl: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl + example: C023 + example_extras: + - '478' + fairsharing: + abbreviation: ORDO + description: Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. + id: '426' + name: Orphanet Rare Diseases Ontology + prefix: FAIRsharing.pbbnwa + subjects: + - Health Science + - Biomedical Science + mappings: + biocontext: ORPHANET.ORDO + biolink: ORPHA + bioportal: ORDO + cellosaurus: ORDO + fairsharing: FAIRsharing.pbbnwa + miriam: orphanet.ordo + n2t: orphanet.ordo + ols: ordo + miriam: + deprecated: false + description: "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." + homepage: https://www.ebi.ac.uk/ols/ontologies/ordo + id: '00000532' + name: Orphanet Rare Disease Ontology + namespaceEmbeddedInLui: false + pattern: ^Orphanet(_|:)C?\d+$ + prefix: orphanet.ordo + sampleId: Orphanet_C023 + uri_format: https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$1 + n2t: + description: The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10). + example: Orphanet_C023 + homepage: https://www.ebi.ac.uk/ols/ontologies/ordo + name: ORDO via OLS + namespaceEmbeddedInLui: false + pattern: ^Orphanet(_|:)C?\d+$ + prefix: orphanet.ordo + uri_format: https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$1 + ols: + description: The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). + download: http://www.orphadata.org/data/ORDO/ordo_orphanet.owl + name: Orphanet Rare Disease Ontology + prefix: ordo + version: '4.0' + version.iri: http://www.orpha.net/version4.0 + pattern: ^C?\d+$ + synonyms: + - ordo + uri_format: http://www.orpha.net/ORDO/Orphanet_$1 +orth: + bioportal: + name: Orthology Ontology + prefix: ORTH + contact: + email: jfernand@um.es + github: jesualdotomasfernandezbreis + name: Jesualdo Tomás Fernández-Breis + orcid: 0000-0002-7558-2880 + download_owl: https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl + example: HomologyRelation + fairsharing: + abbreviation: ORTH + description: ORTH ontology is designed to describe sequence homology data such as gene region, gene and protein-centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures in a single terminology. + id: '77' + name: Orthology Ontology + prefix: FAIRsharing.4877h0 + subjects: + - Comparative Genomics + homepage: https://github.com/qfo/OrthologyOntology + mappings: + bioportal: ORTH + fairsharing: FAIRsharing.4877h0 + ols: orth + ols: + description: 'The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.' + download: http://purl.org/net/orth + homepage: http://purl.org/net/orth + name: Orthology Ontology + prefix: orth + version: >- + This ontology is the second version of the orthology ontology first + published in 2015 and available at + http://purl.bioontology.org/ontology/ORTH . + + @authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov, C. Dessimoz and F. Villiers. + version.iri: http://purl.org/net/orth/2.0 + repository: https://github.com/qfo/OrthologyOntology +orthodb: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORTHODB + uri_format: http://identifiers.org/orthodb/$1 + fairsharing: + abbreviation: OrthoDB + description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. + id: '2080' + name: Database of Orthologous Groups + prefix: FAIRsharing.x989d5 + subjects: + - Life Science + homepage: https://www.orthodb.org + mappings: + biocontext: ORTHODB + fairsharing: FAIRsharing.x989d5 + miriam: orthodb + n2t: orthodb + prefixcommons: orthodb + uniprot: OrthoDB + miriam: + deprecated: false + description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups + homepage: http://cegg.unige.ch/orthodb4 + id: '00000221' + name: OrthoDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: orthodb + sampleId: Q9P0K8 + uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1 + n2t: + description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups + example: Q9P0K8 + homepage: http://cegg.unige.ch/orthodb4 + name: OrthoDB at Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: orthodb + uri_format: http://cegg.unige.ch/orthodb/results?searchtext=$1 + prefixcommons: + description: OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. + example: EOG9VMFMQ + homepage: http://cegg.unige.ch/orthodb/browse + keywords: + - eukaryotic + - protein + - DNA + name: Database of Orthologous Groups + pattern: ^EOG[A-Z,0-9]+$ + prefix: orthodb + pubmed_ids: + - '20972218' + uri_format: http://cegg.unige.ch/orthodb3/results?searchtext=$1 + provides: uniprot + uniprot: + category: Phylogenomic databases + identifier: '143' + link_is_explicit: 'true' + name: Database of Orthologous Groups + prefix: OrthoDB + uri_format: https://www.orthodb.org/?query=$1 +oryzabase.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORYZABASE.GENE + uri_format: http://identifiers.org/oryzabase.gene/$1 + mappings: + biocontext: ORYZABASE.GENE + miriam: oryzabase.gene + n2t: oryzabase.gene + miriam: + deprecated: false + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + id: '00000482' + name: Oryzabase Gene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.gene + sampleId: '117' + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1 + n2t: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. + example: '117' + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + name: Oryzabase v4 Gene at National Institute of Genetics (Japan) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.gene + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1 +oryzabase.mutant: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORYZABASE.MUTANT + uri_format: http://identifiers.org/oryzabase.mutant/$1 + mappings: + biocontext: ORYZABASE.MUTANT + miriam: oryzabase.mutant + n2t: oryzabase.mutant + miriam: + deprecated: false + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + id: '00000483' + name: Oryzabase Mutant + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.mutant + sampleId: '21393' + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1 + n2t: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. + example: '21393' + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + name: Oryzabase v4 Mutant at National Institute of Genetics (Japan) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.mutant + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1 +oryzabase.reference: + mappings: + miriam: oryzabase.reference + n2t: oryzabase.reference + miriam: + deprecated: false + description: The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + id: '00000689' + name: Oryzabase + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.reference + sampleId: '42840' + uri_format: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1 + n2t: + description: The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. + example: '42840' + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + name: Oryzabase + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.reference + uri_format: https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1 + name: Oryzabase Reference +oryzabase.stage: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORYZABASE.STAGE + uri_format: http://identifiers.org/oryzabase.stage/$1 + mappings: + biocontext: ORYZABASE.STAGE + miriam: oryzabase.stage + n2t: oryzabase.stage + miriam: + deprecated: false + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information. + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + id: '00000485' + name: Oryzabase Stage + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.stage + sampleId: '34' + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1 + n2t: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information. + example: '34' + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + name: Oryzabase v4 Stage at National Institute of Genetics (Japan) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.stage + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1 +oryzabase.strain: + biocontext: + is_identifiers: true + is_obo: false + prefix: ORYZABASE.STRAIN + uri_format: http://identifiers.org/oryzabase.strain/$1 + mappings: + biocontext: ORYZABASE.STRAIN + miriam: oryzabase.strain + n2t: oryzabase.strain + miriam: + deprecated: false + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + id: '00000484' + name: Oryzabase Strain + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.strain + sampleId: '1' + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 + n2t: + description: Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. + example: '1' + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + name: Oryzabase v4 Strain at National Institute of Genetics (Japan) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: oryzabase.strain + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 +otl: + biocontext: + is_identifiers: true + is_obo: false + prefix: OTL + uri_format: http://identifiers.org/otl/$1 + fairsharing: + abbreviation: OTL + description: Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library. + id: '1829' + name: Oryza Tag Line + prefix: FAIRsharing.61c2x6 + subjects: + - Life Science + mappings: + biocontext: OTL + fairsharing: FAIRsharing.61c2x6 + miriam: otl + n2t: otl + prefixcommons: otl + miriam: + deprecated: false + description: Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. + homepage: http://oryzatagline.cirad.fr/ + id: '00000486' + name: Oryza Tag Line + namespaceEmbeddedInLui: false + pattern: ^A[A-Z]+\d+$ + prefix: otl + sampleId: AADB12 + uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 + n2t: + description: Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. + example: AADB12 + homepage: http://oryzatagline.cirad.fr/ + name: Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI + namespaceEmbeddedInLui: false + pattern: ^A[A-Z]+\d+$ + prefix: otl + uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 + prefixcommons: + description: Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Génoplante rice insertion line library. + example: AGFC04 + homepage: http://urgi.versailles.inra.fr/OryzaTagLine/ + keywords: + - DNA + name: 'Oryza Tag Line: An integrated database for the functional analysis of the rice genome' + pattern: ^A[A-Z]+\d+$ + prefix: otl + uri_format: http://urgi.versailles.inra.fr/OryzaTagLine/cgi-bin/general_mutant.pl?line=$1 +ovae: + biocontext: + is_identifiers: false + is_obo: true + prefix: OVAE + uri_format: http://purl.obolibrary.org/obo/OVAE_$1 + bioportal: + name: Ontology of Vaccine Adverse Events + prefix: OVAE + example: '0000609' + fairsharing: + abbreviation: OVAE + description: The Ontology of Vaccine Adverse Events (OVAE) is a biomedical ontology in the area of vaccine adverse events. While they are extremely useful in decreasing infection prevalence in human populations, vaccines may also induce some unintended adverse events. As vaccine usage increases, the risk of adverse events proportionally increases. To protect public health, it is necessary to represent, study, and analyze various vaccine adverse events (VAES). Two existing ontologies are closely related to the VAE studies. The Ontology of Adverse Events (OAE) is a community-based biomedical ontology in the area of adverse events. The Vaccine Ontology (VO) represents various vaccines, vaccine components, and vaccinations. Both OAE and VO are OBO Foundry candidate ontologies and are developed by following the OBO Foundry principles. To better represent various VAEs and support vaccine safety study, we developed the Ontology of Vaccine Adverse Events (OVAE) as an extension of the biomedical ontologies OAE and VO. + id: '1240' + name: Ontology of Vaccine Adverse Events + prefix: FAIRsharing.w4x6n4 + subjects: + - Biomedical Science + mappings: + biocontext: OVAE + bioportal: OVAE + fairsharing: FAIRsharing.w4x6n4 + obofoundry: ovae + ols: ovae + ontobee: OVAE + obofoundry: + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqunh He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: A biomedical ontology in the domain of vaccine adverse events. + download.owl: http://purl.obolibrary.org/obo/ovae.owl + homepage: http://www.violinet.org/ovae/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Ontology of Vaccine Adverse Events + preferredPrefix: OVAE + prefix: ovae + repository: https://github.com/OVAE-Ontology/ovae + ols: + description: 'OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ' + download: http://purl.obolibrary.org/obo/ovae.owl + homepage: http://www.violinet.org/ovae/ + name: 'OVAE: Ontology of Vaccine Adverse Events' + prefix: ovae + version: 1.0.34 + ontobee: + library: Library + name: Ontology of Vaccine Adverse Events + prefix: OVAE + pattern: ^\d{7}$ +owl: + biocontext: + is_identifiers: false + is_obo: false + prefix: owl + uri_format: http://www.w3.org/2002/07/owl#$1 + description: 'Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ' + example: Ontology + fairsharing: + abbreviation: OWL + description: The Web Ontology Language (OWL) is a family of knowledge representation languages or ontology languages for authoring ontologies or knowledge bases. The languages are characterized by formal semantics and RDF/XML-based serializations for the Semantic Web. OWL is endorsed by the World Wide Web Consortium (W3C) and has attracted academic, medical and commercial interest. The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information written in RDF, and OWL 2 ontologies themselves are primarily exchanged as RDF documents. + id: '409' + name: Web Ontology Language + prefix: FAIRsharing.atygwy + subjects: + - Informatics + - Computer Science + - Subject Agnostic + - Ontology and Terminology + homepage: https://www.w3.org/TR/owl-features/ + mappings: + biocontext: owl + fairsharing: FAIRsharing.atygwy + name: Web Ontology Language + uri_format: http://www.w3.org/2002/07/owl#$1 +p3db.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: P3DB.PROTEIN + uri_format: http://identifiers.org/p3db.protein/$1 + mappings: + biocontext: P3DB.PROTEIN + miriam: p3db.protein + n2t: p3db.protein + miriam: + deprecated: false + description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. + homepage: http://www.p3db.org/ + id: '00000501' + name: P3DB Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: p3db.protein + sampleId: '70' + uri_format: http://www.p3db.org/protein.php?id=$1&ref=0 + n2t: + description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. + example: '70' + homepage: http://www.p3db.org/ + name: P3DB Protein at University of Missouri + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: p3db.protein + uri_format: http://www.p3db.org/protein.php?id=$1&ref=0 +p3db.site: + biocontext: + is_identifiers: true + is_obo: false + prefix: P3DB.SITE + uri_format: http://identifiers.org/p3db.site/$1 + mappings: + biocontext: P3DB.SITE + miriam: p3db.site + n2t: p3db.site + miriam: + deprecated: false + description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. + homepage: http://www.p3db.org/ + id: '00000502' + name: P3DB Site + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: p3db.site + sampleId: '65' + uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0 + n2t: + description: Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. + example: '65' + homepage: http://www.p3db.org/ + name: P3DB Site at University of Missouri + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: p3db.site + uri_format: http://www.p3db.org/phosphosite.php?id=$1&ref=0 +paleodb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PALEODB + uri_format: http://identifiers.org/paleodb/$1 + mappings: + biocontext: PALEODB + miriam: paleodb + n2t: paleodb + prefixcommons: paleodb + miriam: + deprecated: false + description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. + homepage: http://paleodb.org/ + id: '00000197' + name: PaleoDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paleodb + sampleId: '83088' + uri_format: http://fossilworks.org/?a=taxonInfo&taxon_no=$1 + n2t: + description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. + example: '83088' + homepage: http://paleodb.org/ + name: PaleoDB at Macquarie University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paleodb + uri_format: http://fossilworks.org/?a=taxonInfo&taxon_no=$1 + name: Paleobiology Database + prefixcommons: + description: The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. + example: '83088' + keywords: + - taxonomy + name: Paleobiology Database + pattern: ^\d+$ + prefix: paleodb + uri_format: http://paleodb.geology.wisc.edu/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$1 +panorama: + description: Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible. + example: FxnI151FMs + fairsharing: + abbreviation: Panorama Public + description: Panorama Public is a data repository for sharing and disseminating results from analyzing mass spectrometry data with the Skyline software. Skyline supports targeted analysis of proteomics or metabolomics data from a variety of mass spectrometry data acquisition techniques. As a member of the ProteomeXchange Consortium, Panorama Public can assign ProteomeXchange accessions to submitted proteomics datasets. + id: '3016' + name: Panorama Public + prefix: FAIRsharing.uBpQ1q + subjects: + - Proteomics + - Life Science + - Metabolomics + homepage: https://panoramaweb.org + mappings: + fairsharing: FAIRsharing.uBpQ1q + name: Panorama Public + uri_format: https://panoramaweb.org/$1.url +panther.family: + biocontext: + is_identifiers: true + is_obo: false + prefix: PANTHER.FAMILY + uri_format: http://identifiers.org/panther.family/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: PANTHER.FAMILY + uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1 + go: + homepage: http://www.pantherdb.org/ + name: Protein ANalysis THrough Evolutionary Relationships Classification System + prefix: PANTHER + uri_format: http://www.pantherdb.org/panther/lookupId.jsp?id=$1 + mappings: + biocontext: PANTHER.FAMILY + biolink: PANTHER.FAMILY + go: PANTHER + miriam: panther.family + n2t: panther.family + miriam: + deprecated: false + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families. + homepage: http://www.pantherdb.org/ + id: '00000060' + name: PANTHER Family + namespaceEmbeddedInLui: false + pattern: ^PTHR\d{5}(\:SF\d{1,3})?$ + prefix: panther.family + sampleId: PTHR12345 + uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1 + n2t: + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families. + example: PTHR12345 + homepage: http://www.pantherdb.org/ + name: PANTHER Family at USC (Los Angeles) + namespaceEmbeddedInLui: false + pattern: ^PTHR\d{5}(\:SF\d{1,3})?$ + prefix: panther.family + uri_format: http://www.pantherdb.org/panther/family.do?clsAccession=$1 + part_of: panther +panther.node: + biocontext: + is_identifiers: true + is_obo: false + prefix: PANTHER.NODE + uri_format: http://identifiers.org/panther.node/$1 + mappings: + biocontext: PANTHER.NODE + miriam: panther.node + n2t: panther.node + miriam: + deprecated: false + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes. + homepage: http://pantree.org/ + id: '00000374' + name: PANTHER Node + namespaceEmbeddedInLui: false + pattern: ^PTN\d{9}$ + prefix: panther.node + sampleId: PTN000000026 + uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1 + n2t: + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes. + example: PTN000000026 + homepage: http://pantree.org/ + name: PANTHER Node at USC (Los Angeles) + namespaceEmbeddedInLui: false + pattern: ^PTN\d{9}$ + prefix: panther.node + uri_format: http://www.pantree.org/node/annotationNode.jsp?id=$1 + part_of: panther +panther.pathway: + biocontext: + is_identifiers: true + is_obo: false + prefix: PANTHER.PATHWAY + uri_format: http://identifiers.org/panther.pathway/$1 + mappings: + biocontext: PANTHER.PATHWAY + miriam: panther.pathway + n2t: panther.pathway + miriam: + deprecated: false + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. + homepage: http://www.pantherdb.org/ + id: '00000363' + name: PANTHER Pathway + namespaceEmbeddedInLui: false + pattern: ^P\d{5}$ + prefix: panther.pathway + sampleId: P00024 + uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1 + n2t: + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. + example: P00024 + homepage: http://www.pantherdb.org/ + name: PANTHER Pathway at USC (Los Angeles) + namespaceEmbeddedInLui: false + pattern: ^P\d{5}$ + prefix: panther.pathway + uri_format: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1 + part_of: panther +panther.pthcmp: + biocontext: + is_identifiers: true + is_obo: false + prefix: PANTHER.PTHCMP + uri_format: http://identifiers.org/panther.pthcmp/$1 + mappings: + biocontext: PANTHER.PTHCMP + miriam: panther.pthcmp + n2t: panther.pthcmp + miriam: + deprecated: false + description: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation." + homepage: http://www.pantherdb.org/ + id: '00000422' + name: PANTHER Pathway Component + namespaceEmbeddedInLui: false + pattern: ^G|P|U|C|S\d{5}$ + prefix: panther.pthcmp + sampleId: P00266 + uri_format: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1 + n2t: + description: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation. + example: P00266 + homepage: http://www.pantherdb.org/ + name: PANTHER Pathway Component at USC (Los Angeles) + namespaceEmbeddedInLui: false + pattern: ^G|P|U|C|S\d{5}$ + prefix: panther.pthcmp + uri_format: http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1 + part_of: panther + pattern: ^(G|P|U|C|S)\d{5}$ +pao: + biocontext: + is_identifiers: false + is_obo: true + prefix: PAO + uri_format: http://purl.obolibrary.org/obo/PAO_$1 + mappings: + biocontext: PAO + obofoundry: pao + obofoundry: + contact: jaiswalp@science.oregonstate.edu + contact.github: jaiswalp + contact.label: Pankaj Jaiswal + contact.orcid: 0000-0002-1005-8383 + deprecated: true + homepage: http://www.plantontology.org + name: Plant Anatomy Ontology + prefix: pao +pass2: + biocontext: + is_identifiers: true + is_obo: false + prefix: PASS2 + uri_format: http://identifiers.org/pass2/$1 + deprecated: true + homepage: http://caps.ncbs.res.in/pass2 + mappings: + biocontext: PASS2 + miriam: pass2 + n2t: pass2 + prefixcommons: pass2 + miriam: + deprecated: false + description: The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. + homepage: http://caps.ncbs.res.in/pass2/ + id: '00000468' + name: PASS2 + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pass2 + sampleId: '46977' + uri_format: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1 + n2t: + description: The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. + example: '46977' + homepage: http://caps.ncbs.res.in/pass2/ + name: PASS2 at National centre for Biological Sciences (India) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pass2 + uri_format: http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1 + name: Protein Alignment organised as Structural Superfamily + prefixcommons: + description: PASS2 is an automatic version of the original superfamily alignment database, CAMPASS. The current version contains 628 multi member superfamilies and 566 structure based sequence annotated single member superfamilies. Sequence members for the superfamilies in different genomes have been listed and aligned. + example: '47391' + homepage: http://www.ncbs.res.in/~faculty/mini/campass/pass2.html + keywords: + - structure + - DNA + - genome + - classification + name: Protein Alignments organised as Structural Superfamilies + pattern: ^\d+$ + prefix: pass2 + uri_format: http://caps.ncbs.res.in/cgi-bin/mini/databases/campass/pass/pass.cgi?code=$1 +pathbank: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. + example: SMP0000219 + fairsharing: + abbreviation: PathBank + description: PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics, and systems biology. All PathBank pathways include information on the relevant organelles, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures, and protein complex quaternary structures. The database is easily browsed and supports full text, sequence, and chemical structure searching. + id: '2831' + name: PathBank + prefix: FAIRsharing.3xwMon + subjects: + - Endocrinology + - Molecular biology + - Animal Genetics + - Cheminformatics + - Bioinformatics + - Genetics + - Proteomics + - Drug Metabolism + - Human Genetics + - Molecular Microbiology + - Metabolomics + - Transcriptomics + - Cell Biology + - Database Management + - Microbiology + - Biology + - Systems Biology + - Medical Informatics + - Plant Genetics + homepage: https://pathbank.org + mappings: + fairsharing: FAIRsharing.3xwMon + name: PathBank + pattern: ^(SMP|PW)\d+$ + uri_format: https://pathbank.org/view/$1 +pathwaycommons: + biocontext: + is_identifiers: true + is_obo: false + prefix: PATHWAYCOMMONS + uri_format: http://identifiers.org/pathwaycommons/$1 + mappings: + biocontext: PATHWAYCOMMONS + miriam: pathwaycommons + n2t: pathwaycommons + prefixcommons: pathwaycommons + uniprot: PathwayCommons + miriam: + deprecated: false + description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. + homepage: http://www.pathwaycommons.org/pc/ + id: '00000073' + name: Pathway Commons + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pathwaycommons + sampleId: '485991' + uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1 + n2t: + description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. + example: '485991' + homepage: http://www.pathwaycommons.org/pc/ + name: Pathway Commons + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pathwaycommons + uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1 + prefixcommons: + description: Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases + example: '485991' + homepage: http://www.pathwaycommons.org/pc/ + keywords: + - pathway + name: Pathway Commons + pattern: ^\d+$ + prefix: pathwaycommons + uri_format: http://www.pathwaycommons.org/pc/record2.do?id=$1 + uniprot: + category: Enzyme and pathway databases + identifier: '253' + link_is_explicit: 'true' + name: Pathway Commons web resource for biological pathway data + prefix: PathwayCommons + uri_format: http://apps.pathwaycommons.org/search?q=$1 +pato: + biocontext: + is_identifiers: false + is_obo: true + prefix: PATO + uri_format: http://purl.obolibrary.org/obo/PATO_$1 + bioportal: + name: Phenotypic Quality Ontology + prefix: PATO + fairsharing: + abbreviation: PATO + description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily phenotype annotation. This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. + id: '1287' + name: Phenotypic QualiTy Ontology + prefix: FAIRsharing.ezwdhz + subjects: + - Biodiversity + - Biology + go: + homepage: http://www.obofoundry.org/ontology/pato.html + name: Phenotypic quality ontology + prefix: PATO + mappings: + biocontext: PATO + bioportal: PATO + fairsharing: FAIRsharing.ezwdhz + go: PATO + miriam: pato + n2t: pato + obofoundry: pato + ols: pato + ontobee: PATO + prefixcommons: pato + miriam: + deprecated: false + description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. + homepage: https://www.ebi.ac.uk/ols/ontologies/pato + id: '00000112' + name: PATO + namespaceEmbeddedInLui: true + pattern: ^PATO:\d{7}$ + prefix: pato + sampleId: '0001998' + uri_format: https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1 + n2t: + description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. + example: '0001998' + homepage: http://bioportal.bioontology.org/ontologies/PATO + name: PATO through BioPortal + namespaceEmbeddedInLui: true + pattern: ^PATO:\d{7}$ + prefix: pato + uri_format: http://purl.bioontology.org/ontology/PATO/PATO:$1 + obofoundry: + appears_in: + - agro + - aism + - cdno + - cl + - colao + - ecocore + - ecto + - fovt + - lepao + - mco + - ms + - pcl + - pco + - phipo + - planp + - rbo + - xpo + - zp + contact: g.gkoutos@gmail.com + contact.github: gkoutos + contact.label: George Gkoutos + contact.orcid: 0000-0002-2061-091X + deprecated: false + description: An ontology of phenotypic qualities (properties, attributes or characteristics) + download.json: http://purl.obolibrary.org/obo/pato.json + download.obo: http://purl.obolibrary.org/obo/pato.obo + download.owl: http://purl.obolibrary.org/obo/pato.owl + homepage: https://github.com/pato-ontology/pato/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Phenotype And Trait Ontology + preferredPrefix: PATO + prefix: pato + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/28387809 + title: 'The anatomy of phenotype ontologies: principles, properties and applications' + - id: https://www.ncbi.nlm.nih.gov/pubmed/15642100 + title: Using ontologies to describe mouse phenotypes + repository: https://github.com/pato-ontology/pato + ols: + description: An ontology of phenotypic qualities (properties, attributes or characteristics). + download: http://purl.obolibrary.org/obo/pato.owl + homepage: https://github.com/pato-ontology/pato/ + name: PATO - the Phenotype And Trait Ontology + prefix: pato + version: 2022-02-20 + version.iri: http://purl.obolibrary.org/obo/pato/releases/2022-02-20/pato.owl + ontobee: + library: Foundry + name: Phenotype And Trait Ontology + prefix: PATO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1107' + description: PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. + example: PATO:0001998 + homepage: http://obofoundry.org/wiki/index.php/PATO:Main_Page + keywords: + - obo + - ontology + - quality + - phenotype + name: PATO + pattern: ^PATO:\d{7}$ + prefix: pato + uri_format: http://www.ebi.ac.uk/ontology-lookup/?termId=$1 +pav: + biocontext: + is_identifiers: false + is_obo: false + prefix: pav + uri_format: http://purl.org/pav/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: pav + uri_format: http://purl.org/pav/$1 + bioportal: + name: PAV Provenance, Authoring and Versioning + prefix: PAV + contributor: + github: matentzn + name: Nico Matentzoglu + orcid: 0000-0002-7356-1779 + contributor_extras: + - email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. + example: authoredBy + fairsharing: + abbreviation: PAV + description: PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. This ontology describes the defined PAV properties and their usage. Note that PAV does not define any explicit classes or domain/ranges, as every property is meant to be used directly on the described online resource. + id: '678' + name: Provenance, Authoring and Versioning Ontology + prefix: FAIRsharing.nbfwwv + subjects: + - Data Management + - Subject Agnostic + homepage: https://pav-ontology.github.io/pav/ + mappings: + biocontext: pav + biolink: pav + bioportal: PAV + fairsharing: FAIRsharing.nbfwwv + name: Provenance, Authoring, and Versioning Vocabulary + pattern: ^[a-z][a-zA-Z]+$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + uri_format: http://purl.org/pav/$1 +paxdb.organism: + biocontext: + is_identifiers: true + is_obo: false + prefix: PAXDB.ORGANISM + uri_format: http://identifiers.org/paxdb.organism/$1 + mappings: + biocontext: PAXDB.ORGANISM + miriam: paxdb.organism + n2t: paxdb.organism + miriam: + deprecated: false + description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. + homepage: http://pax-db.org/ + id: '00000488' + name: PaxDb Organism + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paxdb.organism + sampleId: '9606' + uri_format: http://pax-db.org/#!species/$1 + n2t: + description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. + example: '9606' + homepage: http://pax-db.org/ + name: PaxDb v3 at University of Zurich + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paxdb.organism + uri_format: http://pax-db.org/#!species/$1 +paxdb.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: PAXDB.PROTEIN + uri_format: http://identifiers.org/paxdb.protein/$1 + mappings: + biocontext: PAXDB.PROTEIN + miriam: paxdb.protein + n2t: paxdb.protein + miriam: + deprecated: false + description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. + homepage: http://pax-db.org/ + id: '00000489' + name: PaxDb Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paxdb.protein + sampleId: '977869' + uri_format: http://pax-db.org/#!protein/$1 + n2t: + description: PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. + example: '977869' + homepage: http://pax-db.org/ + name: PaxDb v3 at University of Zurich + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: paxdb.protein + uri_format: http://pax-db.org/#!protein/$1 +pazar: + biocontext: + is_identifiers: true + is_obo: false + prefix: PAZAR + uri_format: http://identifiers.org/pazar/$1 + fairsharing: + abbreviation: PAZAR + description: PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data. + id: '2032' + name: PAZAR + prefix: FAIRsharing.33yggg + subjects: + - Life Science + mappings: + biocontext: PAZAR + fairsharing: FAIRsharing.33yggg + miriam: pazar + n2t: pazar + prefixcommons: pazar + miriam: + deprecated: false + description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. + homepage: http://www.pazar.info/ + id: '00000306' + name: Pazar Transcription Factor + namespaceEmbeddedInLui: false + pattern: ^TF\w+$ + prefix: pazar + sampleId: TF0001053 + uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1 + n2t: + description: The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. + example: TF0001053 + homepage: http://www.pazar.info/ + name: Pazar Transcription Factor at University of British Columbia + namespaceEmbeddedInLui: false + pattern: ^TF\w+$ + prefix: pazar + uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1 + prefixcommons: + description: PAZAR is a software framework for the construction and maintenance of regulatory sequence data annotations; a framework which allows multiple boutique databases to function independently within a larger system (or information mall). The goal of PAZAR is to be the public repository for regulatory data. + example: TF0000448 + homepage: http://www.pazar.info/ + keywords: + - regulation + - DNA + - RNA + name: PAZAR + pattern: ^TF\d+$ + prefix: pazar + uri_format: http://www.pazar.info/cgi-bin/tf_search.cgi?searchtab=tfs&ID_list=PAZAR_TF&geneID=$1 +pba: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A controlled vocabulary to support the study of transcription in the primate brain + download_obo: https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo + example: '128011350' + homepage: https://www.blueprintnhpatlas.org/ + name: Primate Brain Atlas + pattern: ^\d+$ + preferred_prefix: PBA +pcl: + bioportal: + name: Provisional Cell Ontology + prefix: PCL + example: '0011124' + mappings: + bioportal: PCL + obofoundry: pcl + ols: pcl + obofoundry: + contact: davidos@ebi.ac.uk + contact.github: dosumis + contact.label: David Osumi-Sutherland + contact.orcid: 0000-0002-7073-9172 + depends_on: + - bfo + - chebi + - cl + - go + - nbo + - ncbitaxon + - omo + - pato + - pr + - ro + - so + - uberon + deprecated: false + description: Cell types that are provisionally defined by experimental techniques such as single cell or single nucleus transcriptomics rather than a straightforward & coherent set of properties. + download.json: http://purl.obolibrary.org/obo/pcl.json + download.obo: http://purl.obolibrary.org/obo/pcl.obo + download.owl: http://purl.obolibrary.org/obo/pcl.owl + homepage: https://github.com/obophenotype/provisional_cell_ontology + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: Provisional Cell Ontology + preferredPrefix: PCL + prefix: pcl + repository: https://github.com/obophenotype/provisional_cell_ontology + ols: + description: Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties. + download: https://raw.githubusercontent.com/obophenotype/provisional_cell_ontology/master/pcl-full.owl + name: Provisional Cell Ontology + prefix: pcl + version: 2022-04-27 + version.iri: http://purl.obolibrary.org/obo/pcl/releases/2022-04-27/pcl-full.owl + pattern: ^\d{7}$ +pco: + biocontext: + is_identifiers: false + is_obo: true + prefix: PCO + uri_format: http://purl.obolibrary.org/obo/PCO_$1 + bioportal: + name: Population and Community Ontology + prefix: PCO + example: '0000021' + fairsharing: + abbreviation: PCO + description: Population and Community Ontology (PCO) is an ontology standard for describing the collective and interacting species of any taxa such as humans or plants. PCO has useful application in community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies. + id: '1053' + name: Population and Community Ontology + prefix: FAIRsharing.vq28qp + subjects: + - Ecology + - Biodiversity + - Community Care + - Social and Behavioural Science + - Population Genetics + mappings: + biocontext: PCO + bioportal: PCO + fairsharing: FAIRsharing.vq28qp + obofoundry: pco + ols: pco + ontobee: PCO + obofoundry: + appears_in: + - ecocore + - envo + contact: rlwalls2008@gmail.com + contact.github: ramonawalls + contact.label: Ramona Walls + contact.orcid: 0000-0001-8815-0078 + depends_on: + - bfo + - bfo + - caro + - envo + - go + - iao + - ncbitaxon + - pato + - ro + deprecated: false + description: An ontology about groups of interacting organisms such as populations and communities + download.owl: http://purl.obolibrary.org/obo/pco.owl + homepage: https://github.com/PopulationAndCommunityOntology/pco + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Population and Community Ontology + preferredPrefix: PCO + prefix: pco + repository: https://github.com/PopulationAndCommunityOntology/pco + ols: + description: The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. + download: http://purl.obolibrary.org/obo/pco.owl + homepage: https://github.com/PopulationAndCommunityOntology/pco + name: Population and Community Ontology + prefix: pco + version: 2021-05-03 + version.iri: http://purl.obolibrary.org/obo/pco/releases/2021-05-03/pco.owl + ontobee: + library: Library + name: Population and Community Ontology + prefix: PCO + pattern: ^\d{7}$ +pd_st: + biocontext: + is_identifiers: false + is_obo: true + prefix: PD_ST + uri_format: http://purl.obolibrary.org/obo/PD_ST_$1 + mappings: + biocontext: PD_ST + obofoundry: pd_st + obofoundry: + contact: henrich@embl.de + contact.label: Thorsten Heinrich + deprecated: true + homepage: http://4dx.embl.de/platy + name: Platynereis stage ontology + prefix: pd_st +pdb: + biocontext: + is_identifiers: false + is_obo: false + prefix: PDB + uri_format: http://www.ebi.ac.uk/pdbsum/$1 + fairsharing: + abbreviation: wwPDB + description: The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The wwPDB is composed of the RCSB PDB, PDBe, PDBj and BMRB. + id: '2207' + name: Worldwide Protein Data Bank + prefix: FAIRsharing.mckkb4 + subjects: + - Structural Biology + - Life Science + go: + homepage: https://www.rcsb.org/pdb/ + name: Protein Data Bank + prefix: PDB + uri_format: https://www.rcsb.org/structure/$1 + mappings: + biocontext: PDB + fairsharing: FAIRsharing.mckkb4 + go: PDB + miriam: pdb + n2t: pdb + ncbi: PDB + prefixcommons: pdbj + uniprot: RCSB-PDB + miriam: + deprecated: false + description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. + homepage: https://www.wwpdb.org/ + id: '00000020' + name: Protein Data Bank + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: pdb + providers: + - code: CURATOR_REVIEW + description: Proteopedia + homepage: http://www.proteopedia.org/ + name: Proteopedia + uri_format: http://proteopedia.org/wiki/index.php/$1 + - code: ebi + description: Protein Databank through PDBsum + homepage: https://www.ebi.ac.uk/pdbsum/ + name: Protein Databank through PDBsum + uri_format: https://www.ebi.ac.uk/pdbsum/$1 + - code: rcsb + description: RCSB PDB + homepage: https://www.rcsb.org/ + name: RCSB PDB + uri_format: https://www.rcsb.org/structure/$1 + - code: pdbj + description: Protein Data Bank Japan (PDBj) + homepage: http://www.pdbj.org/ + name: Protein Data Bank Japan (PDBj) + uri_format: https://pdbj.org/mine/summary/$1 + - code: pdbe + description: Protein Databank in Europe (PDBe) + homepage: http://www.pdbe.org/ + name: Protein Databank in Europe (PDBe) + uri_format: https://www.ebi.ac.uk/pdbe/entry/pdb/$1 + sampleId: 2gc4 + uri_format: https://www.wwpdb.org/pdb?id=$1 + n2t: + description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. + example: 2gc4 + homepage: https://www.pdb.org/ + name: RCSB PDB + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: pdb + uri_format: https://www.rcsb.org/pdb/explore/explore.do?structureId=$1 + name: PDB Structure + ncbi: + example: 12GS + homepage: http://www.rcsb.org/pdb/ + name: Biological macromolecule three dimensional structure database + prefix: PDB + prefixcommons: + description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. + example: 2OM1 + homepage: http://www.pdbj.org/ + keywords: + - protein + - structure + name: Protein Data Bank Japan + pattern: ^\d+[A-Z]+$ + prefix: pdbj + uri_format: http://service.pdbj.org/mine/Detail?PDBID=$1&PAGEID=Summary + synonyms: + - RCSB_PDB + - pdbe + - pdbj + - wwpdb + uniprot: + category: 3D structure databases + identifier: '171' + name: Protein Data Bank RCSB + prefix: RCSB-PDB + uri_format: https://www.rcsb.org/structure/$1 + wikidata: + database: Q766195 + database.label: Protein Data Bank + homepage: https://www.rcsb.org/ + name: PDB structure ID + pattern: '[0-9][0-9A-Za-z]{3}' + prefix: P638 + uri_format: https://rdf.wwpdb.org/pdb/$1 +pdb-ccd: + biocontext: + is_identifiers: true + is_obo: false + prefix: PDB-CCD + uri_format: http://identifiers.org/pdb-ccd/$1 + comment: might be same as pdb.ligand, not sure though + contributor_extras: + - email: bmeldal@ebi.ac.uk + github: bmeldal-eg + name: Birgit Meldal + orcid: 0000-0003-4062-6158 + example_extras: + - A + - PI + has_canonical: pdb.ligand + mappings: + biocontext: PDB-CCD + miriam: pdb-ccd + n2t: pdb-ccd + miriam: + deprecated: false + description: The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. + homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ + id: '00000113' + name: Chemical Component Dictionary + namespaceEmbeddedInLui: false + pattern: ^\w{1,3}$ + prefix: pdb-ccd + sampleId: AB0 + uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 + n2t: + description: The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. + example: AB0 + homepage: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ + name: Protein Data Bank Chemical Component Dictionary at EBI + namespaceEmbeddedInLui: false + pattern: ^\w{3}$ + prefix: pdb-ccd + uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 + pattern: ^\w{1,3}$ + synonyms: + - pdbechem + uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 +pdb.ligand: + biocontext: + is_identifiers: true + is_obo: false + prefix: PDB.LIGAND + uri_format: http://identifiers.org/pdb.ligand/$1 + mappings: + biocontext: PDB.LIGAND + miriam: pdb.ligand + n2t: pdb.ligand + prefixcommons: pdbligand + miriam: + deprecated: false + description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. + homepage: http://www.pdb.org/ + id: '00000490' + name: Protein Data Bank Ligand + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: pdb.ligand + providers: + - code: CURATOR_REVIEW + description: PDB Ligand at Protein Databank in Europe (PDBe) + homepage: https://www.pdbe.org/ + name: PDB Ligand at Protein Databank in Europe (PDBe) + uri_format: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 + sampleId: TRQ + uri_format: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1 + n2t: + description: The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. + example: TRQ + homepage: http://www.pdb.org/ + name: PDB Ligand at RCSB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: pdb.ligand + uri_format: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1 + prefixcommons: + description: PDB-Ligand is a three dimensional structure database of small molecular ligands that are bound to larger biolomocules deposited in the Protein Data Bank (PDB). + example: 1iij + homepage: http://www.idrtech.com/PDB-Ligand/ + keywords: + - small molecule + - protein + - interaction + - structure + name: PDB-Ligand + pattern: ^[A-Z,0-9]+$ + prefix: pdbligand + synonyms: + - PDB_CHEM_ID + wikidata: + prefix: P3636 +pdro: + biocontext: + is_identifiers: false + is_obo: true + prefix: PDRO + uri_format: http://purl.obolibrary.org/obo/PDRO_$1 + bioportal: + name: The Prescription of Drugs Ontology + prefix: PDRO + example: '0010039' + fairsharing: + abbreviation: PDRO + description: PDRO is a realist ontology that aims to represent the domain of drug prescriptions. Such an ontology is currently missing in the OBOFoundry and is highly relevant to the domains of existing ontologies like DRON, OMRSE and OAE. PDRO’s central focus is the structure of a drug prescription, which is represented as a mereology of informational entities. Our current use cases are (1) refining this structure (e.g., adding closure axioms, cardinality, datatype bindings, etc) for prospectively standardizing local electronic prescriptions and (2) annotating prescription data of differing EHRs for detecting inappropriate prescriptions using a central semantic framework. Future ontological work will include aligning PDRO more closely with the Document Acts Ontology. + id: '526' + name: The Prescription of Drugs Ontology + prefix: FAIRsharing.9te3ev + subjects: + - Primary Health Care + mappings: + biocontext: PDRO + bioportal: PDRO + fairsharing: FAIRsharing.9te3ev + obofoundry: pdro + ols: pdro + ontobee: PDRO + obofoundry: + contact: paul.fabry@usherbrooke.ca + contact.github: pfabry + contact.label: Paul Fabry + contact.orcid: 0000-0002-3336-2476 + deprecated: false + description: An ontology to describe entities related to prescription of drugs + download.owl: http://purl.obolibrary.org/obo/pdro.owl + homepage: https://github.com/OpenLHS/PDRO + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: The Prescription of Drugs Ontology + preferredPrefix: PDRO + prefix: pdro + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/34831777 + title: 'The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts' + repository: https://github.com/OpenLHS/PDRO + ols: + description: An ontology to describe entities related to prescription of drugs + download: http://purl.obolibrary.org/obo/pdro.owl + homepage: https://github.com/OpenLHS/PDRO + name: The Prescription of Drugs Ontology + prefix: pdro + version: 2021-06-08 + version.iri: http://purl.obolibrary.org/obo/pdro/2021-06-08/pdro.owl + ontobee: + library: Library + name: The Prescription of Drugs Ontology + prefix: PDRO + pattern: ^\d{7}$ +pdumdv: + biocontext: + is_identifiers: false + is_obo: true + prefix: PDUMDV + uri_format: http://purl.obolibrary.org/obo/PDUMDV_$1 + bioportal: + name: Platynereis Developmental Stages + prefix: PDUMDV + example: '0001410' + fairsharing: + abbreviation: PDUMDV + description: Life cycle stages for Platynereis dumerilii. The status of this resource is "in development", confirmed via developer remarks within the GitHub project stating that the ontology is not ready. + id: '1126' + name: Platynereis Developmental Stages + prefix: FAIRsharing.493qns + subjects: + - Developmental Biology + - Life Science + mappings: + biocontext: PDUMDV + bioportal: PDUMDV + fairsharing: FAIRsharing.493qns + obofoundry: pdumdv + ols: pdumdv + ontobee: PDUMDV + obofoundry: + contact: frederic.bastian@unil.ch + contact.github: fbastian + contact.label: Frédéric Bastian + contact.orcid: 0000-0002-9415-5104 + deprecated: false + description: Life cycle stages for Platynereis dumerilii + download.obo: http://purl.obolibrary.org/obo/pdumdv.obo + download.owl: http://purl.obolibrary.org/obo/pdumdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Platynereis Developmental Stages + preferredPrefix: PdumDv + prefix: pdumdv + repository: https://github.com/obophenotype/developmental-stage-ontologies + ols: + description: Life cycle stages for Platynereis dumerilii + download: http://purl.obolibrary.org/obo/pdumdv.owl + homepage: https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv + name: Platynereis Developmental Stages + prefix: pdumdv + version: 2020-03-10 + version.iri: http://purl.obolibrary.org/obo/pdumdv/releases/2020-03-10/pdumdv.owl + ontobee: + library: Library + name: Platynereis Developmental Stages + prefix: PDUMDV + pattern: ^\d{7}$ + synonyms: + - PdumDv +peco: + biocontext: + is_identifiers: false + is_obo: true + prefix: PECO + uri_format: http://purl.obolibrary.org/obo/PECO_$1 + bioportal: + name: Plant Experimental Conditions Ontology + prefix: PECO + download_obo: https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo + example: '0007114' + fairsharing: + abbreviation: PECO + description: PECO is a structured, controlled vocabulary for the representation of plant experimental conditions. It describes the treatments, growing conditions, and/or study types used in various types of plant biology experiments. + id: '1184' + name: Plant Experimental Condition Ontology + prefix: FAIRsharing.6yNXYK + subjects: + - Botany + mappings: + biocontext: PECO + bioportal: PECO + fairsharing: FAIRsharing.6yNXYK + obofoundry: peco + ols: peco + ontobee: PECO + obofoundry: + appears_in: + - agro + - mco + contact: jaiswalp@science.oregonstate.edu + contact.github: jaiswalp + contact.label: Pankaj Jaiswal + contact.orcid: 0000-0002-1005-8383 + deprecated: false + description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. + download.obo: http://purl.obolibrary.org/obo/peco.obo + download.owl: http://purl.obolibrary.org/obo/peco.owl + homepage: http://planteome.org/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Plant Experimental Conditions Ontology + preferredPrefix: PECO + prefix: peco + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 + title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' + repository: https://github.com/Planteome/plant-experimental-conditions-ontology + ols: + description: A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. + download: http://purl.obolibrary.org/obo/peco.owl + homepage: http://planteome.org/ + name: Plant Experimental Conditions Ontology + prefix: peco + version: 2020-08-21 + version.iri: http://purl.obolibrary.org/obo/peco/releases/2020-08-21/peco.owl + ontobee: + library: Library + name: Plant Experimental Conditions Ontology + prefix: PECO + pattern: ^\d{7}$ + preferred_prefix: PECO +ped: + fairsharing: + abbreviation: PED + description: Original standard text format for sample pedigree information and genotype calls. + id: '418' + name: PED + prefix: FAIRsharing.31385c + subjects: + - Bioinformatics + - Virology + - Life Science + - Epidemiology + mappings: + fairsharing: FAIRsharing.31385c + miriam: ped + miriam: + deprecated: false + description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. + homepage: https://proteinensemble.org/ + id: '00000777' + name: Protein Ensemble Database + namespaceEmbeddedInLui: false + pattern: ^PED\d{5}$ + prefix: ped + sampleId: PED00037 + uri_format: https://proteinensemble.org/$1 +ped.ensemble: + mappings: + miriam: ped.ensemble + miriam: + deprecated: false + description: The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. + homepage: https://proteinensemble.org/ + id: '00000795' + name: Protein Ensemble Database ensemble + namespaceEmbeddedInLui: false + pattern: ^PED\d{5}e\d{3}$ + prefix: ped.ensemble + sampleId: PED00017e001 + uri_format: https://proteinensemble.org/$1 + part_of: ped +peff: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + download_obo: https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo + example: '0001011' + homepage: https://www.psidev.info/peff + name: PSI Extended File Format + pattern: ^\d{7}$ +peptideatlas: + biocontext: + is_identifiers: true + is_obo: false + prefix: PEPTIDEATLAS + uri_format: http://identifiers.org/peptideatlas/$1 + fairsharing: + abbreviation: PeptideAtlas + description: The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and sequence and spectral library searches are applied. Analyses are performed to produce a probability of correct identification for all results in a uniform manner, together with false discovery rates at the whole-atlas level. + id: '1927' + name: PeptideAtlas + prefix: FAIRsharing.dvyrsz + subjects: + - Proteomics + mappings: + biocontext: PEPTIDEATLAS + fairsharing: FAIRsharing.dvyrsz + miriam: peptideatlas + n2t: peptideatlas + prefixcommons: peptideatlas + uniprot: PeptideAtlas + miriam: + deprecated: false + description: The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. + homepage: http://www.peptideatlas.org/ + id: '00000053' + name: PeptideAtlas + namespaceEmbeddedInLui: false + pattern: ^PAp[0-9]{8}$ + prefix: peptideatlas + sampleId: PAp00000009 + uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1 + n2t: + description: The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. + example: PAp00000009 + homepage: http://www.peptideatlas.org/ + name: PeptideAtlas at ISB + namespaceEmbeddedInLui: false + pattern: ^PAp[0-9]{8}$ + prefix: peptideatlas + uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1 + prefixcommons: + description: The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. + example: PAp00000009 + homepage: http://www.peptideatlas.org + keywords: + - mass spectrometry + - protein + - structure + name: PeptideAtlas + pattern: ^PAp[0-9]{8}$ + prefix: peptideatlas + pubmed_ids: + - '18451766' + uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?atlas_build_id=242&protein_name=$1&action=QUERY + uniprot: + category: Proteomic databases + identifier: '71' + link_is_explicit: 'true' + name: PeptideAtlas + prefix: PeptideAtlas + uri_format: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=$1 +peptideatlas.dataset: + mappings: + miriam: peptideatlas.dataset + n2t: peptideatlas.dataset + miriam: + deprecated: false + description: Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas. + homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary + id: '00000690' + name: PeptideAtlas Dataset + namespaceEmbeddedInLui: false + pattern: ^PASS\d{5}$ + prefix: peptideatlas.dataset + sampleId: PASS01237 + uri_format: http://www.peptideatlas.org/PASS/$1 + n2t: + description: Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas. + example: PASS01237 + homepage: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary + name: PeptideAtlas Dataset + namespaceEmbeddedInLui: false + pattern: ^PASS\d{5}$ + prefix: peptideatlas.dataset + uri_format: http://www.peptideatlas.org/PASS/$1 +perkinelmer: + cellosaurus: + category: Cell line collections + homepage: https://www.perkinelmer.com/ + name: PerkinElmer cell line collection + prefix: PerkinElmer + uri_format: https://www.perkinelmer.com/searchresult?searchName=$1 + example: SCC111 + mappings: + cellosaurus: PerkinElmer +peroxibase: + biocontext: + is_identifiers: true + is_obo: false + prefix: PEROXIBASE + uri_format: http://identifiers.org/peroxibase/$1 + fairsharing: + abbreviation: PeroxiBase + description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. + id: '2051' + name: PeroxiBase + prefix: FAIRsharing.z1czxj + subjects: + - Life Science + mappings: + biocontext: PEROXIBASE + fairsharing: FAIRsharing.z1czxj + miriam: peroxibase + n2t: peroxibase + prefixcommons: peroxibase + uniprot: PeroxiBase + miriam: + deprecated: false + description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. + homepage: http://peroxibase.toulouse.inra.fr/ + id: '00000222' + name: Peroxibase + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: peroxibase + sampleId: '5282' + uri_format: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1 + n2t: + description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. + example: '5282' + homepage: http://peroxibase.toulouse.inra.fr/ + name: Peroxibase at University of Geneva + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: peroxibase + uri_format: http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1 + prefixcommons: + description: Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. + example: '5282' + homepage: http://peroxibase.toulouse.inra.fr/ + keywords: + - enzyme + - protein + - regulation + name: PeroxiBase, a peroxidase database + pattern: ^\d+$ + prefix: peroxibase + pubmed_ids: + - '19112168' + uri_format: http://peroxibase.toulouse.inra.fr/listing.php?action=view&id=$1 + uniprot: + category: Protein family/group databases + identifier: '72' + link_is_explicit: 'true' + name: PeroxiBase, a peroxidase database + prefix: PeroxiBase + uri_format: http://peroxibase.toulouse.inra.fr/display_perox/view_perox/$1 +pesticides: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients. + example: derivatives%2Fthiocyclam%20hydrochloride + homepage: http://www.alanwood.net/pesticides + name: Alan Wood's Pesticides + uri_format: http://www.alanwood.net/pesticides/$1.html +pfam: + biocontext: + is_identifiers: true + is_obo: false + prefix: PFAM + uri_format: http://identifiers.org/pfam/$1 + example: PF11779 + fairsharing: + abbreviation: Pfam + description: The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM. + id: '1625' + name: Protein Families + prefix: FAIRsharing.y3scf6 + subjects: + - Biology + go: + description: Pfam is a collection of protein families represented by sequence alignments and hidden Markov models (HMMs) + homepage: http://pfam.xfam.org + name: Pfam database of protein families + prefix: Pfam + mappings: + biocontext: PFAM + fairsharing: FAIRsharing.y3scf6 + go: Pfam + miriam: pfam + n2t: pfam + ncbi: PFAM + prefixcommons: pfam + uniprot: Pfam + wikidata: P3519 + miriam: + deprecated: false + description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. + homepage: https://pfam.xfam.org/ + id: '00000028' + name: Pfam + namespaceEmbeddedInLui: false + pattern: ^PF\d{5}$ + prefix: pfam + sampleId: PF01234 + uri_format: https://pfam.xfam.org/family/$1 + n2t: + description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. + example: PF01234 + homepage: https://pfam.xfam.org/ + name: Pfam at EMBL-EBI + namespaceEmbeddedInLui: false + pattern: ^PF\d{5}$ + prefix: pfam + uri_format: https://pfam.xfam.org/family/$1 + name: Pfam + ncbi: + example: PF00003 + homepage: http://pfam.xfam.org/ + name: Collection of protein families + prefix: PFAM + prefixcommons: + description: The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. + example: PF01234 + homepage: http://pfam.sanger.ac.uk/ + keywords: + - domain + - protein + name: Sanger Pfam Mirror + pattern: ^PF\d{5}$ + prefix: pfam + pubmed_ids: + - '9847196' + - '14681378' + - '11752314' + - '10592242' + - '9399864' + - '9223186' + uri_format: http://pfam.sanger.ac.uk/family?entry=$1 + synonyms: + - PF + uniprot: + category: Family and domain databases + identifier: '73' + link_is_explicit: 'true' + name: Pfam protein domain database + prefix: Pfam + uri_format: https://pfam.xfam.org/family/$1 + wikidata: + database: Q906796 + database.homepage: http://pfam.xfam.org/ + database.label: Pfam + homepage: https://pfam.xfam.org/ + name: Pfam ID + pattern: (PF\d{5}|CL\d{4}) + prefix: P3519 + uri_format: http://pfam.xfam.org/family?acc=$1 +pfam.clan: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Higher order grouping of Pfam families + example: CL0192 + homepage: https://pfam.xfam.org + name: Pfam Clans + pattern: ^CL\d+$ + uri_format: https://pfam.xfam.org/clan/$1 +pfr: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. + example: '1001' + fairsharing: + abbreviation: TDR + description: The Texas Data Repository is a platform for publishing and archiving datasets (and other data products) created by faculty, staff, and students at Texas higher education institutions. The repository is built in an open-source application called Dataverse, developed and used by Harvard University. The repository is hosted by the Texas Digital Library, a consortium of academic libraries in Texas with a proven history of providing shared technology services that support secure, reliable access to digital collections of research and scholarship. Researchers deposit data within the TDR to, for example, comply with funding requirements and ensure reliable, managed access for data. + id: '2558' + name: Texas Data Repository + prefix: FAIRsharing.wqsxtg + subjects: + - Data Management + - Subject Agnostic + homepage: http://repository.topdownproteomics.org/proteoforms + mappings: + fairsharing: FAIRsharing.wqsxtg + name: Proteoform Atlas + pattern: ^\d+$ + synonyms: + - TDR + uri_format: http://repository.topdownproteomics.org/proteoforms/$1 +pgdso: + biocontext: + is_identifiers: false + is_obo: true + prefix: PGDSO + uri_format: http://purl.obolibrary.org/obo/PGDSO_$1 + mappings: + biocontext: PGDSO + obofoundry: pgdso + obofoundry: + contact: po-discuss@plantontology.org + contact.label: Plant Ontology Administrators + deprecated: true + homepage: http://www.plantontology.org + name: Plant Growth and Development Stage + prefix: pgdso +pgs: + mappings: + miriam: pgs + miriam: + deprecated: false + description: The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation. + homepage: http://pgscatalog.org + id: '00000753' + name: Polygenic Score Catalog + namespaceEmbeddedInLui: false + pattern: ^PGS[0-9]{6}$ + prefix: pgs + sampleId: PGS000018 + uri_format: https://www.pgscatalog.org/pgs/$1/ + uri_format: https://www.pgscatalog.org/pgs/$1 +pgx: + biocontext: + is_identifiers: true + is_obo: false + prefix: PGX + uri_format: http://identifiers.org/pgx/$1 + cellosaurus: + category: Polymorphism and mutation databases + homepage: https://progenetix.org/ + name: Cancer genome data @ progenetix.org + prefix: Progenetix + uri_format: https://progenetix.org/biosamples/by-curie/cellosaurus:$1 + fairsharing: + abbreviation: Progenetix + description: The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. Progenetix is the largest curated database for whole genome copy number profiles in cancer. The current dataset contains more than 130'000 profiles from genomic CNV screening experiments. This data covers 700 diagnostic entities according to the NCIt Neoplasm Core and the International Classification of Disease in Oncology (ICD-O 3). Additionally, the website attempts to lists all publications referring to cancer genome profiling experiments. + id: '2134' + name: Progenetix + prefix: FAIRsharing.65tdnz + subjects: + - Genomics + - Biomedical Science + mappings: + biocontext: PGX + cellosaurus: Progenetix + fairsharing: FAIRsharing.65tdnz + miriam: pgx + n2t: pgx + miriam: + deprecated: false + description: The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt "neoplasm" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs. + homepage: https://progenetix.org/ + id: '00000600' + name: Progenetix + namespaceEmbeddedInLui: false + pattern: ^\w{3,15}[-_]\w[\w.-]{3,128}$ + prefix: pgx + sampleId: pgxbs-kftva5zv + uri_format: https://progenetix.org/services/ids/$1 + n2t: + description: The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32317 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1026 articles and represents 364 different cancer types, according to the International classification of Diseases in Oncology (ICD-O). + example: icdom:8500_3 + homepage: http://progenetix.org/ + name: Progenetix + namespaceEmbeddedInLui: false + pattern: ^[\w\-:,]{3,64}$ + prefix: pgx + uri_format: http://progenetix.org/pgx:$1 + synonyms: + - Progenetix +pharmacodb.cell: + cellosaurus: + category: Chemistry resources + homepage: https://pharmacodb.ca/ + name: PharmacoDB integrative pharmacogenomic database + prefix: PharmacoDB + uri_format: https://pharmacodb.ca/cell_lines/$1 + description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line. + example: 22RV1_12_2019 + homepage: https://pharmacodb.ca/cell_lines + mappings: + cellosaurus: PharmacoDB + name: PharmacoDB Cells + uri_format: https://pharmacodb.ca/cell_lines/$1 +pharmacodb.dataset: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset. + example: '1' + homepage: https://pharmacodb.ca/datasets + name: PharmacoDB Datasets + pattern: ^\d+$ + uri_format: https://pharmacodb.ca/datasets/$1 +pharmacodb.tissue: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue. + example: '13' + homepage: https://pharmacodb.ca/tissues + name: PharmacoDB Tissues + pattern: ^\d+$ + uri_format: https://pharmacodb.ca/tissues/$1 +pharmgkb.disease: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHARMGKB.DISEASE + uri_format: http://identifiers.org/pharmgkb.disease/$1 + mappings: + biocontext: PHARMGKB.DISEASE + miriam: pharmgkb.disease + n2t: pharmgkb.disease + prefixcommons: pharmgkb.disease + miriam: + deprecated: false + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + homepage: http://www.pharmgkb.org/ + id: '00000090' + name: PharmGKB Disease + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.disease + sampleId: PA447218 + uri_format: http://www.pharmgkb.org/disease/$1 + n2t: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + example: PA447218 + homepage: http://www.pharmgkb.org/ + name: PharmGKB Disease at Stanford + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.disease + uri_format: http://www.pharmgkb.org/disease/$1 + prefixcommons: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + example: PA447218 + keywords: + - pharmacogenomics + name: PharmGKB Disease + pattern: ^PA\d+$ + prefix: pharmgkb.disease + pubmed_ids: + - '11908751' + - '22103613' + uri_format: http://www.pharmgkb.org/disease/$1 + wikidata: + prefix: P7001 +pharmgkb.drug: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHARMGKB.DRUG + uri_format: http://identifiers.org/pharmgkb.drug/$1 + mappings: + biocontext: PHARMGKB.DRUG + miriam: pharmgkb.drug + n2t: pharmgkb.drug + prefixcommons: pharmgkb.drug + miriam: + deprecated: false + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + homepage: http://www.pharmgkb.org/ + id: '00000091' + name: PharmGKB Drug + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.drug + sampleId: PA448710 + uri_format: http://www.pharmgkb.org/drug/$1 + n2t: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + example: PA448710 + homepage: http://www.pharmgkb.org/ + name: PharmGKB Drug at Stanford + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.drug + uri_format: http://www.pharmgkb.org/drug/$1 + prefixcommons: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + example: PA448710 + keywords: + - drug + - pharmacogenomics + name: PharmGKB Drug + pattern: ^PA\d+$ + prefix: pharmgkb.drug + pubmed_ids: + - '11908751' + - '22103613' + uri_format: http://www.pharmgkb.org/drug/$1 + wikidata: + prefix: P7001 +pharmgkb.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHARMGKB.GENE + uri_format: http://identifiers.org/pharmgkb.gene/$1 + bioportal: + name: PharmGKB Ontology + prefix: PHARMGKB + go: + homepage: https://www.pharmgkb.org + name: Pharmacogenetics and Pharmacogenomics Knowledge Base + prefix: PharmGKB + uri_format: https://www.pharmgkb.org/do/serve?objId=$1 + mappings: + biocontext: PHARMGKB.GENE + bioportal: PHARMGKB + go: PharmGKB + miriam: pharmgkb.gene + n2t: pharmgkb.gene + prefixcommons: pharmgkb.gene + miriam: + deprecated: false + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + homepage: http://www.pharmgkb.org/ + id: '00000245' + name: PharmGKB Gene + namespaceEmbeddedInLui: false + pattern: ^PA\w+$ + prefix: pharmgkb.gene + sampleId: PA131 + uri_format: http://www.pharmgkb.org/gene/$1 + n2t: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + example: PA131 + homepage: http://www.pharmgkb.org/ + name: PharmGKB Gene at Stanford + namespaceEmbeddedInLui: false + pattern: ^PA\w+$ + prefix: pharmgkb.gene + uri_format: http://www.pharmgkb.org/gene/$1 + prefixcommons: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. + example: PA131 + keywords: + - gene + - pharmacogenomics + name: PharmGKB Gene + pattern: ^PA\w+$ + prefix: pharmgkb.gene + pubmed_ids: + - '22103613' + uri_format: http://www.pharmgkb.org/gene/$1 + wikidata: + prefix: P7001 +pharmgkb.pathways: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHARMGKB.PATHWAYS + uri_format: http://identifiers.org/pharmgkb.pathways/$1 + mappings: + biocontext: PHARMGKB.PATHWAYS + miriam: pharmgkb.pathways + n2t: pharmgkb.pathways + prefixcommons: pharmgkb.pathways + miriam: + deprecated: false + description: "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies." + homepage: http://www.pharmgkb.org/ + id: '00000089' + name: PharmGKB Pathways + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.pathways + sampleId: PA146123006 + uri_format: http://www.pharmgkb.org/pathway/$1 + n2t: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies. + example: PA146123006 + homepage: http://www.pharmgkb.org/ + name: PharmGKB at Stanford + namespaceEmbeddedInLui: false + pattern: ^PA\d+$ + prefix: pharmgkb.pathways + uri_format: http://www.pharmgkb.org/pathway/$1 + prefixcommons: + description: The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies. + example: PA146123006 + keywords: + - pathway + - pharmacogenomics + name: PharmGKB Pathways + pattern: ^PA\d+$ + prefix: pharmgkb.pathways + pubmed_ids: + - '11908751' + - '22103613' + uri_format: http://www.pharmgkb.org/pathway/$1 + wikidata: + prefix: P7001 +phenolexplorer: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHENOLEXPLORER + uri_format: http://identifiers.org/phenolexplorer/$1 + mappings: + biocontext: PHENOLEXPLORER + miriam: phenolexplorer + n2t: phenolexplorer + miriam: + deprecated: false + description: Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. + homepage: http://www.phenol-explorer.eu/foods/ + id: '00000268' + name: Phenol-Explorer + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: phenolexplorer + sampleId: '75' + uri_format: http://phenol-explorer.eu/foods/$1 + n2t: + description: Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. + example: '75' + homepage: http://www.phenol-explorer.eu/foods/ + name: Phenol-Explorer Database on Phenol content of foods + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: phenolexplorer + uri_format: http://phenol-explorer.eu/foods/$1 +phenx: + bioportal: + name: PhenX Phenotypic Terms + prefix: PHENX + description: A Web-based catalog of recommended measurement protocols + example: '130502' + fairsharing: + abbreviation: PhenX + description: Standard measures related to complex diseases, phenotypic traits and environmental exposures. + id: '894' + name: PhenX Phenotypic Terms + prefix: FAIRsharing.y5jcwa + subjects: + - Environmental Science + - Life Science + - Biomedical Science + homepage: https://www.phenxtoolkit.org/ + mappings: + bioportal: PHENX + fairsharing: FAIRsharing.y5jcwa + name: PhenX Toolkit + pattern: ^\d+$ + uri_format: https://www.phenxtoolkit.org/protocols/view/$1 +phipo: + bioportal: + name: Pathogen Host Interaction Phenotype Ontology + prefix: PHIPO + example: '0000001' + mappings: + bioportal: PHIPO + obofoundry: phipo + ols: phipo + ontobee: PHIPO + obofoundry: + contact: alayne.cuzick@rothamsted.ac.uk + contact.github: CuzickA + contact.label: Alayne Cuzick + contact.orcid: 0000-0001-8941-3984 + depends_on: + - pato + deprecated: false + description: PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions. + download.obo: http://purl.obolibrary.org/obo/phipo.obo + download.owl: http://purl.obolibrary.org/obo/phipo.owl + homepage: https://github.com/PHI-base/phipo + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Pathogen Host Interaction Phenotype Ontology + preferredPrefix: PHIPO + prefix: phipo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/34788826 + title: 'PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions' + repository: https://github.com/PHI-base/phipo + ols: + description: Ontology of species-neutral phenotypes observed in pathogen-host interactions. + download: http://purl.obolibrary.org/obo/phipo.owl + homepage: https://github.com/PHI-base/phipo + name: Pathogen Host Interactions Phenotype Ontology + prefix: phipo + version: 2021-07-14 + version.iri: http://purl.obolibrary.org/obo/phipo/releases/2021-07-14/phipo.owl + ontobee: + library: Library + name: Pathogen Host Interaction Phenotype Ontology + prefix: PHIPO + pattern: ^\d{7}$ +phosphopoint.kinase: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHOSPHOPOINT.KINASE + uri_format: http://identifiers.org/phosphopoint.kinase/$1 + mappings: + biocontext: PHOSPHOPOINT.KINASE + miriam: phosphopoint.kinase + n2t: phosphopoint.kinase + miriam: + deprecated: false + description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. + homepage: http://kinase.bioinformatics.tw/ + id: '00000385' + name: PhosphoPoint Kinase + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phosphopoint.kinase + sampleId: AURKA + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 + n2t: + description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. + example: AURKA + homepage: http://kinase.bioinformatics.tw/ + name: PhosphoPoint Kinase at National Taiwan University + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phosphopoint.kinase + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 +phosphopoint.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHOSPHOPOINT.PROTEIN + uri_format: http://identifiers.org/phosphopoint.protein/$1 + mappings: + biocontext: PHOSPHOPOINT.PROTEIN + miriam: phosphopoint.protein + n2t: phosphopoint.protein + miriam: + deprecated: false + description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. + homepage: http://kinase.bioinformatics.tw/ + id: '00000386' + name: PhosphoPoint Phosphoprotein + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phosphopoint.protein + sampleId: AURKA + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 + n2t: + description: PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. + example: AURKA + homepage: http://kinase.bioinformatics.tw/ + name: PhosphoPoint Phosphoprotein at National Taiwan University + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phosphopoint.protein + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 +phosphosite.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHOSPHOSITE.PROTEIN + uri_format: http://identifiers.org/phosphosite.protein/$1 + mappings: + biocontext: PHOSPHOSITE.PROTEIN + miriam: phosphosite.protein + n2t: phosphosite.protein + miriam: + deprecated: false + description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. + homepage: http://www.phosphosite.org/homeAction.do + id: '00000105' + name: PhosphoSite Protein + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: phosphosite.protein + sampleId: '12300' + uri_format: http://www.phosphosite.org/proteinAction.do?id=$1 + n2t: + description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. + example: '12300' + homepage: http://www.phosphosite.org/homeAction.do + name: PhosphoSite + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: phosphosite.protein + uri_format: http://www.phosphosite.org/proteinAction.do?id=$1 +phosphosite.residue: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHOSPHOSITE.RESIDUE + uri_format: http://identifiers.org/phosphosite.residue/$1 + mappings: + biocontext: PHOSPHOSITE.RESIDUE + miriam: phosphosite.residue + n2t: phosphosite.residue + miriam: + deprecated: false + description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. + homepage: http://www.phosphosite.org/homeAction.do + id: '00000125' + name: PhosphoSite Residue + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: phosphosite.residue + sampleId: '2842' + uri_format: http://www.phosphosite.org/siteAction.do?id=$1 + n2t: + description: PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. + example: '2842' + homepage: http://www.phosphosite.org/homeAction.do + name: PhosphoSite Residue + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: phosphosite.residue + uri_format: http://www.phosphosite.org/siteAction.do?id=$1 +phylomedb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHYLOMEDB + uri_format: http://identifiers.org/phylomedb/$1 + fairsharing: + abbreviation: PhylomeDB + description: 'PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed, genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interests. The v5 release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies ' + id: '1838' + name: PhylomeDB + prefix: FAIRsharing.7hxxc4 + subjects: + - Taxonomy + - Phylogeny + - Phylogenetics + - Phylogenomics + - Life Science + mappings: + biocontext: PHYLOMEDB + fairsharing: FAIRsharing.7hxxc4 + miriam: phylomedb + n2t: phylomedb + prefixcommons: phylomedb + uniprot: PhylomeDB + miriam: + deprecated: false + description: PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. + homepage: http://phylomedb.org/ + id: '00000223' + name: PhylomeDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phylomedb + sampleId: Phy000CLXM_RAT + uri_format: http://phylomedb.org/?seqid=$1 + n2t: + description: PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. + example: Phy000CLXM_RAT + homepage: http://phylomedb.org/ + name: PhylomeDB at Centro de Investigación Príncipe Felipe + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: phylomedb + uri_format: http://phylomedb.org/?seqid=$1 + prefixcommons: + description: PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. + example: Phy000CLXM_RAT + homepage: http://phylomedb.bioinfo.cipf.es + keywords: + - genome + - protein + - taxonomy + name: Database for complete collections of gene phylogenies + pattern: ^\w+$ + prefix: phylomedb + pubmed_ids: + - '17962297' + uri_format: http://phylomedb.org/?seqid=$d + uniprot: + category: Phylogenomic databases + identifier: '144' + link_is_explicit: 'true' + name: Database for complete collections of gene phylogenies + prefix: PhylomeDB + uri_format: http://phylomedb.org/search_phylome/?seqid=$1 +phytozome.locus: + biocontext: + is_identifiers: true + is_obo: false + prefix: PHYTOZOME.LOCUS + uri_format: http://identifiers.org/phytozome.locus/$1 + mappings: + biocontext: PHYTOZOME.LOCUS + miriam: phytozome.locus + n2t: phytozome.locus + ncbi: Phytozome + miriam: + deprecated: false + description: Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information. + homepage: http://www.phytozome.net/ + id: '00000432' + name: Phytozome Locus + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: phytozome.locus + sampleId: Glyma0021s00410 + uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 + n2t: + description: Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information. + example: Glyma0021s00410 + homepage: http://www.phytozome.net/ + name: Phytozome Locus at Joint Genome Institute + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: phytozome.locus + uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 + ncbi: + example: Glyma0021s00410 + homepage: http://phytozome.jgi.doe.gov/pz/portal.html + name: Plant Genome Network + prefix: Phytozome + synonyms: + - JGI Phytozome +pictar: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + example: hsa-let-7a + homepage: https://pictar.mdc-berlin.de/ + name: PicTar + synonyms: + - pictar-vert +pid.pathway: + biocontext: + is_identifiers: true + is_obo: false + prefix: PID.PATHWAY + uri_format: http://identifiers.org/pid.pathway/$1 + example: eff796f3-6195-11e5-8ac5-06603eb7f303 + fairsharing: + abbreviation: PID + description: The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. + id: '1959' + name: Pathway Interaction Database + prefix: FAIRsharing.ncgh1j + subjects: + - Life Science + mappings: + biocontext: PID.PATHWAY + fairsharing: FAIRsharing.ncgh1j + miriam: pid.pathway + n2t: pid.pathway + prefixcommons: pid + miriam: + deprecated: false + description: The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information. + homepage: http://pid.nci.nih.gov/ + id: '00000133' + name: 'NCI Pathway Interaction Database: Pathway' + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: pid.pathway + sampleId: pi3kcipathway + uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1 + n2t: + description: The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information. + example: pi3kcipathway + homepage: http://pid.nci.nih.gov/ + name: NCI Pathway Interaction Database (Pathway) + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: pid.pathway + uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1 + pattern: ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ + prefixcommons: + description: The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways + example: p38alphabetadownstreampathway + homepage: http://pid.nci.nih.gov/ + keywords: + - pathway + - small molecule + - gene + - protein + name: Pathway Interaction Database + pattern: ^\w+$ + prefix: pid + pubmed_ids: + - '18832364' + uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1 + synonyms: + - pid +pigqtldb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PIGQTLDB + uri_format: http://identifiers.org/pigqtldb/$1 + mappings: + biocontext: PIGQTLDB + miriam: pigqtldb + n2t: pigqtldb + prefixcommons: pigqtldb + miriam: + deprecated: false + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs. + homepage: https://www.animalgenome.org/QTLdb + id: '00000506' + name: Animal Genome Pig QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pigqtldb + sampleId: '14' + uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 + n2t: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs. + example: '14' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/SS/index + name: Animal QTL Pig at Iowa State University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pigqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1 + part_of: qtldb + prefixcommons: + description: This Pig Quantitative Trait Locus (QTL) database (Pig QTLdb) has gathered all pig QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on pig chromosomes the most feasible location for genes responsible for quantitative trait important to pig production. + example: '66' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/SS/index + keywords: + - DNA + - genome + name: Pig Quantitative Trait Locus database + pattern: ^\d+$ + prefix: pigqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1 +pina: + biocontext: + is_identifiers: true + is_obo: false + prefix: PINA + uri_format: http://identifiers.org/pina/$1 + fairsharing: + abbreviation: PINA + description: Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. In particular, it provides a variety of built-in tools to filter and analyze the networks for gaining biological and functional insights into the network. + id: '1627' + name: Protein Interaction Network Analysis platform + prefix: FAIRsharing.7q4gsz + subjects: + - Life Science + - Data Visualization + mappings: + biocontext: PINA + fairsharing: FAIRsharing.7q4gsz + miriam: pina + n2t: pina + miriam: + deprecated: false + description: Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. + homepage: http://cbg.garvan.unsw.edu.au/pina/ + id: '00000359' + name: PINA + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: pina + sampleId: Q13485 + uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null + n2t: + description: Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. + example: Q13485 + homepage: http://cbg.garvan.unsw.edu.au/pina/ + name: Protein Interaction Network Analysis (PINA) at Garvan Institute + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: pina + uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null + name: Protein Interaction Network Analysis + provides: uniprot + uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1 +piroplasma: + biocontext: + is_identifiers: true + is_obo: false + prefix: PIROPLASMA + uri_format: http://identifiers.org/piroplasma/$1 + mappings: + biocontext: PIROPLASMA + miriam: piroplasma + n2t: piroplasma + miriam: + deprecated: false + description: PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: http://piroplasmadb.org/ + id: '00000351' + name: PiroplasmaDB + namespaceEmbeddedInLui: false + pattern: ^TA\d+$ + prefix: piroplasma + sampleId: TA14985 + uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + n2t: + description: PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: TA14985 + homepage: http://piroplasmadb.org/ + name: PiroplasmaBD at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^TA\d+$ + prefix: piroplasma + uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +pirsf: + biocontext: + is_identifiers: true + is_obo: false + prefix: PIRSF + uri_format: http://identifiers.org/pirsf/$1 + fairsharing: + abbreviation: PIRSF + description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. + id: '2035' + name: PIR SuperFamily + prefix: FAIRsharing.vssch2 + subjects: + - Proteomics + - Life Science + go: + homepage: http://pir.georgetown.edu/pirsf/ + name: PIR Superfamily Classification System + prefix: PIRSF + uri_format: http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 + mappings: + biocontext: PIRSF + fairsharing: FAIRsharing.vssch2 + go: PIRSF + miriam: pirsf + n2t: pirsf + prefixcommons: pirsf + uniprot: PIRSF + miriam: + deprecated: false + description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. + homepage: https://pir.georgetown.edu/ + id: '00000017' + name: PIRSF + namespaceEmbeddedInLui: false + pattern: ^PIRSF\d{6}$ + prefix: pirsf + sampleId: PIRSF000100 + uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 + n2t: + description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. + example: PIRSF000100 + homepage: https://pir.georgetown.edu/ + name: PIRSF + namespaceEmbeddedInLui: false + pattern: ^PIRSF\d{6}$ + prefix: pirsf + uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 + prefixcommons: + description: The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. + example: PIRSF000100 + homepage: http://pir.georgetown.edu/pirsf/ + keywords: + - protein + - structure + name: PIRSF; a whole-protein classification database + pattern: ^PIRSF\d{6}$ + prefix: pirsf + pubmed_ids: + - '14681371' + uri_format: http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 + uniprot: + category: Family and domain databases + identifier: '79' + link_is_explicit: 'true' + name: PIRSF; a whole-protein classification database + prefix: PIRSF + uri_format: https://proteininformationresource.org/cgi-bin/ipcSF?id=$1 +pkdb: + fairsharing: + abbreviation: PK-DB + description: PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. + id: '3196' + name: Pharmacokinetics Database + prefix: FAIRsharing.AYegqK + subjects: + - Clinical Veterinary Medicine + - Clinical Studies + - Personalized Medicine + - Pharmacology + - Life Science + - Pharmacogenomics + - Preclinical Studies + mappings: + fairsharing: FAIRsharing.AYegqK + miriam: pkdb + miriam: + deprecated: false + description: 'PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ' + homepage: https://www.hu-berlin.de/?set_language=en&cl=en + id: '00000708' + name: PK-DB + namespaceEmbeddedInLui: false + pattern: ^PKDB[0-9]{5}$ + prefix: pkdb + sampleId: PKDB00198 + uri_format: https://pk-db.com/data/$1 +plana: + biocontext: + is_identifiers: false + is_obo: true + prefix: PLANA + uri_format: http://purl.obolibrary.org/obo/PLANA_$1 + bioportal: + name: Planarian Anatomy and Developmental Stage Ontolgoy + prefix: PLANA + example: '0000001' + fairsharing: + abbreviation: PLANA + description: Anatomy ontology for planaria and terms specific to the developmental stages of the planarian Schmidtea mediterranea. As the regenerative flatworm Schmidtea mediterranea gains popularity as a developmental research organism the need for standard nomenclature and a centralized repository of anatomical terms has become increasingly apparent. Utilization of a controlled vocabulary creates opportunities to catalogue genes and expression data for computational searches across research groups and cross-species comparisons, all while establishing a framework for integration of new terms. We created a Planarian Anatomy Ontology containing 327 terms and definitions for cellular organelles, cell types, tissues, organ systems, anatomical entities, life cycle stages and developmental processes described in the literature. Where possible, extant terms and definitions from Uberon and other open source anatomy ontologies were imported into the ontology to strengthen cross-species queries. + id: '1171' + name: Planarian Anatomy and Developmental Stage Ontology + prefix: FAIRsharing.g1qrqs + subjects: + - Anatomy + - Developmental Biology + - Life Science + mappings: + biocontext: PLANA + bioportal: PLANA + fairsharing: FAIRsharing.g1qrqs + obofoundry: plana + ols: plana + ontobee: PLANA + name: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology + obofoundry: + appears_in: + - planp + contact: smr@stowers.org + contact.github: srobb1 + contact.label: Sofia Robb + contact.orcid: 0000-0002-3528-5267 + depends_on: + - ro + - uberon + deprecated: false + description: PLANA, the planarian anatomy ontology, encompasses the anatomy and life cycle stages for both __Schmidtea mediterranea__ biotypes. + download.obo: http://purl.obolibrary.org/obo/plana.obo + download.owl: http://purl.obolibrary.org/obo/plana.owl + homepage: https://github.com/obophenotype/planaria-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: planaria-ontology + preferredPrefix: PLANA + prefix: plana + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/34318308 + title: 'Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms' + repository: https://github.com/obophenotype/planaria-ontology + ols: + description: PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. + download: http://purl.obolibrary.org/obo/plana.owl + name: Planarian Anatomy Ontology (PLANA) + prefix: plana + version: 2022-03-02 + version.iri: http://purl.obolibrary.org/obo/plana/releases/2022-03-02 + ontobee: + library: Library + name: planaria-ontology + prefix: PLANA + pattern: ^\d{7}$ +planp: + bioportal: + name: Planarian Phenotype Ontology + prefix: PLANP + example: '0000001' + mappings: + bioportal: PLANP + obofoundry: planp + ols: planp + ontobee: PLANP + obofoundry: + contact: smr@stowers.org + contact.github: srobb1 + contact.label: Sofia Robb + contact.orcid: 0000-0002-3528-5267 + depends_on: + - go + - pato + - plana + - ro + deprecated: false + description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. + download.obo: http://purl.obolibrary.org/obo/planp.obo + download.owl: http://purl.obolibrary.org/obo/planp.owl + homepage: https://github.com/obophenotype/planarian-phenotype-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Planarian Phenotype Ontology + preferredPrefix: PLANP + prefix: planp + repository: https://github.com/obophenotype/planarian-phenotype-ontology + ols: + description: Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. + download: http://purl.obolibrary.org/obo/planp.owl + homepage: https://github.com/obophenotype/planarian-phenotype-ontology + name: Planarian Phenotype Ontology (PLANP) + prefix: planp + version: 2020-03-28 + version.iri: http://purl.obolibrary.org/obo/planp/releases/2020-03-28/planp.owl + ontobee: + library: Library + name: Planarian Phenotype Ontology + prefix: PLANP + pattern: ^\d+$ +planttfdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PLANTTFDB + uri_format: http://identifiers.org/planttfdb/$1 + fairsharing: + abbreviation: PlantTFDB + description: Plant Transcription Factor Database (PlantTFDB) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, It contains 320 370 TFs, classified into 58 families, from 165 species. Abundant functional and evolutionary annotations (e.g., GO, functional description, binding motifs, cis-element, regulation, references, orthologous groups and phylogenetic tree, etc.) are provided for identified TFs. In addition, multiple online tools are set up for TF identification, regulation prediction and functional enrichment analyses. + id: '1807' + name: Plant Transcription Factor Database + prefix: FAIRsharing.ex3fqk + subjects: + - Life Science + mappings: + biocontext: PLANTTFDB + fairsharing: FAIRsharing.ex3fqk + miriam: planttfdb + n2t: planttfdb + prefixcommons: planttfdb + miriam: + deprecated: false + description: The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. + homepage: http://planttfdb.cbi.pku.edu.cn + id: '00000579' + name: Plant Transcription Factor Database + namespaceEmbeddedInLui: false + pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ + prefix: planttfdb + sampleId: Ath_AT1G01030.1 + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 + n2t: + description: The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. + example: Ath_AT1G01030.1 + homepage: http://planttfdb.cbi.pku.edu.cn + name: PlantTFDB at Peking University + namespaceEmbeddedInLui: false + pattern: ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ + prefix: planttfdb + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 + prefixcommons: + description: Plant Transcription Factor Database collected 40976 transcription factors from 39 species, and they are classified into 58 families. + example: Ath005712 + homepage: http://planttfdb.cbi.pku.edu.cn + keywords: + - regulation + - DNA + - RNA + - small molecule + - protein + - gene + name: Plant Transcription Factor Database + pattern: ^[a-z]+\d+$ + prefix: planttfdb + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=[?species_name]&did=$1 +plasmodb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PLASMODB + uri_format: http://identifiers.org/plasmodb/$1 + fairsharing: + abbreviation: PlasmoDB + description: PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria. + id: '1882' + name: PlasmoDB + prefix: FAIRsharing.g4n8sw + subjects: [] + go: + homepage: https://plasmodb.org + name: PlasmoDB + prefix: PlasmoDB + uri_format: https://plasmodb.org/plasmo/app/record/gene/$1 + mappings: + biocontext: PLASMODB + fairsharing: FAIRsharing.g4n8sw + go: PlasmoDB + miriam: plasmodb + n2t: plasmodb + ncbi: ApiDB_PlasmoDB + prefixcommons: plasmodb + miriam: + deprecated: false + description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: http://plasmodb.org/plasmo/ + id: '00000150' + name: PlasmoDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: plasmodb + sampleId: PF11_0344 + uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + n2t: + description: AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: PF11_0344 + homepage: http://plasmodb.org/plasmo/ + name: PlasmoDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: plasmodb + uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + ncbi: + example: PF11_0344 + homepage: http://www.plasmodb.org/plasmo/home.jsp + name: Plasmodium Genome Resources + prefix: ApiDB_PlasmoDB + prefixcommons: + description: PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria. + example: PFA0765c + homepage: http://PlasmoDB.org + keywords: + - genome + name: PlasmoDB + pattern: ^PF[A-Z,0-9]+$ + prefix: plasmodb + pubmed_ids: + - '18957442' + uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1&project_id=PlasmoDB + synonyms: + - ApiDB_PlasmoDB +plo: + biocontext: + is_identifiers: false + is_obo: true + prefix: PLO + uri_format: http://purl.obolibrary.org/obo/PLO_$1 + mappings: + biocontext: PLO + obofoundry: plo + name: Plasmodium Life Cycle + obofoundry: + contact: mb4@sanger.ac.uk + contact.label: Matt Berriman + deprecated: true + homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ + name: Plasmodium life cycle + prefix: plo +pmap.cutdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PMAP.CUTDB + uri_format: http://identifiers.org/pmap.cutdb/$1 + mappings: + biocontext: PMAP.CUTDB + miriam: pmap.cutdb + n2t: pmap.cutdb + prefixcommons: pmap.cutdb + miriam: + deprecated: false + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). + homepage: http://cutdb.burnham.org + id: '00000225' + name: CutDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pmap.cutdb + sampleId: '25782' + uri_format: http://cutdb.burnham.org/relation/show/$1 + n2t: + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). + example: '25782' + homepage: http://cutdb.burnham.org + name: CutDB at The Burnham Institute for Medical Research + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pmap.cutdb + uri_format: http://cutdb.burnham.org/relation/show/$1 + prefixcommons: + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). + example: pmap.21243 + homepage: http://www.proteolysis.org/ + keywords: + - pathway + - protein + - enzyme + name: CutDB - Proteolytic event database + pattern: ^pmap.\d+$ + prefix: pmap.cutdb + pubmed_ids: + - '17142225' + uri_format: http://www.proteolysis.org/proteases/m_summarypg/$1 +pmap.substratedb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PMAP.SUBSTRATEDB + uri_format: http://identifiers.org/pmap.substratedb/$1 + mappings: + biocontext: PMAP.SUBSTRATEDB + miriam: pmap.substratedb + n2t: pmap.substratedb + prefixcommons: pmap.substratedb + miriam: + deprecated: false + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. + homepage: http://substrate.burnham.org/ + id: '00000224' + name: SubstrateDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pmap.substratedb + sampleId: '1915' + uri_format: http://substrate.burnham.org/protein/annotation/$1/html + n2t: + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. + example: '1915' + homepage: http://substrate.burnham.org/ + name: SubstrateDB at The Burnham Institute for Medical Research + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pmap.substratedb + uri_format: http://substrate.burnham.org/protein/annotation/$1/html + prefixcommons: + description: The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. + example: '1915' + keywords: + - domain + - protein + - reaction + name: SubstrateDB - Protease substrates + pattern: ^\w+$ + prefix: pmap.substratedb + pubmed_ids: + - '18842634' + uri_format: http://substrate.burnham.org/protein/annotation/$1/html +pmc: + biocontext: + is_identifiers: false + is_obo: false + prefix: PMCID + uri_format: http://www.ncbi.nlm.nih.gov/pmc/$1 + fairsharing: + abbreviation: PMC + description: PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) digital archive of biomedical and life sciences journal literature. + id: '1987' + name: PubMed Central + prefix: FAIRsharing.wpt5mp + subjects: + - Environmental Science + - Earth Science + - Virology + - Life Science + - Biomedical Science + - Epidemiology + go: + homepage: https://www.ncbi.nlm.nih.gov/pmc/ + name: Pubmed Central + prefix: PMCID + synonyms: + - PMC + uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1 + mappings: + biocontext: PMCID + fairsharing: FAIRsharing.wpt5mp + go: PMCID + miriam: pmc + n2t: pmc + prefixcommons: pmc + miriam: + deprecated: false + description: PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. + homepage: http://europepmc.org/ + id: '00000147' + name: PMC International + namespaceEmbeddedInLui: false + pattern: PMC\d+ + prefix: pmc + providers: + - code: ncbi + description: PubMed Central + homepage: https://www.ncbi.nlm.nih.gov/pmc/ + name: PubMed Central + uri_format: https://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pubmed + sampleId: PMC3084216 + uri_format: http://europepmc.org/articles/$1 + n2t: + description: PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. + example: PMC3084216 + homepage: http://europepmc.org/ + name: Europe PMC + namespaceEmbeddedInLui: false + pattern: PMC\d+ + prefix: pmc + uri_format: http://europepmc.org/articles/$1 + prefixcommons: + description: PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) digital archive of biomedical and life sciences journal literature. + example: PMC3084216 + homepage: http://www.pubmedcentral.nih.gov/ + keywords: + - bibliography + name: Pubmed Central + pattern: ^PMC\d+$ + prefix: pmc + uri_format: http://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pmcentrez + synonyms: + - PMC + - PMCID + wikidata: + prefix: P932 +pmdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PMDB + uri_format: http://identifiers.org/pmdb/$1 + fairsharing: + abbreviation: PMDB + description: The Protein Model DataBase (PMDB) is a database that stores three dimensional protein models obtained by structure prediction techniques. + id: '1946' + name: Protein Model Database + prefix: FAIRsharing.wkaakq + subjects: + - Structural Biology + mappings: + biocontext: PMDB + fairsharing: FAIRsharing.wkaakq + miriam: pmdb + n2t: pmdb + prefixcommons: pmdb + miriam: + deprecated: false + description: The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. + homepage: https://bioinformatics.cineca.it/PMDB/ + id: '00000190' + name: Protein Model Database + namespaceEmbeddedInLui: false + pattern: ^PM\d{7} + prefix: pmdb + sampleId: PM0012345 + uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1 + n2t: + description: The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. + example: PM0012345 + homepage: https://bioinformatics.cineca.it/PMDB/ + name: Protein Model Database at University of Rome + namespaceEmbeddedInLui: false + pattern: ^PM\d{7} + prefix: pmdb + uri_format: https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1 + prefixcommons: + description: The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. + example: PM0012345 + homepage: http://www.caspur.it/PMDB/ + keywords: + - protein + - structure + name: Protein Model Database + pattern: ^PM\d{7}$ + prefix: pmdb + uri_format: http://mi.caspur.it/PMDB/user/search.php?idsearch=$1 +pmp: + biocontext: + is_identifiers: true + is_obo: false + prefix: PMP + uri_format: http://identifiers.org/pmp/$1 + mappings: + biocontext: PMP + miriam: pmp + n2t: pmp + prefixcommons: pmp + miriam: + deprecated: false + description: The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. + id: '00000227' + name: PMP + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: pmp + sampleId: Q0VCA6 + n2t: + description: The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. + example: Q0VCA6 + homepage: http://www.proteinmodelportal.org/ + name: PMP at University of Basel + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: pmp + uri_format: http://www.proteinmodelportal.org/query/uniprot/$1 + name: Protein Model Portal + prefixcommons: + description: The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models. + example: Q0VCA6 + homepage: http://www.proteinmodelportal.org/ + keywords: + - prediction + - protein + - structure + name: Protein Model Portal + pattern: ^\d+$ + prefix: pmp + pubmed_ids: + - '19037750' + uri_format: http://www.proteinmodelportal.org/query/uniprot/$1 + provides: uniprot +pmr: + bioportal: + name: Physical Medicine and Rehabilitation + prefix: PMR + fairsharing: + abbreviation: PMR + description: The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository’s content via web services. + id: '2261' + name: Physiome Model Repository + prefix: FAIRsharing.bcjrnq + subjects: + - Mathematics + - Life Science + - Physiology + - Biomedical Science + - Systems Biology + mappings: + bioportal: PMR + fairsharing: FAIRsharing.bcjrnq + miriam: pmr + miriam: + deprecated: false + description: Resource for the community to store, retrieve, search, reference, and reuse CellML models. + homepage: https://www.auckland.ac.nz/en.html + id: '00000845' + name: Physiome Model Repository + namespaceEmbeddedInLui: false + pattern: ^[a-z0-9]{32,32}$ + prefix: pmr + sampleId: ebf69ca24298b28b2361e7d43eb52d6c + uri_format: https://models.physiomeproject.org/exposure/$1 +po: + biocontext: + is_identifiers: false + is_obo: true + prefix: PO + uri_format: http://purl.obolibrary.org/obo/PO_$1 + bioportal: + name: Plant Ontology + prefix: PO + fairsharing: + abbreviation: PO + description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants. + id: '237' + name: Plant Ontology + prefix: FAIRsharing.3ngg40 + subjects: + - Botany + - Life Science + - Plant Anatomy + go: + homepage: http://www.planteome.org/ + name: Plant Ontology + prefix: PO + mappings: + biocontext: PO + bioportal: PO + fairsharing: FAIRsharing.3ngg40 + go: PO + miriam: po + n2t: po + obofoundry: po + ols: po + ontobee: PO + prefixcommons: po + miriam: + deprecated: false + description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. + homepage: http://www.plantontology.org/ + id: '00000307' + name: Plant Ontology + namespaceEmbeddedInLui: true + pattern: ^PO:\d+$ + prefix: po + sampleId: '0009089' + uri_format: http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1 + n2t: + description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. + example: '0009089' + homepage: http://bioportal.bioontology.org/ontologies/PO + name: Plant Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^PO:\d+$ + prefix: po + uri_format: http://purl.bioontology.org/ontology/PO/PO:$1 + obofoundry: + appears_in: + - agro + - ecocore + - envo + - genepio + contact: jaiswalp@science.oregonstate.edu + contact.github: jaiswalp + contact.label: Pankaj Jaiswal + contact.orcid: 0000-0002-1005-8383 + deprecated: false + description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. + download.obo: http://purl.obolibrary.org/obo/po.obo + download.owl: http://purl.obolibrary.org/obo/po.owl + homepage: http://browser.planteome.org/amigo + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Plant Ontology + preferredPrefix: PO + prefix: po + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/23220694 + title: The plant ontology as a tool for comparative plant anatomy and genomic analyses. + - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 + title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' + repository: https://github.com/Planteome/plant-ontology + twitter: planteome + ols: + description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. + download: http://purl.obolibrary.org/obo/po.owl + homepage: http://browser.planteome.org/amigo + name: Plant Ontology + prefix: po + version: 2021-08-13 + version.iri: http://purl.obolibrary.org/obo/po/releases/2021-08-13/po.owl + ontobee: + library: Foundry + name: Plant Ontology + prefix: PO + pattern: ^\d+$ + prefixcommons: + bioportal: '1587' + description: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants. + example: PO:0006220 + homepage: http://www.plantontology.org/ + keywords: + - ontology + - structure + - classification + name: Plant Ontology + pattern: ^PO:\d+$ + prefix: po + uri_format: http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$1 +pocketome: + biocontext: + is_identifiers: true + is_obo: false + prefix: POCKETOME + uri_format: http://identifiers.org/pocketome/$1 + fairsharing: + abbreviation: Pocketome + description: The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is involved in transient interactions with small molecules and peptides. + id: '1631' + name: 'Pocketome: an encyclopedia of small-molecule binding sites in 4D' + prefix: FAIRsharing.tc6df8 + subjects: + - Life Science + mappings: + biocontext: POCKETOME + fairsharing: FAIRsharing.tc6df8 + miriam: pocketome + n2t: pocketome + miriam: + deprecated: false + description: Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. + homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall + id: '00000400' + name: Pocketome + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+ + prefix: pocketome + sampleId: 1433C_TOBAC_1_252 + uri_format: http://www.pocketome.org/files/$1.html + n2t: + description: Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. + example: 1433C_TOBAC_1_252 + homepage: http://www.pocketome.org/sfSearch.cgi?act=browseall + name: Pocketome at UCSD Skaggs School + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z_0-9]+ + prefix: pocketome + uri_format: http://www.pocketome.org/files/$1.html +polbase: + biocontext: + is_identifiers: true + is_obo: false + prefix: POLBASE + uri_format: http://identifiers.org/polbase/$1 + fairsharing: + abbreviation: Polbase + description: Polbase is an open and searchable database providing information from published and unpublished sources on the biochemical, genetic, and structural information of DNA polymerases. + id: '1632' + name: Polbase + prefix: FAIRsharing.s9ztmd + subjects: + - Biochemistry + - Genetics + - Life Science + mappings: + biocontext: POLBASE + fairsharing: FAIRsharing.s9ztmd + miriam: polbase + n2t: polbase + miriam: + deprecated: false + description: Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. + homepage: http://polbase.neb.com/ + id: '00000355' + name: PolBase + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9]+$ + prefix: polbase + sampleId: 19-T4 + uri_format: https://polbase.neb.com/polymerases/$1#sequences + n2t: + description: Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. + example: 19-T4 + homepage: http://polbase.neb.com/ + name: PolBase at New England BioLabs + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9]+$ + prefix: polbase + uri_format: https://polbase.neb.com/polymerases/$1#sequences +pombase: + biocontext: + is_identifiers: false + is_obo: false + prefix: PomBase + uri_format: https://www.pombase.org/spombe/result/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: PomBase + uri_format: https://www.pombase.org/gene/$1 + fairsharing: + abbreviation: PomBase + description: PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets. + id: '1683' + name: PomBase + prefix: FAIRsharing.8jsya3 + subjects: + - Life Science + go: + homepage: https://www.pombase.org/ + name: PomBase + prefix: PomBase + uri_format: https://www.pombase.org/gene/$1 + mappings: + biocontext: PomBase + biolink: PomBase + fairsharing: FAIRsharing.8jsya3 + go: PomBase + miriam: pombase + n2t: pombase + ncbi: PomBase + prefixcommons: pombase + uniprot: PomBase + wikidata: P6245 + miriam: + deprecated: false + description: PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. + homepage: http://www.pombase.org/ + id: '00000335' + name: PomBase + namespaceEmbeddedInLui: false + pattern: ^S\w+(\.)?\w+(\.)?$ + prefix: pombase + sampleId: SPCC13B11.01 + uri_format: http://www.pombase.org/spombe/result/$1 + n2t: + description: PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. + example: SPCC13B11.01 + homepage: http://www.pombase.org/ + name: PomBase at University of Cambridge + namespaceEmbeddedInLui: false + pattern: ^S\w+(\.)?\w+(\.)?$ + prefix: pombase + uri_format: http://www.pombase.org/spombe/result/$1 + name: PomBase + ncbi: + example: SPBC11B10.09 + homepage: http://www.pombase.org/ + name: Database of Structural and Functional Data for Schizosaccaromyces pombe + prefix: PomBase + prefixcommons: + description: PomBase is a model organism database for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. + example: SPCC13B11.01 + homepage: http://www.pombase.org + name: Schizosaccharomyces pombe database + pattern: ^S\w+(\.)?\w+(\.)?$ + prefix: pombase + pubmed_ids: + - '22039153' + synonyms: + - PomBase + uniprot: + category: Organism-specific databases + comment: Replacement for GeneDB_Spombe + identifier: '31' + link_is_explicit: 'true' + name: Schizosaccharomyces pombe database + prefix: PomBase + uri_format: https://www.pombase.org/spombe/result/$1 + wikidata: + database: Q25304673 + database.homepage: https://www.pombase.org/ + database.label: PomBase + name: PomBase systematic ID + prefix: P6245 + uri_format: https://www.pombase.org/gene/$1 +poro: + biocontext: + is_identifiers: false + is_obo: true + prefix: PORO + uri_format: http://purl.obolibrary.org/obo/PORO_$1 + bioportal: + name: Porifera Ontology + prefix: PORO + example: '0000550' + fairsharing: + abbreviation: PORO + description: An ontology covering the anatomy of Porifera (sponges) + id: '448' + name: Porifera Ontology + prefix: FAIRsharing.93g1th + subjects: [] + mappings: + biocontext: PORO + bioportal: PORO + fairsharing: FAIRsharing.93g1th + obofoundry: poro + ols: poro + ontobee: PORO + obofoundry: + contact: robert.thacker@stonybrook.edu + contact.github: bobthacker + contact.label: Bob Thacker + contact.orcid: 0000-0002-9654-0073 + depends_on: + - ro + - uberon + deprecated: false + description: An ontology covering the anatomy of the taxon Porifera (sponges) + download.obo: http://purl.obolibrary.org/obo/poro.obo + download.owl: http://purl.obolibrary.org/obo/poro.owl + homepage: https://github.com/obophenotype/porifera-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Porifera Ontology + preferredPrefix: PORO + prefix: poro + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/25276334 + title: 'The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology' + repository: https://github.com/obophenotype/porifera-ontology + ols: + description: An ontology describing the anatomical structures and characteristics of Porifera (sponges) + download: http://purl.obolibrary.org/obo/poro.owl + homepage: https://github.com/obophenotype/porifera-ontology + name: Porifera (sponge) ontology + prefix: poro + version: 2016-10-06 + version.iri: http://purl.obolibrary.org/obo/poro/releases/2016-10-06/poro.owl + ontobee: + library: Library + name: Porifera Ontology + prefix: PORO + pattern: ^\d{7}$ +ppdb: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. ' + example: '1484' + fairsharing: + abbreviation: ppdb + description: Genome-wide plant promoter database for several plant species, including Arabidopsis thaliana, rice, poplar, and Physcomitrella patens. + id: '2133' + name: Plant Promoter Database + prefix: FAIRsharing.7k8zh0 + subjects: + - Life Science + homepage: https://sitem.herts.ac.uk/aeru/ppdb/ + mappings: + fairsharing: FAIRsharing.7k8zh0 + name: Pesticide Properties DataBase + pattern: ^\d+$ + uri_format: https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm +ppo: + biocontext: + is_identifiers: false + is_obo: true + prefix: PPO + uri_format: http://purl.obolibrary.org/obo/PPO_$1 + bioportal: + name: Plant Phenology Ontology + prefix: PPO + example: '0002058' + fairsharing: + abbreviation: PPO + description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. + id: '441' + name: Plant Phenology Ontology + prefix: FAIRsharing.hakg7c + subjects: + - Botany + mappings: + biocontext: PPO + bioportal: PPO + fairsharing: FAIRsharing.hakg7c + obofoundry: ppo + ols: ppo + ontobee: PPO + obofoundry: + contact: rlwalls2008@gmail.com + contact.github: ramonawalls + contact.label: Ramona Walls + contact.orcid: 0000-0001-8815-0078 + deprecated: false + description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. + download.owl: http://purl.obolibrary.org/obo/ppo.owl + homepage: https://github.com/PlantPhenoOntology/PPO + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Plant Phenology Ontology + preferredPrefix: PPO + prefix: ppo + repository: https://github.com/PlantPhenoOntology/PPO + ols: + contact: ppo-discuss@googlegroups.com + description: An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. + download: http://purl.obolibrary.org/obo/ppo.owl + homepage: https://github.com/PlantPhenoOntology/PPO + name: Plant Phenology Ontology + prefix: ppo + version: 2018-10-26 + version.iri: https://raw.githubusercontent.com/PlantPhenoOntology/ppo/master/releases/2018-10-26/ppo.owl + ontobee: + library: Library + name: Plant Phenology Ontology + prefix: PPO + pattern: ^\d{7}$ +ppr: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000. + example: ppr103739 + homepage: https://europepmc.org + name: Europe PMC Preprints + uri_format: https://europepmc.org/article/ppr/$1 +pr: + biocontext: + is_identifiers: false + is_obo: true + prefix: PR + uri_format: http://purl.obolibrary.org/obo/PR_$1 + bioportal: + name: Protein Ontology + prefix: PR + fairsharing: + abbreviation: PRO + description: 'Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).' + id: '1229' + name: PRotein Ontology + prefix: FAIRsharing.4ndncv + subjects: + - Biology + go: + homepage: https://proconsortium.org/ + name: Protein Ontology + prefix: PR + synonyms: + - PRO + uri_format: https://proconsortium.org/app/entry/PR_$1 + mappings: + biocontext: PR + bioportal: PR + fairsharing: FAIRsharing.4ndncv + go: PR + miriam: pr + n2t: pr + obofoundry: pr + ols: pr + ontobee: PR + prefixcommons: pr + uniprot: PRO + wikidata: P4926 + miriam: + deprecated: false + description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. + homepage: https://proconsortium.org/ + id: '00000141' + name: Protein Ontology + namespaceEmbeddedInLui: true + pattern: ^PR:P?\d+$ + prefix: pr + sampleId: '000000024' + uri_format: https://proconsortium.org/app/entry/PR:$1 + n2t: + description: The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. + example: '000000024' + homepage: https://proconsortium.org/ + name: Protein Ontology at Georgetown + namespaceEmbeddedInLui: true + pattern: ^PR\:P?\d+$ + prefix: pr + uri_format: https://proconsortium.org/app/entry/PR:$1 + name: Protein Ontology + obofoundry: + appears_in: + - chiro + - cl + - pcl + - uberon + - scdo + contact: dan5@georgetown.edu + contact.github: nataled + contact.label: Darren Natale + contact.orcid: 0000-0001-5809-9523 + deprecated: false + description: An ontological representation of protein-related entities + download.obo: http://purl.obolibrary.org/obo/pr.obo + download.owl: http://purl.obolibrary.org/obo/pr.owl + homepage: http://proconsortium.org + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: PRotein Ontology (PRO) + preferredPrefix: PR + prefix: pr + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/27899649 + title: 'Protein Ontology (PRO): enhancing and scaling up the representation of protein entities' + repository: https://github.com/PROconsortium/PRoteinOntology + ols: + description: An ontological representation of protein-related entities + download: http://purl.obolibrary.org/obo/pr.owl + homepage: http://proconsortium.org + name: PRotein Ontology (PRO) + prefix: pr + version: '65.0' + version.iri: http://purl.obolibrary.org/obo/pr/65.0/pr.owl + ontobee: + library: Foundry + name: PRotein Ontology (PRO) + prefix: PR + pattern: ^\d+$ + prefixcommons: + bioportal: '1062' + description: 'PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).' + example: PR:000000024 + homepage: http://pir.georgetown.edu/pro/ + keywords: + - obo + - protein + name: PRotein Ontology (PRO) + pattern: ^PR\:\d+$ + prefix: pr + pubmed_ids: + - '18047702' + uri_format: http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$1 + synonyms: + - PR + - PRO + uniprot: + category: Miscellaneous databases + identifier: '181' + link_is_explicit: 'true' + name: Protein Ontology + prefix: PRO + uri_format: https://proconsortium.org/app/entry/$1 + wikidata: + database: Q55118584 + database.homepage: http://pir.georgetown.edu/pro + database.label: Protein Ontology + homepage: https://pir.georgetown.edu/pro/pro.shtml + name: PRotein Ontology ID + pattern: PR:\d* + prefix: P4926 + uri_format: https://proconsortium.org/app/entry/$1/ +prefixcommons: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A registry of life science prefxes + example: ChEBI + homepage: https://prefixcommons.org + name: Prefix Commons + uri_format: https://bioregistry.io/metaregistry/prefixcommons/$1 +pride: + biocontext: + is_identifiers: true + is_obo: false + prefix: PRIDE + uri_format: http://identifiers.org/pride/$1 + cellosaurus: + category: Proteomic databases + homepage: https://www.ebi.ac.uk/pride/archive/ + name: PRoteomics IDEntifications archive + prefix: PRIDE + uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1 + fairsharing: + abbreviation: PRIDE + description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. + id: '1863' + name: PRoteomics IDEntifications database + prefix: FAIRsharing.e1byny + subjects: + - Proteomics + - Life Science + mappings: + biocontext: PRIDE + cellosaurus: PRIDE + fairsharing: FAIRsharing.e1byny + miriam: pride + n2t: pride + ols: pride + prefixcommons: pride + uniprot: PRIDE + miriam: + deprecated: false + description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. + homepage: https://www.ebi.ac.uk/pride/ + id: '00000065' + name: PRIDE + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pride + sampleId: '1' + uri_format: https://www.ebi.ac.uk/pride/archive/assays/$1 + n2t: + description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. + example: '1' + homepage: https://www.ebi.ac.uk/pride/ + name: PRIDE at EBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pride + uri_format: https://www.ebi.ac.uk/pride/archive/assays/$1 + ols: + description: The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. + download: https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo + homepage: https://github.com/PRIDE-Utilities/pride-ontology + name: PRIDE Controlled Vocabulary + prefix: pride + prefixcommons: + description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. + example: '1' + homepage: http://www.ebi.ac.uk/pride/ + keywords: + - protein + name: PRoteomics IDEntifications database + pattern: ^\d+$ + prefix: pride + pubmed_ids: + - '16381953' + - '16041671' + - '18033805' + - '18428683' + uri_format: http://www.ebi.ac.uk/pride/experimentLink.do?experimentAccessionNumber=$1 + repository: https://github.com/PRIDE-Utilities/pride-ontology + uniprot: + category: Proteomic databases + identifier: '130' + link_is_explicit: 'true' + name: PRoteomics IDEntifications database + prefix: PRIDE + uri_format: https://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=$1 +pride.project: + biocontext: + is_identifiers: true + is_obo: false + prefix: PRIDE.PROJECT + uri_format: http://identifiers.org/pride.project/$1 + mappings: + biocontext: PRIDE.PROJECT + miriam: pride.project + n2t: pride.project + miriam: + deprecated: false + description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. + homepage: https://www.ebi.ac.uk/pride/ + id: '00000515' + name: PRIDE Project + namespaceEmbeddedInLui: false + pattern: ^P(X|R)D\d{6}$ + prefix: pride.project + providers: + - code: omicsdi + description: PRIDE Project through OmicsDI + homepage: https://www.omicsdi.org/ + name: PRIDE Project through OmicsDI + uri_format: https://www.omicsdi.org/dataset/pride/$1 + sampleId: PXD000440 + uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1 + n2t: + description: The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. + example: PXD000440 + homepage: https://www.ebi.ac.uk/pride/ + name: PRIDE Project at EBI + namespaceEmbeddedInLui: false + pattern: ^P(X|R)D\d{6}$ + prefix: pride.project + uri_format: https://www.ebi.ac.uk/pride/archive/projects/$1 +prints: + biocontext: + is_identifiers: true + is_obo: false + prefix: PRINTS + uri_format: http://identifiers.org/prints/$1 + fairsharing: + abbreviation: PRINTS + description: PRINTS is a collection of groups of conserved protein motifs, called fingerprints, used to define a protein family. A fingerprint is a group of conserved motifs used to characterize a protein family. Usually, the motifs do not overlap, though they may be contiguous in 3D space. Fingerprints can encode protein folds and functionalities more flexibly than single motifs. Please note that the last release of this database on the PRINTS website was in 2007. + id: '2099' + name: PRINTS + prefix: FAIRsharing.h8r843 + subjects: + - Structural Biology + - Biology + go: + homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/ + name: PRINTS compendium of protein fingerprints + prefix: PRINTS + uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1 + mappings: + biocontext: PRINTS + fairsharing: FAIRsharing.h8r843 + go: PRINTS + miriam: prints + n2t: prints + uniprot: PRINTS + miriam: + deprecated: false + description: PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. + homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ + id: '00000061' + name: PRINTS + namespaceEmbeddedInLui: false + pattern: ^PR\d{5}$ + prefix: prints + sampleId: PR00001 + uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off + n2t: + description: PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. + example: PR00001 + homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ + name: PRINTS through SPRINT + namespaceEmbeddedInLui: false + pattern: ^PR\d{5}$ + prefix: prints + uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off + uniprot: + category: Family and domain databases + comment: Replacement for PRINT + identifier: '82' + link_is_explicit: 'true' + name: Protein Motif fingerprint database; a protein domain database + prefix: PRINTS + uri_format: http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=$1 +probonto: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROBONTO + uri_format: http://identifiers.org/probonto/$1 + fairsharing: + abbreviation: ProbOnto + description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 150 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for model annotation and facilitates the encoding of distribution-based models, related functions and quantities. ProbOnto is both an ontology and a knowledge base, however its primary focus is the knowledge base. + id: '2298' + name: Ontology and Knowledge Base of Probability Distributions + prefix: FAIRsharing.8zqzm9 + subjects: + - Statistics + - Mathematics + - Computational Biology + - Systems Biology + mappings: + biocontext: PROBONTO + fairsharing: FAIRsharing.8zqzm9 + miriam: probonto + n2t: probonto + ols: probonto + miriam: + deprecated: false + description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. + homepage: https://www.ebi.ac.uk/ols/ontologies/probonto + id: '00000575' + name: ProbOnto + namespaceEmbeddedInLui: false + pattern: ^PROB_c\d+$ + prefix: probonto + sampleId: PROB_c0000005 + uri_format: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1 + n2t: + description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. + example: PROB_c0000005 + homepage: https://www.ebi.ac.uk/ols/ontologies/probonto + name: ProbOnto through OLS + namespaceEmbeddedInLui: false + pattern: ^PROB_c\d+$ + prefix: probonto + uri_format: https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1 + ols: + contact: probonto.dev@gmail.com + description: ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than eighty uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulas. + download: https://raw.githubusercontent.com/probonto/ontology/master/probonto4ols.owl + homepage: http://probonto.org + name: Probability Distribution Ontology + prefix: probonto + version: 2.5.0 +prodom: + biocontext: + is_identifiers: true + is_obo: false + prefix: PRODOM + uri_format: http://identifiers.org/prodom/$1 + fairsharing: + abbreviation: ProDom + description: ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database. + id: '1910' + name: ProDom + prefix: FAIRsharing.a8z6gz + subjects: + - Life Science + mappings: + biocontext: PRODOM + fairsharing: FAIRsharing.a8z6gz + miriam: prodom + n2t: prodom + prefixcommons: prodom + miriam: + deprecated: false + description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. + homepage: http://prodom.prabi.fr/prodom/current/html/home.php + id: '00000117' + name: ProDom + namespaceEmbeddedInLui: false + pattern: ^PD\d+$ + prefix: prodom + sampleId: PD10000 + uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1 + n2t: + description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. + example: PD10000 + homepage: http://prodom.prabi.fr/prodom/current/html/home.php + name: ProDom Protein Domain Database + namespaceEmbeddedInLui: false + pattern: ^PD\d+$ + prefix: prodom + uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1 + prefixcommons: + description: ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database + example: PD10000 + homepage: http://prodom.prabi.fr/ + keywords: + - protein + - classification + name: ProDom; a protein domain database + pattern: ^PD\d+$ + prefix: prodom + pubmed_ids: + - '15608179' + uri_format: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1 +proglyc: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROGLYC + uri_format: http://identifiers.org/proglyc/$1 + mappings: + biocontext: PROGLYC + miriam: proglyc + n2t: proglyc + miriam: + deprecated: false + description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. + homepage: http://www.proglycprot.org/ + id: '00000354' + name: ProGlycProt + namespaceEmbeddedInLui: false + pattern: ^[A-Z]C\d{1,3}$ + prefix: proglyc + sampleId: AC119 + uri_format: http://www.proglycprot.org/detail.aspx?ProId=$1 + n2t: + description: ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. + example: AC119 + homepage: http://www.proglycprot.org/ + name: ProGlycProt at IMT + namespaceEmbeddedInLui: false + pattern: ^[A-Z]C\d{1,3}$ + prefix: proglyc + uri_format: http://www.proglycprot.org/detail.aspx?ProId=$1 +propreo: + biocontext: + is_identifiers: false + is_obo: true + prefix: PROPREO + uri_format: http://purl.obolibrary.org/obo/PROPREO_$1 + bioportal: + name: Proteomics Data and Process Provenance Ontology + prefix: PROPREO + mappings: + biocontext: PROPREO + bioportal: PROPREO + obofoundry: propreo + prefixcommons: propreo + obofoundry: + contact: satya30@uga.edu + contact.label: Satya S. Sahoo + deprecated: true + homepage: http://lsdis.cs.uga.edu/projects/glycomics/propreo/ + name: Proteomics data and process provenance + prefix: propreo + prefixcommons: + bioportal: '1039' + description: A comprehensive proteomics data and process provenance ontology. + example: protein + homepage: http://knoesis.wright.edu/research/semsci/application_domain/sem_life_sci/glycomics/resources/ontologies/propreo/ + keywords: + - owl + - proteomics + name: Proteomics data and process provenance + pattern: ^\w+$ + prefix: propreo +prosite: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROSITE + uri_format: http://identifiers.org/prosite/$1 + fairsharing: + abbreviation: PROSITE + description: PROSITE is a database of protein families and domains. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. + id: '2060' + name: PROSITE + prefix: FAIRsharing.vwc6bd + subjects: + - Biology + go: + homepage: https://prosite.expasy.org/ + name: Prosite database of protein families and domains + prefix: Prosite + uri_format: https://prosite.expasy.org/$1 + mappings: + biocontext: PROSITE + fairsharing: FAIRsharing.vwc6bd + go: Prosite + miriam: prosite + n2t: prosite + prefixcommons: prosite + uniprot: PROSITE + wikidata: P4355 + miriam: + deprecated: false + description: PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. + homepage: https://www.expasy.org/prosite/ + id: '00000032' + name: PROSITE + namespaceEmbeddedInLui: false + pattern: ^PS\d{5}$ + prefix: prosite + sampleId: PS00001 + uri_format: https://prosite.expasy.org/$1 + n2t: + description: PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. + example: PS00001 + homepage: https://www.expasy.org/prosite/ + name: ExPASy PROSITE + namespaceEmbeddedInLui: false + pattern: ^PS\d{5}$ + prefix: prosite + uri_format: https://prosite.expasy.org/$1 + name: PROSITE + prefixcommons: + description: PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them + example: PS00001 + homepage: http://www.expasy.org/prosite + keywords: + - protein + - structure + name: PROSITE; a protein domain and family database + pattern: ^PS\d{5}$ + prefix: prosite + pubmed_ids: + - '16381852' + uri_format: http://www.expasy.org/cgi-bin/nicesite.pl?$1 + uniprot: + category: Family and domain databases + identifier: '84' + link_is_explicit: 'true' + name: PROSITE; a protein domain and family database + prefix: PROSITE + uri_format: https://prosite.expasy.org/doc/$1 + wikidata: + database: Q899676 + database.homepage: http://prosite.expasy.org/ + database.label: PROSITE + name: PROSITE documentation ID + pattern: PDOC\d{5} + prefix: P4355 + uri_format: http://prosite.expasy.org/$1 +protclustdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROTCLUSTDB + uri_format: http://identifiers.org/protclustdb/$1 + fairsharing: + abbreviation: ProtClustDB + description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. + id: '1988' + name: NCBI Protein Clusters Database + prefix: FAIRsharing.da493y + subjects: + - Genomics + - Genetics + - Life Science + mappings: + biocontext: PROTCLUSTDB + fairsharing: FAIRsharing.da493y + miriam: protclustdb + n2t: protclustdb + prefixcommons: protclustdb + miriam: + deprecated: false + description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. + homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters + id: '00000226' + name: ProtClustDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: protclustdb + sampleId: O80725 + uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1 + n2t: + description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. + example: O80725 + homepage: https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters + name: ProtClustDB at NCBI + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: protclustdb + uri_format: https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1 + prefixcommons: + description: ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. + example: '2728498' + homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters + keywords: + - protein + - structure + name: ProtClustDB + pattern: ^\d+$ + prefix: protclustdb + pubmed_ids: + - '18940865' + uri_format: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=ShowDetailView&TermToSearch=$1 +proteomicsdb.peptide: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROTEOMICSDB.PEPTIDE + uri_format: http://identifiers.org/proteomicsdb.peptide/$1 + comment: The fact that this has .peptide as a subspace is a bit of a misnomer. Its original registration with MIRIAM uses a subview over the protein to point to peptides, but the identifiers in this semantic space seem to be about proteins. + mappings: + biocontext: PROTEOMICSDB.PEPTIDE + miriam: proteomicsdb.peptide + n2t: proteomicsdb.peptide + miriam: + deprecated: false + description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. + homepage: https://www.proteomicsdb.org/#peptideSearch + id: '00000525' + name: ProteomicsDB Peptide + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: proteomicsdb.peptide + sampleId: '53504' + uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/peptides/ + n2t: + description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. + example: '53504' + homepage: https://www.proteomicsdb.org/#peptideSearch + name: Proteomics DB Peptide at Center for Integrated Protein Science + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: proteomicsdb.peptide + uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/peptides/ + uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1 +proteomicsdb.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROTEOMICSDB.PROTEIN + uri_format: http://identifiers.org/proteomicsdb.protein/$1 + mappings: + biocontext: PROTEOMICSDB.PROTEIN + miriam: proteomicsdb.protein + n2t: proteomicsdb.protein + miriam: + deprecated: false + description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. + homepage: https://www.proteomicsdb.org/#human + id: '00000524' + name: ProteomicsDB Protein + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: proteomicsdb.protein + sampleId: '53504' + uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary + n2t: + description: ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. + example: '53504' + homepage: https://www.proteomicsdb.org/#human + name: Proteomics DB Protein at Center for Integrated Protein Science + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: proteomicsdb.protein + uri_format: https://www.proteomicsdb.org/#human/proteinDetails/$1/summary +protonet.cluster: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROTONET.CLUSTER + uri_format: http://identifiers.org/protonet.cluster/$1 + mappings: + biocontext: PROTONET.CLUSTER + miriam: protonet.cluster + n2t: protonet.cluster + prefixcommons: protonet.cluster + miriam: + deprecated: false + description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. + homepage: http://www.protonet.cs.huji.ac.il/ + id: '00000229' + name: ProtoNet Cluster + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: protonet.cluster + sampleId: '4349895' + uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1 + n2t: + description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. + example: '4349895' + homepage: http://www.protonet.cs.huji.ac.il/ + name: ProtoNet at Hebrew University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: protonet.cluster + uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1 + prefixcommons: + description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. + example: '4349895' + keywords: + - classification + - clustering + - protein + name: ProtoNet Cluster + pattern: ^\d+$ + prefix: protonet.cluster + pubmed_ids: + - '16672244' + uri_format: http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1 +protonet.proteincard: + biocontext: + is_identifiers: true + is_obo: false + prefix: PROTONET.PROTEINCARD + uri_format: http://identifiers.org/protonet.proteincard/$1 + mappings: + biocontext: PROTONET.PROTEINCARD + miriam: protonet.proteincard + n2t: protonet.proteincard + prefixcommons: protonet.proteincard + miriam: + deprecated: false + description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. + homepage: http://www.protonet.cs.huji.ac.il/ + id: '00000228' + name: ProtoNet ProteinCard + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: protonet.proteincard + sampleId: '16941567' + uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 + n2t: + description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. + example: '16941567' + homepage: http://www.protonet.cs.huji.ac.il/ + name: ProtoNet at Hebrew University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: protonet.proteincard + uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 + prefixcommons: + description: ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. + example: '16941567' + keywords: + - protein + name: ProtoNet ProteinCard + pattern: ^\d+$ + prefix: protonet.proteincard + pubmed_ids: + - '16672244' + uri_format: http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 +prov: + biocontext: + is_identifiers: false + is_obo: false + prefix: prov + uri_format: http://www.w3.org/ns/prov#$1 + biolink: + is_identifiers: false + is_obo: false + prefix: prov + uri_format: http://www.w3.org/ns/prov#$1 + description: The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web. + example: Activity + homepage: https://www.w3.org/ns/prov + mappings: + biocontext: prov + biolink: prov + ols: prov + name: PROV Namespace + ols: + download: https://www.w3.org/ns/prov-o + homepage: https://www.w3.org/TR/prov-o/ + name: Provenance Ontology (PROV-O) + prefix: prov + version: 2013-04-30 + version.iri: http://www.w3.org/ns/prov-o-20130430 + uri_format: http://www.w3.org/ns/prov#$1 +pscdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: PSCDB + uri_format: http://identifiers.org/pscdb/$1 + fairsharing: + abbreviation: PSCDB + description: The Protein Structural Change DataBase (PSCDB) presents the structural changes found in proteins, represented by pairs of ligand-free and ligand-bound structures of identical proteins, and links these changes to ligand-binding. + id: '1638' + name: Protein Structure Change Database + prefix: FAIRsharing.3d4jx0 + subjects: + - Life Science + mappings: + biocontext: PSCDB + fairsharing: FAIRsharing.3d4jx0 + miriam: pscdb + n2t: pscdb + miriam: + deprecated: false + description: The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. + homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html + id: '00000370' + name: PSCDB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pscdb + sampleId: '051' + uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html + n2t: + description: The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. + example: '051' + homepage: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html + name: PSCDB at Nagoya University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pscdb + uri_format: http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html + name: Protein Structural Change Database +psdo: + bioportal: + name: Performance Summary Display Ontology + prefix: PSDO + example: '0000055' + mappings: + bioportal: PSDO + obofoundry: psdo + ols: psdo + ontobee: PSDO + obofoundry: + contact: zachll@umich.edu + contact.github: zachll + contact.label: Zach Landis-Lewis + contact.orcid: 0000-0002-9117-9338 + depends_on: + - bfo + - iao + - ro + - stato + deprecated: false + description: Ontology to reproducibly study visualizations of clinical performance + download.owl: http://purl.obolibrary.org/obo/psdo.owl + homepage: https://github.com/Display-Lab/psdo + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Performance Summary Display Ontology + preferredPrefix: PSDO + prefix: psdo + repository: https://github.com/Display-Lab/psdo + ols: + description: Performance Summary Display Ontology (PSDO) (pronounced "pseudo" or "sudo") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed. + download: http://purl.obolibrary.org/obo/psdo.owl + homepage: https://github.com/Display-Lab/psdo + name: Performance Summary Display Ontology + prefix: psdo + version: 1.0.0 + version.iri: http://purl.obolibrary.org/obo/2020-12-04/psdo.owl + ontobee: + library: Library + name: Performance Summary Display Ontology + prefix: PSDO + pattern: ^\d{7}$ +pseudogene: + bioportal: + name: Pseudogene + prefix: pseudo + description: This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. + example: PGOHUM00000289843 + homepage: http://www.pseudogene.org + mappings: + bioportal: pseudo + prefixcommons: pseudogene + name: PseudoGene + prefixcommons: + description: Pseudogene is a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. + example: '4' + homepage: http://www.pseudogene.org/ + keywords: + - gene + name: PseudoGene + pattern: ^\d+$ + prefix: pseudogene + uri_format: http://tables.pseudogene.org/[?species_name]/$1 + synonyms: + - pseudogene.org + wikidata: + database: Q7254809 +pseudomonas: + biocontext: + is_identifiers: true + is_obo: false + prefix: PSEUDOMONAS + uri_format: http://identifiers.org/pseudomonas/$1 + mappings: + biocontext: PSEUDOMONAS + miriam: pseudomonas + n2t: pseudomonas + miriam: + deprecated: false + description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. + homepage: http://www.pseudomonas.com/ + id: '00000180' + name: Pseudomonas Genome Database + namespaceEmbeddedInLui: false + pattern: ^P\w+$ + prefix: pseudomonas + sampleId: PSEEN0001 + uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1 + n2t: + description: The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. + example: PSEEN0001 + homepage: http://www.pseudomonas.com/ + name: Pseudomonas Genome Database at Simon Fraser University + namespaceEmbeddedInLui: false + pattern: ^P\w+$ + prefix: pseudomonas + uri_format: http://www.pseudomonas.com/feature/show/?locus_tag=$1 +psipar: + biocontext: + is_identifiers: true + is_obo: false + prefix: PSIPAR + uri_format: http://identifiers.org/psipar/$1 + mappings: + biocontext: PSIPAR + miriam: psipar + n2t: psipar + miriam: + deprecated: false + description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. + homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR + id: '00000533' + name: Protein Affinity Reagents + namespaceEmbeddedInLui: false + pattern: ^PAR:\d+$ + prefix: psipar + sampleId: PAR:0116 + uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1 + n2t: + description: Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. + example: PAR:0116 + homepage: https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR + name: Protein Affinity Reagents through OLS + namespaceEmbeddedInLui: false + pattern: ^PAR:\d+$ + prefix: psipar + uri_format: https://www.ebi.ac.uk/ontology-lookup/?termId=$1 +pso: + bioportal: + name: PatientSafetyOntology + prefix: PSO + example: '0000013' + fairsharing: + abbreviation: PSO + description: It is the ontology embedding PRIME (Prospective Risk Analysis in Medical Environments) in related issues of patient safety research and activities. It classifies terms and express relations between them. The ontology building in an ongoing process. Any comments are welcome. + id: '588' + name: PatientSafetyOntology + prefix: FAIRsharing.dyj433 + subjects: [] + mappings: + bioportal: PSO + fairsharing: FAIRsharing.dyj433 + obofoundry: pso + ols: pso + ontobee: PSO + obofoundry: + contact: cooperl@oregonstate.edu + contact.github: cooperl09 + contact.label: Laurel Cooper + contact.orcid: 0000-0002-6379-8932 + depends_on: + - ro + deprecated: false + description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. + download.obo: http://purl.obolibrary.org/obo/pso.obo + download.owl: http://purl.obolibrary.org/obo/pso.owl + homepage: https://github.com/Planteome/plant-stress-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Plant Stress Ontology + preferredPrefix: PSO + prefix: pso + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 + title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' + repository: https://github.com/Planteome/plant-stress-ontology + ols: + description: The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. + download: http://purl.obolibrary.org/obo/pso.owl + homepage: https://github.com/Planteome/plant-stress-ontology + name: Plant Stress Ontology + prefix: pso + version: 2020-05-19 + version.iri: http://purl.obolibrary.org/obo/pso/releases/2020-05-19/pso.owl + ontobee: + library: Library + name: Plant Stress Ontology + prefix: PSO + pattern: ^\d{7}$ +pspub: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Documentation of the Phenoscape Curation Workflow + homepage: https://wiki.phenoscape.org/wiki/Curation_workflow + name: Phenoscape Publication +pubchem.bioassay: + biocontext: + is_identifiers: true + is_obo: false + prefix: PUBCHEM.BIOASSAY + uri_format: http://identifiers.org/pubchem.bioassay/$1 + go: + homepage: https://pubchem.ncbi.nlm.nih.gov + name: NCBI PubChem database of bioassay records + prefix: PubChem_BioAssay + uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1 + mappings: + biocontext: PUBCHEM.BIOASSAY + go: PubChem_BioAssay + miriam: pubchem.bioassay + n2t: pubchem.bioassay + prefixcommons: pubchem.bioassay + miriam: + deprecated: false + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay + id: '00000072' + name: PubChem-bioassay + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubchem.bioassay + sampleId: '1018' + uri_format: https://pubchem.ncbi.nlm.nih.gov/bioassay/$1 + n2t: + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. + example: '1018' + homepage: 'https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay ' + name: PubChem Bioassay at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubchem.bioassay + uri_format: https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$1 + prefixcommons: + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. + example: '1018' + homepage: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay + keywords: + - small molecule + name: 'Pubchem: Bioassays' + pattern: ^\d+$ + prefix: pubchem.bioassay + pubmed_ids: + - '17170002' + uri_format: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$1 +pubchem.compound: + biocontext: + is_identifiers: false + is_obo: false + prefix: CID + uri_format: http://pubchem.ncbi.nlm.nih.gov/compound/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: CID + uri_format: http://pubchem.ncbi.nlm.nih.gov/compound/$1 + cellosaurus: + category: Chemistry resources + homepage: https://pubchem.ncbi.nlm.nih.gov + name: PubChem compound database + prefix: PubChem + uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1 + cheminf: + description: [] + name: PubChem compound identifier (CID) + obsolete: false + prefix: '000140' + fairsharing: + abbreviation: CID + description: In addition to data used in on-going collaborations, this database host images from France Bio Imaging microscopy facility with public access either associated to publications, either that make interest from an image processing point of view (such as challenges for developpers or for use in metrology). This resource requires a log in account, however some projects are available with a guest account. + id: '2306' + name: Curie Image Database + prefix: FAIRsharing.g63c77 + subjects: + - Life Science + go: + homepage: https://pubchem.ncbi.nlm.nih.gov + name: NCBI PubChem database of chemical structures + prefix: PubChem_Compound + uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1 + mappings: + biocontext: CID + biolink: CID + cellosaurus: PubChem + cheminf: '000140' + fairsharing: FAIRsharing.g63c77 + go: PubChem_Compound + miriam: pubchem.compound + n2t: pubchem.compound + prefixcommons: pubchem.compound + scholia: pubchem + wikidata: P662 + miriam: + deprecated: false + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. + homepage: https://pubchem.ncbi.nlm.nih.gov/ + id: '00000034' + name: PubChem-compound + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubchem.compound + providers: + - code: scholia + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + homepage: https://scholia.toolforge.org/ + name: Scholia + uri_format: https://scholia.toolforge.org/pubchem/$1 + sampleId: '100101' + uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1 + n2t: + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. + example: '100101' + homepage: https://pubchem.ncbi.nlm.nih.gov/ + name: NCBI PubChem Compound + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubchem.compound + uri_format: https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$1 + prefixcommons: + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. + example: '100101' + keywords: + - chemical + - metabolite + - structure + name: 'Pubchem: Compounds' + pattern: ^\d+$ + prefix: pubchem.compound + uri_format: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?db=pccompound&term=$1 + synonyms: + - CID + - DSSTox_CID + - PUBCHEM_CID + - PubChem_Compound_CID + - Pubchem + - pubchem_id + wikidata: + database: Q278487 + database.homepage: http://pubchem.ncbi.nlm.nih.gov + database.label: PubChem + format.rdf: http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1 + homepage: http://pubchem.ncbi.nlm.nih.gov + name: PubChem CID + pattern: '[1-9]\d{0,8}' + prefix: P662 + uri_format: https://pubchem.ncbi.nlm.nih.gov/compound/$1 +pubchem.element: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number. + example: '1' + homepage: https://pubchem.ncbi.nlm.nih.gov/periodic-table + name: PubChem Element + pattern: ^\d+$ + uri_format: https://pubchem.ncbi.nlm.nih.gov/element/$1 +pubchem.substance: + biocontext: + is_identifiers: true + is_obo: false + prefix: PUBCHEM.SUBSTANCE + uri_format: http://identifiers.org/pubchem.substance/$1 + cheminf: + description: [] + name: PubChem substance identifier (SID) + obsolete: false + prefix: '000141' + go: + homepage: https://pubchem.ncbi.nlm.nih.gov + name: NCBI PubChem database of chemical substances + prefix: PubChem_Substance + uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1 + mappings: + biocontext: PUBCHEM.SUBSTANCE + cheminf: '000141' + go: PubChem_Substance + miriam: pubchem.substance + n2t: pubchem.substance + prefixcommons: pubchem.substance + wikidata: P2153 + miriam: + deprecated: false + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. + homepage: https://pubchem.ncbi.nlm.nih.gov/ + id: '00000033' + name: PubChem-substance + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubchem.substance + sampleId: '100101' + uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1 + n2t: + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. + example: '100101' + homepage: https://pubchem.ncbi.nlm.nih.gov/ + name: NCBI PubChem Substance + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubchem.substance + uri_format: https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$1 + prefixcommons: + description: PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. + example: '100101' + keywords: + - small molecule + - protein + - structure + name: 'Pubchem: Substances' + pattern: ^\d+$ + prefix: pubchem.substance + pubmed_ids: + - '17170002' + uri_format: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=$1 + synonyms: + - DSSTox_Generic_SID + wikidata: + database: Q278487 + database.homepage: http://pubchem.ncbi.nlm.nih.gov + database.label: PubChem + format.rdf: http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID$1 + homepage: https://www.ncbi.nlm.nih.gov/pcsubstance + name: PubChem Substance ID (SID) + pattern: '[1-9]\d*' + prefix: P2153 + uri_format: https://pubchem.ncbi.nlm.nih.gov/substance/$1 +publons.researcher: + biolink: + is_identifiers: false + is_obo: false + prefix: ResearchID + uri_format: https://publons.com/researcher/$1 + description: Database of researchers to track publications, citation metrics, peer reviews, and journal editing work. + example: '1981638' + homepage: https://publons.com/researcher + mappings: + biolink: ResearchID + name: Publons Researcher + pattern: ^\d+$ + uri_format: https://publons.com/researcher/$1 +pubmed: + biocontext: + is_identifiers: false + is_obo: false + prefix: PMID + uri_format: http://www.ncbi.nlm.nih.gov/pubmed/$1 + cellosaurus: + category: Reference resources + homepage: https://www.ncbi.nlm.nih.gov/pubmed + name: PubMed + prefix: PubMed + uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1 + cheminf: + description: [] + name: PubMed Identifier + obsolete: false + prefix: '000302' + fairsharing: + abbreviation: PubMed + description: PubMed is a search engine of biomedical literature, provided as a service of the U.S. National Library of Medicine and includes more than 25 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. + id: '1990' + name: PubMed + prefix: FAIRsharing.a5sv8m + subjects: + - Environmental Science + - Traditional Medicine + - Earth Science + - Life Science + - Biomedical Science + go: + homepage: https://www.ncbi.nlm.nih.gov/pubmed + name: PubMed + prefix: PMID + synonyms: + - PUBMED + uri_format: http://www.ncbi.nlm.nih.gov/pubmed/$1 + mappings: + biocontext: PMID + cellosaurus: PubMed + cheminf: '000302' + fairsharing: FAIRsharing.a5sv8m + go: PMID + miriam: pubmed + n2t: pubmed + prefixcommons: pubmed + scholia: pubmed + miriam: + deprecated: false + description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. + homepage: https://www.ncbi.nlm.nih.gov/PubMed/ + id: '00000015' + name: PubMed + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubmed + providers: + - code: hubmed + description: HubMed + homepage: http://www.hubmed.org/ + name: HubMed + uri_format: http://www.hubmed.org/display.cgi?uids=$1 + - code: epmc + description: Europe PMC + homepage: http://europepmc.org/ + name: Europe PMC + uri_format: http://europepmc.org/abstract/MED/$1 + - code: CURATOR_REVIEW + description: PubMed through Linkedlife data + homepage: http://linkedlifedata.com/ + name: PubMed through Linkedlife data + uri_format: http://linkedlifedata.com/resource/pubmed/id/$1 + - code: scholia + description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata. + homepage: https://scholia.toolforge.org/ + name: Scholia + uri_format: https://scholia.toolforge.org/pubmed/$1 + sampleId: '16333295' + uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1 + n2t: + description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. + example: '16333295' + homepage: https://www.ncbi.nlm.nih.gov/PubMed/ + name: NCBI PubMed + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: pubmed + uri_format: https://www.ncbi.nlm.nih.gov/pubmed/$1 + prefixcommons: + description: PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. + example: '23735196' + homepage: http://www.ncbi.nlm.nih.gov/pubmed/ + keywords: + - bibliography + name: PubMed + pattern: ^\d+$ + prefix: pubmed + pubmed_ids: + - '16381840' + uri_format: http://www.ncbi.nlm.nih.gov/pubmed/$1 + synonyms: + - MEDLINE + - PMID + - pmid + wikidata: + prefix: P698 +pw: + biocontext: + is_identifiers: false + is_obo: true + prefix: PW + uri_format: http://purl.obolibrary.org/obo/PW_$1 + bioportal: + name: Pathway Ontology + prefix: PW + download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo + example: '0000423' + fairsharing: + abbreviation: PW + description: 'The goal of the Pathway Ontology is to cover all types of biological pathways, including altered and disease pathways, and to capture the relationships between them within the hierarchical structure of a Directed Acyclic Graph (DAG). The five nodes of the ontology are: classic metabolic, regulatory, signaling, drug and disease pathways. An extensive survey of the review literature along with searches of existing pathway databases have been used to choose terms and their position within the tree. The ontology is continually expanding along with the development of Pathway and Disease Portals at RGD.' + id: '1182' + name: Pathway Ontology + prefix: FAIRsharing.f73xhd + subjects: + - Drug Metabolism + - Life Science + mappings: + biocontext: PW + bioportal: PW + fairsharing: FAIRsharing.f73xhd + miriam: pw + n2t: pw + obofoundry: pw + ols: pw + ontobee: PW + prefixcommons: pw + miriam: + deprecated: false + description: 'The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.' + homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html + id: '00000242' + name: Pathway Ontology + namespaceEmbeddedInLui: true + pattern: ^PW:\d{7}$ + prefix: pw + sampleId: '0000208' + uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1 + n2t: + description: 'The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.' + example: '0000208' + homepage: http://bioportal.bioontology.org/ontologies/PW + name: Pathway Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^PW:\d{7}$ + prefix: pw + uri_format: http://purl.bioontology.org/ontology/PW/PW:$1 + obofoundry: + contact: gthayman@mcw.edu + contact.github: gthayman + contact.label: G. Thomas Hayman + contact.orcid: 0000-0002-9553-7227 + deprecated: false + description: A controlled vocabulary for annotating gene products to pathways. + download.obo: http://purl.obolibrary.org/obo/pw.obo + download.owl: http://purl.obolibrary.org/obo/pw.owl + homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Pathway ontology + preferredPrefix: PW + prefix: pw + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/21478484 + title: The Rat Genome Database pathway portal. + - id: https://www.ncbi.nlm.nih.gov/pubmed/24499703 + title: The pathway ontology - updates and applications. + repository: https://github.com/rat-genome-database/PW-Pathway-Ontology + ols: + description: A controlled vocabulary for annotating gene products to pathways. + download: http://purl.obolibrary.org/obo/pw.owl + homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html + name: Pathway ontology + prefix: pw + version: 2019-10-23 + version.iri: http://purl.obolibrary.org/obo/pw/7.52/pw.owl + ontobee: + library: Library + name: Pathway ontology + prefix: PW + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1035' + description: 'The goal of the Pathway Ontology is to capture the various kinds of biological networks, the relationships between them and the alterations or malfunctioning of such networks within a hierarchical structure. The five nodes are: classic metabolic pathways, regulatory pathways, signaling pathways, drug pathways and disease pathways for complex human conditions.' + example: PW_0000002 + homepage: ftp://rgd.mcw.edu/pub/data_release/ontology_obo_files/ + keywords: + - obo + - pathway + - human + name: Pathway ontology + pattern: ^PW_\d{7}$ + prefix: pw + pubmed_ids: + - '21478484' + uri_format: http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=$1 + wikidata: + database: Q28864280 + prefix: P7333 +px: + biocontext: + is_identifiers: true + is_obo: false + prefix: PX + uri_format: http://identifiers.org/px/$1 + mappings: + biocontext: PX + miriam: px + n2t: px + miriam: + deprecated: false + description: The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. + homepage: http://www.proteomexchange.org/ + id: '00000513' + name: ProteomeXchange + namespaceEmbeddedInLui: false + pattern: ^(R)?PXD\d{6}$ + prefix: px + sampleId: PXD000500 + uri_format: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1 + n2t: + description: The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. + example: PXD000500 + homepage: http://www.proteomexchange.org/ + name: ProteomeXchange at Seattle + namespaceEmbeddedInLui: false + pattern: ^(R)?PXD\d{6}$ + prefix: px + uri_format: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1 +pypi: + mappings: + miriam: pypi + miriam: + deprecated: false + description: The Python Package Index (PyPI) is a repository for Python packages. + homepage: https://www.python.org/psf/ + id: '00000863' + name: PyPI + namespaceEmbeddedInLui: false + pattern: ^[a-zA-Z_][a-zA-Z0-9\-_]+$ + prefix: pypi + sampleId: numpy + uri_format: https://pypi.org/project/$1/ + uri_format: https://pypi.org/project/$1 +qtldb: + mappings: + miriam: qtldb + miriam: + deprecated: false + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent. + homepage: https://www.animalgenome.org/QTLdb + id: '00000798' + name: Animal Genome QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: qtldb + sampleId: '4685' + uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 +qudt: + biolink: + is_identifiers: false + is_obo: false + prefix: qud + uri_format: http://qudt.org/1.1/schema/qudt#$1 + bioportal: + name: Quantities, Units, Dimensions, and Types Ontology + prefix: QUDT + description: Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types. + example: baseDimensionEnumeration + fairsharing: + abbreviation: QUDT + description: The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. QUDT provides a unified model of measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units. Originally developed by TopQuadrant for the NASA Exploration Initiatives Ontology Models (NExIOM) project, they now form the basis of the NASA QUDT Handbook. QUDT aims to improve interoperability of data and the specification of information structures through industry standards for Units of Measure, Quantity Kinds, Dimensions and Data Types. + id: '1198' + name: Quantities, Units, Dimensions and Types + prefix: FAIRsharing.d3pqw7 + subjects: + - Astrophysics and Astronomy + homepage: https://qudt.org + mappings: + biolink: qud + bioportal: QUDT + fairsharing: FAIRsharing.d3pqw7 + name: Quantities, Units, Dimensions, and Types Ontology + uri_format: http://qudt.org/schema/qudt#$1 +radiomics: + bioportal: + name: Radiomics Ontology + prefix: RO + description: The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal] + example: LK99 + homepage: http://www.radiomics.org/RO + mappings: + bioportal: RO +rapdb.locus: + mappings: + miriam: rapdb.locus + miriam: + deprecated: false + description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB. + homepage: https://rapdb.dna.affrc.go.jp/ + id: '00000702' + name: RAP-DB Locus + namespaceEmbeddedInLui: false + pattern: ^Os\S+g\d{7}$ + prefix: rapdb.locus + sampleId: Os01g0883800 + uri_format: https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1 + synonyms: + - irgsp +rapdb.transcript: + mappings: + miriam: rapdb.transcript + miriam: + deprecated: false + description: Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB. + homepage: https://rapdb.dna.affrc.go.jp/ + id: '00000762' + name: RAP-DB Transcript + namespaceEmbeddedInLui: false + pattern: ^Os\S+t\d{7}-\d{2}$ + prefix: rapdb.transcript + sampleId: Os01t0883800-02 + uri_format: https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1 +rbk: + biocontext: + is_identifiers: true + is_obo: false + prefix: RBK + uri_format: http://identifiers.org/rbk/$1 + fairsharing: + abbreviation: RBK + description: This site contains data generated by (Re)Building a Kidney (RBK), an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. RBK's goal is to coordinate and support studies that will result in the ability to generate or repair nephrons that can function within the kidney. This resource includes data from both the RBK project and the GenitoUrinary Development Molecular Anatomy Project (GUDMAP). Data submission is restricted to members of the Consortium only. + id: '3323' + name: (Re)Building a Kidney + prefix: FAIRsharing.78d3ad + subjects: + - Molecular biology + - Genomics + - Developmental Biology + - Cell Biology + mappings: + biocontext: RBK + fairsharing: FAIRsharing.78d3ad + miriam: rbk + n2t: rbk + miriam: + deprecated: false + description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. + homepage: https://www.rebuildingakidney.org/ + id: '00000659' + name: Rebuilding a Kidney + namespaceEmbeddedInLui: false + pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ + prefix: rbk + sampleId: Q-2958 + uri_format: https://www.rebuildingakidney.org/id/$1 + n2t: + description: (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. + example: Q-2958 + homepage: https://www.rebuildingakidney.org/ + name: Rebuilding a Kidney + namespaceEmbeddedInLui: false + pattern: ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ + prefix: rbk + uri_format: https://www.rebuildingakidney.org/id/$1 +rbo: + bioportal: + name: Radiation Biology Ontology + prefix: RBO + example: '00000105' + mappings: + bioportal: RBO + obofoundry: rbo + ols: rbo + ontobee: RBO + obofoundry: + contact: daniel.c.berrios@nasa.gov + contact.github: DanBerrios + contact.label: Daniel C. Berrios + contact.orcid: 0000-0003-4312-9552 + depends_on: + - bfo + - chmo + - envo + - obi + - pato + - ro + - uo + deprecated: false + description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. + download.json: http://purl.obolibrary.org/obo/rbo.json + download.obo: http://purl.obolibrary.org/obo/rbo.obo + download.owl: http://purl.obolibrary.org/obo/rbo.owl + homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Radiation Biology Ontology + preferredPrefix: RBO + prefix: rbo + repository: https://github.com/Radiobiology-Informatics-Consortium/RBO + ols: + description: RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. + download: http://purl.obolibrary.org/obo/rbo.owl + homepage: https://github.com/Radiobiology-Informatics-Consortium/RBO + name: Radiation Biology Ontology + prefix: rbo + version: 2022-04-16 + version.iri: http://purl.obolibrary.org/obo/rbo/releases/2022-04-16/rbo.owl + ontobee: + library: Library + name: Radiation Biology Ontology + prefix: RBO + pattern: ^\d{8}$ +rcb: + cellosaurus: + category: Cell line collections + homepage: https://cell.brc.riken.jp/en/rcb + name: RIKEN Bioresource Center Cell Bank + prefix: RCB + uri_format: http://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1&lang=En + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center. + example: RCB0002 + homepage: https://cell.brc.riken.jp/en/rcb + mappings: + cellosaurus: RCB + name: RIKEN Bioresource Center Cell Bank + pattern: ^RCB\d+$ + uri_format: https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1 +rdf: + biocontext: + is_identifiers: false + is_obo: false + prefix: rdf + uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1 + description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts + example: RDF + fairsharing: + abbreviation: RDF + description: 'The Resource Description Framework (RDF) is a framework for representing information in the Web. This document defines an abstract syntax (a data model) which serves to link all RDF-based languages and specifications. The abstract syntax has two key data structures: RDF graphs are sets of subject-predicate-object triples, where the elements may be IRIs, blank nodes, or datatyped literals. They are used to express descriptions of resources. RDF datasets are used to organize collections of RDF graphs, and comprise a default graph and zero or more named graphs. RDF 1.1 Concepts and Abstract Syntax also introduces key concepts and terminology, and discusses datatyping and the handling of fragment identifiers in IRIs within RDF graphs.' + id: '1047' + name: Resource Description Framework + prefix: FAIRsharing.p77ph9 + subjects: + - Computer Science + - Subject Agnostic + homepage: http://www.w3.org/1999/02/22-rdf-syntax-ns + mappings: + biocontext: rdf + fairsharing: FAIRsharing.p77ph9 + name: Resource Description Framework + uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1 +rdfs: + biocontext: + is_identifiers: false + is_obo: false + prefix: rdfs + uri_format: http://www.w3.org/2000/01/rdf-schema#$1 + bioportal: + name: The RDF Schema vocabulary + prefix: RDFS + description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. + example: label + fairsharing: + abbreviation: RDFS + description: RDF Schema (RDFS) is the RDF vocabulary description language. RDFS defines classes and properties that may be used to describe classes, properties and other resources. + id: '982' + name: Resource Description Framework Schema + prefix: FAIRsharing.v9n3gk + subjects: + - Bioinformatics + - Life Science + - Ontology and Terminology + - Linguistics + homepage: https://www.w3.org/TR/rdf-schema/ + mappings: + biocontext: rdfs + bioportal: RDFS + fairsharing: FAIRsharing.v9n3gk + name: RDF Schema + uri_format: http://www.w3.org/2000/01/rdf-schema#$1 +rdo: + bioportal: + name: Reusable Biodiversity Ontology + prefix: RDO + description: Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. + download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo + download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl + example: '9002859' + homepage: https://ratmine.mcw.edu/ontology/disease/ + mappings: + bioportal: RDO + name: RGD Disease_Ontology + pattern: ^\d{7}$ +re3data: + mappings: + miriam: re3data + miriam: + deprecated: false + description: Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines. + homepage: https://datacite.org + id: '00000861' + name: re3data + namespaceEmbeddedInLui: false + pattern: ^r3d\d{9,9}$ + prefix: re3data + sampleId: r3d100010772 + uri_format: https://www.re3data.org/repository/$1 +reactome: + biocontext: + is_identifiers: false + is_obo: false + prefix: REACT + uri_format: http://www.reactome.org/PathwayBrowser/#/$1 + cheminf: + description: Database identifier used by Reactome. + name: Reactome + obsolete: false + prefix: '000411' + example: R-BTA-418592 + go: + homepage: https://www.reactome.org/ + name: Reactome - a curated knowledgebase of biological pathways + prefix: Reactome + synonyms: + - REACTOME + - REAC + uri_format: https://www.reactome.org/content/detail/$1 + mappings: + biocontext: REACT + cheminf: '000411' + go: Reactome + miriam: reactome + n2t: reactome + prefixcommons: reactome + uniprot: Reactome + wikidata: P3937 + miriam: + deprecated: false + description: The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. + homepage: https://www.reactome.org/ + id: '00000018' + name: Reactome + namespaceEmbeddedInLui: false + pattern: (^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$) + prefix: reactome + sampleId: R-HSA-201451 + uri_format: https://reactome.org/content/detail/$1 + n2t: + description: The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. + example: R-HSA-201451 + homepage: https://www.reactome.org/ + name: Reactome, a curated knowledgebase of biological pathways + namespaceEmbeddedInLui: false + pattern: (^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$) + prefix: reactome + uri_format: https://reactome.org/content/detail/$1 + name: Reactome + pattern: ^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$ + prefixcommons: + description: The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. + example: REACT_1590 + homepage: http://www.reactome.org + keywords: + - human + - pathway + - reaction + name: Reactome - a curated knowledgebase of biological pathways + pattern: ^REACT_\d+(\.\d+)?$ + prefix: reactome + pubmed_ids: + - '15608231' + uri_format: http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$1 + providers: + - code: pathwaycommons + description: Pathway diagram drawn with Cytoscape + homepage: https://www.pathwaycommons.org + name: Pathway Commons + uri_format: https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1 + synonyms: + - RE + - REACT + uniprot: + category: Enzyme and pathway databases + comment: Replacement for GK + identifier: '88' + link_is_explicit: 'true' + name: Reactome - a knowledgebase of biological pathways and processes + prefix: Reactome + uri_format: https://www.reactome.org/PathwayBrowser/#%s&FLG=%u + wikidata: + database: Q2134522 + database.homepage: http://www.reactome.org/ + database.label: Reactome + homepage: http://www.reactome.org/ + name: Reactome ID + prefix: P3937 + uri_format: http://identifiers.org/reactome:$1 +reaxys: + description: Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier. + example: '1257009' + homepage: https://www.reaxys.com + name: Reaxys + pattern: ^\d+$ + synonyms: + - Beilstein + - Reaxys + wikidata: + prefix: P1579 +rebase: + biocontext: + is_identifiers: true + is_obo: false + prefix: REBASE + uri_format: http://identifiers.org/rebase/$1 + fairsharing: + abbreviation: REBASE + description: A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. + id: '2009' + name: Restriction enzymes and methylases database + prefix: FAIRsharing.9sb9qh + subjects: + - Life Science + go: + homepage: http://rebase.neb.com/rebase/rebase.html + name: REBASE restriction enzyme database + prefix: REBASE + uri_format: http://rebase.neb.com/rebase/enz/$1.html + mappings: + biocontext: REBASE + fairsharing: FAIRsharing.9sb9qh + go: REBASE + miriam: rebase + n2t: rebase + prefixcommons: rebase + uniprot: REBASE + miriam: + deprecated: false + description: REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. + homepage: http://rebase.neb.com/rebase/ + id: '00000230' + name: REBASE + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rebase + sampleId: '101' + uri_format: http://rebase.neb.com/rebase/enz/$1.html + n2t: + description: REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. + example: '101' + homepage: http://rebase.neb.com/rebase/ + name: REBASE at New England Biolabs + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rebase + uri_format: http://rebase.neb.com/rebase/enz/$1.html + prefixcommons: + description: A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. + example: '101' + homepage: http://rebase.neb.com + keywords: + - enzyme + - protein + - structure + - small molecule + - genome + - DNA + - RNA + name: Restriction enzymes and methylases database + pattern: ^\d+$ + prefix: rebase + pubmed_ids: + - '19846593' + uri_format: http://rebase.neb.com/rebase/enz/$1.html + uniprot: + category: Protein family/group databases + identifier: '89' + link_is_explicit: 'true' + name: Restriction enzymes and methylases database + prefix: REBASE + uri_format: http://rebase.neb.com/rebase/enz/$1.html +receptome.family: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database. + example: '5.1' + homepage: http://www.receptome.org + name: Human Plasma Membrane Receptome Families + uri_format: http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1 +refseq: + biocontext: + is_identifiers: false + is_obo: false + prefix: RefSeq + uri_format: http://www.ncbi.nlm.nih.gov/refseq/?term=$1 + fairsharing: + abbreviation: RefSeq + description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. + id: '1991' + name: Reference Sequence Database + prefix: FAIRsharing.4jg0qw + subjects: + - Genetics + - Computational Biology + - Life Science + go: + homepage: http://www.ncbi.nlm.nih.gov/RefSeq/ + name: RefSeq + prefix: RefSeq + has_canonical: ncbiprotein + mappings: + biocontext: RefSeq + fairsharing: FAIRsharing.4jg0qw + go: RefSeq + miriam: refseq + n2t: refseq + prefixcommons: refseq + uniprot: RefSeq + miriam: + deprecated: false + description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. + homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/ + id: '00000039' + name: RefSeq + namespaceEmbeddedInLui: false + pattern: ^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$ + prefix: refseq + sampleId: NP_012345 + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 + n2t: + description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. + example: NP_012345 + homepage: https://www.ncbi.nlm.nih.gov/projects/RefSeq/ + name: The NCBI Reference Sequence database + namespaceEmbeddedInLui: false + pattern: ^((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?$ + prefix: refseq + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 + name: Reference Sequence Collection + prefixcommons: + description: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. + example: NP_012345 + homepage: http://www.ncbi.nlm.nih.gov/RefSeq/ + keywords: + - protein + - DNA + - RNA + name: Reference Sequence Database + pattern: ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+(\.\d+)?$ + prefix: refseq + pubmed_ids: + - '17130148' + uri_format: http://www.ncbi.nlm.nih.gov/nuccore/[?id] + synonyms: + - REFSEQ_PROT + uniprot: + category: Sequence databases + identifier: '117' + link_is_explicit: 'true' + name: NCBI Reference Sequences + prefix: RefSeq + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 +reo: + comment: 'From James O.: It was an ontology for "reagents" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.' + contact: + email: matt@tislab.org + github: mbrush + name: Matthew Brush + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs. + download_owl: https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl + example: '0000079' + homepage: https://github.com/tis-lab/reagent-ontology + mappings: + ontobee: REO + name: Reagent Ontology + ontobee: + library: Not Specified/No + name: Reagent Ontology + prefix: REO + pattern: ^\d{7}$ + references: + - https://github.com/obi-ontology/obi/issues/1015 + - https://code.google.com/archive/p/reagent-ontology/ + - https://github.com/obi-ontology/obi/issues/1135 + repository: https://github.com/tis-lab/reagent-ontology +repeatsdb.protein: + mappings: + miriam: repeatsdb.protein + miriam: + deprecated: false + description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database. + homepage: https://repeatsdb.org/ + id: '00000792' + name: RepeatsDB Protein + namespaceEmbeddedInLui: false + pattern: ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$ + prefix: repeatsdb.protein + sampleId: P29894 + uri_format: https://repeatsdb.org/protein/$1 + provides: uniprot +repeatsdb.structure: + mappings: + miriam: repeatsdb.structure + miriam: + deprecated: false + description: RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. + homepage: https://repeatsdb.org/ + id: '00000764' + name: RepeatsDB Structure + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$ + prefix: repeatsdb.structure + sampleId: 2gc4E + uri_format: https://repeatsdb.org/structure/$1 +reproduceme: + bioportal: + name: REPRODUCE-ME + prefix: REPRODUCE-ME + example: MicrobeamManipulation + mappings: + bioportal: REPRODUCE-ME + ols: reproduceme + ols: + contact: sheeba.samuel@uni-jena.de + description: The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility. + download: https://sheeba-samuel.github.io/REPRODUCE-ME/doc/reproduce-me.xml + homepage: https://w3id.org/reproduceme/research + name: REPRODUCE-ME Ontology + prefix: reproduceme + version: '1.1' +resid: + biocontext: + is_identifiers: false + is_obo: true + prefix: RESID + uri_format: http://purl.obolibrary.org/obo/RESID_$1 + go: + homepage: https://proteininformationresource.org/resid/resid.shtml + name: RESID Database of Protein Modifications + prefix: RESID + uri_format: https://proteininformationresource.org/cgi-bin/resid?id=$1 + mappings: + biocontext: RESID + go: RESID + miriam: resid + n2t: resid + obofoundry: resid + prefixcommons: resid + miriam: + deprecated: false + description: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. + homepage: http://pir0.georgetown.edu/resid/ + id: '00000046' + name: RESID + namespaceEmbeddedInLui: false + pattern: ^AA\d{4}$ + prefix: resid + sampleId: AA0001 + uri_format: http://pir0.georgetown.edu/cgi-bin/resid?id=$1 + n2t: + description: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. + example: AA0001 + homepage: http://pir0.georgetown.edu/resid/ + name: RESID at Georgetown University + namespaceEmbeddedInLui: false + pattern: ^AA\d{4}$ + prefix: resid + uri_format: http://pir0.georgetown.edu/cgi-bin/resid?id=$1 + obofoundry: + contact: john.garavelli@ebi.ac.uk + contact.label: John Garavelli + deprecated: true + description: For the description of covalent bonds in proteins. + homepage: http://www.ebi.ac.uk/RESID/ + name: Protein covalent bond + prefix: resid + prefixcommons: + description: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. + example: AA0001 + homepage: http://www.ebi.ac.uk/RESID/ + keywords: + - protein + - small molecule + - structure + name: RESID Database of Protein Modifications + pattern: ^AA\d{4}$ + prefix: resid + pubmed_ids: + - '15174124' + uri_format: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$1'] +reto: + bioportal: + name: Regulation of Transcription Ontology + prefix: RETO + download_obo: https://www.bio.ntnu.no/ontology/ReTO/reto.obo + download_owl: https://www.bio.ntnu.no/ontology/ReTO/reto.owl + fairsharing: + abbreviation: ReTO + description: An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI and orthological properties from RO and SIO. + id: '263' + name: Regulation of Transcription Ontolology + prefix: FAIRsharing.4qyf0f + subjects: + - Life Science + - Transcriptomics + mappings: + bioportal: RETO + fairsharing: FAIRsharing.4qyf0f + ols: reto + no_own_terms: true + ols: + contact: vladimir.n.mironov@gmail.com + description: Regulation of Transcription + download: http://www.bio.ntnu.no/ontology/ReTO/reto.rdf + homepage: http://www.semantic-systems-biology.org/apo + name: Regulation of Transcription Ontology + prefix: reto + version: 2019-09-17 +rex: + biocontext: + is_identifiers: false + is_obo: true + prefix: REX + uri_format: http://purl.obolibrary.org/obo/REX_$1 + bioportal: + name: Physico-Chemical Process + prefix: REX + download_owl: http://purl.obolibrary.org/obo/rex.owl + example: '0000512' + fairsharing: + abbreviation: REX + description: REX is an ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. REX includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX. + id: '1085' + name: Physico-chemical process + prefix: FAIRsharing.g0a7s0 + subjects: + - Chemistry + - Life Science + homepage: https://www.ebi.ac.uk/chebi/ + mappings: + biocontext: REX + bioportal: REX + fairsharing: FAIRsharing.g0a7s0 + obofoundry: rex + ols: rex + ontobee: REX + prefixcommons: rex + obofoundry: + deprecated: true + description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. + download.owl: http://purl.obolibrary.org/obo/rex.owl + name: Physico-chemical process + prefix: rex + ols: + description: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. + download: http://purl.obolibrary.org/obo/rex.owl + name: Physico-chemical process + prefix: rex + version: 2017-11-19 + version.iri: http://purl.obolibrary.org/obo/rex/releases/2017-11-19/rex.owl + ontobee: + library: Library + name: Physico-chemical process + prefix: REX + part_of: chebi + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1043' + description: REX is an ontology of physico-chemical processes and includes microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. + example: REX_0000517 + homepage: http://www.ebi.ac.uk/~kirill/REX/ + keywords: + - obo + - biochemistry + name: Physico-chemical process + pattern: ^REX_\d{8}$ + prefix: rex +rexo: + bioportal: + name: Regulation of Gene Expression Ontolology + prefix: REXO + download_obo: https://www.bio.ntnu.no/ontology/ReXO/rexo.obo + download_owl: https://www.bio.ntnu.no/ontology/ReXO/rexo.owl + fairsharing: + abbreviation: ReXO + description: An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, and orthology relations using ontological properties from RO and ISO. + id: '846' + name: Regulation of Gene Expression Ontolology + prefix: FAIRsharing.recas1 + subjects: + - Life Science + mappings: + bioportal: REXO + fairsharing: FAIRsharing.recas1 + ols: rexo + no_own_terms: true + ols: + contact: vladimir.n.mironov@gmail.com + description: Regulation of Gene Expression + download: http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf + homepage: http://www.semantic-systems-biology.org/apo + name: Regulation of Gene Expression Ontology + prefix: rexo + version: 2019-04-11 +rfam: + biocontext: + is_identifiers: true + is_obo: false + prefix: RFAM + uri_format: http://identifiers.org/rfam/$1 + fairsharing: + abbreviation: Rfam + description: 'The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence.' + id: '2396' + name: Rfam + prefix: FAIRsharing.fex4c8 + subjects: + - Genetics + go: + homepage: https://rfam.org + name: Rfam database of RNA families + prefix: Rfam + uri_format: https://rfam.org/family/$1 + mappings: + biocontext: RFAM + fairsharing: FAIRsharing.fex4c8 + go: Rfam + miriam: rfam + n2t: rfam + ncbi: RFAM + miriam: + deprecated: false + description: 'The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.' + homepage: https://rfam.xfam.org/ + id: '00000409' + name: RFAM + namespaceEmbeddedInLui: false + pattern: ^RF\d{5}$ + prefix: rfam + sampleId: RF00230 + uri_format: https://rfam.xfam.org/family/$1 + n2t: + description: 'The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.' + example: RF00230 + homepage: https://rfam.xfam.org/ + name: Rfam at EMBL-EBI + namespaceEmbeddedInLui: false + pattern: ^RF\d{5}$ + prefix: rfam + uri_format: https://rfam.xfam.org/family/$1 + ncbi: + example: RF00230 + homepage: http://www.sanger.ac.uk/Software/Rfam/ + name: RNA families database of alignments and CMs + prefix: RFAM +rgd: + biocontext: + is_identifiers: false + is_obo: false + prefix: RGD + uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 + bioportal: + name: RRB Group D + prefix: RGD + cellosaurus: + category: Organism-specific databases + homepage: https://rgd.mcw.edu + name: Rat Genome Database + prefix: RGD + uri_format: https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 + example: '7499841' + fairsharing: + abbreviation: RGD + description: The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually and via an automated pipeline, giving RGD users integrated access to a wide variety of data to support their research. + id: '1951' + name: Rat Genome Database + prefix: FAIRsharing.pfg82t + subjects: + - Genomics + - Comparative Genomics + go: + homepage: https://rgd.mcw.edu/ + name: Rat Genome Database + prefix: RGD + synonyms: + - RAD + - RGDID + uri_format: https://rgd.mcw.edu/rgdweb/search/search.html?term=$1 + mappings: + biocontext: RGD + bioportal: RGD + cellosaurus: RGD + fairsharing: FAIRsharing.pfg82t + go: RGD + miriam: rgd + n2t: rgd + ncbi: RGD + prefixcommons: rgd + uniprot: RGD + wikidata: P3853 + miriam: + deprecated: false + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. + homepage: http://rgd.mcw.edu/ + id: '00000047' + name: Rat Genome Database + namespaceEmbeddedInLui: false + pattern: ^\d{4,}$ + prefix: rgd + providers: + - code: agr + description: RGD through the Alliance of Genome Resources + homepage: https://www.alliancegenome.org + name: RGD through the Alliance of Genome Resources + uri_format: https://www.alliancegenome.org/gene/RGD:$1 + sampleId: '2018' + uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 + n2t: + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. + example: '2018' + homepage: http://rgd.mcw.edu/ + name: Rat Genome Database + namespaceEmbeddedInLui: false + pattern: ^\d{4,}$ + prefix: rgd + uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 + name: Rat Genome Database + ncbi: + example: '620528' + homepage: http://rgd.mcw.edu/rgdweb/search/search.html + name: Rat Genome Database + prefix: RGD + prefixcommons: + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. + example: '2018' + homepage: http://rgd.mcw.edu/genes/ + keywords: + - genome + - gene + - DNA + name: Rat Genome Database + pattern: ^\d{4,7}$ + prefix: rgd + pubmed_ids: + - '17151068' + uri_format: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$1 + synonyms: + - RGD + uniprot: + category: Organism-specific databases + identifier: '91' + link_is_explicit: 'true' + name: Rat genome database + prefix: RGD + uri_format: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$1 + wikidata: + database: Q7295410 + database.homepage: http://rgd.mcw.edu + database.label: Rat genome database + homepage: http://rgd.mcw.edu/ + name: Rat Genome Database ID + prefix: P3853 + uri_format: http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 +rgd.qtl: + biocontext: + is_identifiers: true + is_obo: false + prefix: RGD.QTL + uri_format: http://identifiers.org/rgd.qtl/$1 + mappings: + biocontext: RGD.QTL + miriam: rgd.qtl + n2t: rgd.qtl + miriam: + deprecated: false + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. + homepage: http://rgd.mcw.edu/ + id: '00000451' + name: Rat Genome Database qTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rgd.qtl + sampleId: '1354581' + uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1 + n2t: + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. + example: '1354581' + homepage: http://rgd.mcw.edu/ + name: Rat Genome Database qTL at Medical College of Wisconsin + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rgd.qtl + uri_format: http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1 +rgd.strain: + biocontext: + is_identifiers: true + is_obo: false + prefix: RGD.STRAIN + uri_format: http://identifiers.org/rgd.strain/$1 + mappings: + biocontext: RGD.STRAIN + miriam: rgd.strain + n2t: rgd.strain + miriam: + deprecated: false + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. + homepage: http://rgd.mcw.edu/ + id: '00000452' + name: Rat Genome Database strain + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rgd.strain + sampleId: '5688061' + uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1 + n2t: + description: Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. + example: '5688061' + homepage: http://rgd.mcw.edu/ + name: Rat Genome Database strain at Medical College of Wisconsin + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: rgd.strain + uri_format: http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1 +rhea: + biocontext: + is_identifiers: true + is_obo: false + prefix: RHEA + uri_format: http://identifiers.org/rhea/$1 + fairsharing: + abbreviation: Rhea + description: Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt. + id: '1639' + name: Rhea + prefix: FAIRsharing.pn1sr5 + subjects: + - Biochemistry + - Life Science + go: + description: Rhea is a manually annotated database of chemical reactions. All data in Rhea is freely accessible and available for anyone to use. + homepage: https://www.rhea-db.org + name: Rhea, the Annotated Reactions Database + prefix: RHEA + uri_format: https://www.rhea-db.org/rhea/$1 + mappings: + biocontext: RHEA + fairsharing: FAIRsharing.pn1sr5 + go: RHEA + miriam: rhea + n2t: rhea + prefixcommons: rhea + miriam: + deprecated: false + description: >2- + Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. + + Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB. + homepage: https://www.rhea-db.org/ + id: '00000082' + name: Rhea + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: rhea + sampleId: '12345' + uri_format: https://www.rhea-db.org/rhea/$1 + n2t: + description: Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed "spontaneous". + example: '12345' + homepage: https://www.rhea-db.org/ + name: Rhea + namespaceEmbeddedInLui: false + pattern: ^\d{5}$ + prefix: rhea + uri_format: https://www.rhea-db.org/reaction?id=$1 + prefixcommons: + description: Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed "spontaneous". + example: '12345' + homepage: http://www.ebi.ac.uk/rhea/ + keywords: + - reaction + - small molecule + name: Reaction database + pattern: ^\d{5}$ + prefix: rhea + uri_format: http://www.ebi.ac.uk/rhea//reaction.xhtml?id=$1 + synonyms: + - RHEA + uri_format: https://www.rhea-db.org/rhea/$1 + wikidata: + database: Q24265951 +ricegap: + biocontext: + is_identifiers: true + is_obo: false + prefix: RICEGAP + uri_format: http://identifiers.org/ricegap/$1 + mappings: + biocontext: RICEGAP + miriam: ricegap + n2t: ricegap + miriam: + deprecated: false + description: The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. + homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml + id: '00000358' + name: Rice Genome Annotation Project + namespaceEmbeddedInLui: false + pattern: ^LOC\_Os\d{1,2}g\d{5}$ + prefix: ricegap + sampleId: LOC_Os02g13300 + uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1 + n2t: + description: The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. + example: LOC_Os02g13300 + homepage: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml + name: Rice Genome Annotation Project at TIGR + namespaceEmbeddedInLui: false + pattern: ^LOC\_Os\d{1,2}g\d{5}$ + prefix: ricegap + uri_format: http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1 +ricenetdb.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: RICENETDB.COMPOUND + uri_format: http://identifiers.org/ricenetdb.compound/$1 + mappings: + biocontext: RICENETDB.COMPOUND + miriam: ricenetdb.compound + n2t: ricenetdb.compound + miriam: + deprecated: false + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + homepage: http://bis.zju.edu.cn/ricenetdb + id: '00000666' + name: RiceNetDB Compound + namespaceEmbeddedInLui: false + pattern: ^OSC\d{4}$ + prefix: ricenetdb.compound + sampleId: OSC1416 + uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1 + n2t: + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + example: OSC1416 + homepage: http://bis.zju.edu.cn/ricenetdb + name: RiceNetDB Compound + namespaceEmbeddedInLui: false + pattern: ^OSC\d{4}$ + prefix: ricenetdb.compound + uri_format: http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1 +ricenetdb.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: RICENETDB.GENE + uri_format: http://identifiers.org/ricenetdb.gene/$1 + mappings: + biocontext: RICENETDB.GENE + miriam: ricenetdb.gene + n2t: ricenetdb.gene + miriam: + deprecated: false + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + homepage: http://bis.zju.edu.cn/ricenetdb/ + id: '00000664' + name: RiceNetDB Gene + namespaceEmbeddedInLui: false + pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$ + prefix: ricenetdb.gene + sampleId: LOC_Os01g49190.1 + uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1 + n2t: + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + example: LOC_Os01g49190.1 + homepage: http://bis.zju.edu.cn/ricenetdb/ + name: RiceNetDB + namespaceEmbeddedInLui: false + pattern: ^LOC\_Os\d{1,2}g\d{5}\.\d$ + prefix: ricenetdb.gene + uri_format: http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1 +ricenetdb.mirna: + biocontext: + is_identifiers: true + is_obo: false + prefix: RICENETDB.MIRNA + uri_format: http://identifiers.org/ricenetdb.miRNA/$1 + mappings: + biocontext: RICENETDB.MIRNA + miriam: ricenetdb.mirna + n2t: ricenetdb.mirna + miriam: + deprecated: false + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + homepage: http://bis.zju.edu.cn/ricenetdb + id: '00000668' + name: RiceNetDB miRNA + namespaceEmbeddedInLui: false + pattern: ^osa-miR\d{3,5}[a-z]{0,1}$ + prefix: ricenetdb.mirna + sampleId: osa-miR446 + uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1 + n2t: + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + example: osa-miR446 + homepage: http://bis.zju.edu.cn/ricenetdb + name: RiceNetDB miRNA + namespaceEmbeddedInLui: false + pattern: ^osa-miR\d{3,5}[a-z]{0,1}$ + prefix: ricenetdb.mirna + uri_format: http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1 +ricenetdb.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: RICENETDB.PROTEIN + uri_format: http://identifiers.org/ricenetdb.protein/$1 + mappings: + biocontext: RICENETDB.PROTEIN + miriam: ricenetdb.protein + n2t: ricenetdb.protein + miriam: + deprecated: false + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + homepage: http://bis.zju.edu.cn/ricenetdb/ + id: '00000665' + name: RiceNetDB Protein + namespaceEmbeddedInLui: false + pattern: ^LOC\_Os\d{1,2}g\d{5}$ + prefix: ricenetdb.protein + sampleId: LOC_Os01g49190 + uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1 + n2t: + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + example: LOC_Os01g49190 + homepage: http://bis.zju.edu.cn/ricenetdb/ + name: RiceNetDB + namespaceEmbeddedInLui: false + pattern: ^LOC\_Os\d{1,2}g\d{5}$ + prefix: ricenetdb.protein + uri_format: http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1 +ricenetdb.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: RICENETDB.REACTION + uri_format: http://identifiers.org/ricenetdb.reaction/$1 + mappings: + biocontext: RICENETDB.REACTION + miriam: ricenetdb.reaction + n2t: ricenetdb.reaction + miriam: + deprecated: false + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + homepage: http://bis.zju.edu.cn/ricenetdb + id: '00000667' + name: RiceNetDB Reaction + namespaceEmbeddedInLui: false + pattern: ^OSR\d{4}$ + prefix: ricenetdb.reaction + sampleId: OSR0818 + uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1 + n2t: + description: 'RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.' + example: OSR0818 + homepage: http://bis.zju.edu.cn/ricenetdb + name: RiceNetDB Reaction + namespaceEmbeddedInLui: false + pattern: ^OSR\d{4}$ + prefix: ricenetdb.reaction + uri_format: http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1 +rnacentral: + biocontext: + is_identifiers: true + is_obo: false + prefix: RNACENTRAL + uri_format: http://identifiers.org/rnacentral/$1 + fairsharing: + abbreviation: RNAcentral + description: RNAcentral is a free, public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of databases representing a broad range of organisms and RNA types. + id: '2891' + name: RNAcentral + prefix: FAIRsharing.KcCjL7 + subjects: + - Bioinformatics + - Biology + go: + description: An international database of ncRNA sequences + homepage: https://rnacentral.org + name: RNAcentral + prefix: RNAcentral + uri_format: https://rnacentral.org/rna/$1 + mappings: + biocontext: RNACENTRAL + fairsharing: FAIRsharing.KcCjL7 + go: RNAcentral + miriam: rnacentral + n2t: rnacentral + ncbi: RNAcentral + miriam: + deprecated: false + description: RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. + homepage: https://rnacentral.org/ + id: '00000630' + name: RNAcentral + namespaceEmbeddedInLui: false + pattern: ^URS[0-9A-F]{10}(\_\d+)?$ + prefix: rnacentral + sampleId: URS0000759CF4 + uri_format: https://rnacentral.org/rna/$1 + n2t: + description: RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. + example: URS0000759CF4 + homepage: https://rnacentral.org/ + name: RNAcentral through EMBL-EBI + namespaceEmbeddedInLui: false + pattern: ^URS[0-9A-F]{10}(\_\d+)?$ + prefix: rnacentral + uri_format: https://rnacentral.org/rna/$1 + ncbi: + example: URS00001B9622_9606 + homepage: http://rnacentral.org + name: Noncoding RNA Sequence Database + prefix: RNAcentral + synonyms: + - LNCRNADB +rnamod: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A comprehensive listing of post-transcriptionally modified nucleosides from RNA - + example: '051' + homepage: http://rna.rega.kuleuven.be/rnamods/ + name: The RNA Modification Database + pattern: ^\d{3}$ + uri_format: http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1 +rnamods: + biocontext: + is_identifiers: true + is_obo: false + prefix: RNAMODS + uri_format: http://identifiers.org/rnamods/$1 + go: + homepage: https://mods.rna.albany.edu/ + name: RNA Modification Database + prefix: RNAmods + synonyms: + - RNAMDB + uri_format: https://mods.rna.albany.edu/mods/modifications/view/$1 + mappings: + biocontext: RNAMODS + go: RNAmods + miriam: rnamods + n2t: rnamods + prefixcommons: rnamods + miriam: + deprecated: false + description: The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. + homepage: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm + id: '00000308' + name: RNA Modification Database + namespaceEmbeddedInLui: false + pattern: ^\d{3}$ + prefix: rnamods + sampleId: '101' + uri_format: http://mods.rna.albany.edu/mods/modifications/view/$1 + n2t: + description: The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. + example: '101' + homepage: http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm + name: RNA Modification Database at University of Utah + namespaceEmbeddedInLui: false + pattern: ^\d{3}$ + prefix: rnamods + uri_format: http://mods.rna.albany.edu/mods/modifications/view/$1 + prefixcommons: + description: The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA and is maintained as an updated version of the initial printed report. + example: '080' + homepage: http://medlib.med.utah.edu/RNAmods/ + keywords: + - RNA + - structure + name: RNA Modification Database + pattern: ^\d+$ + prefix: rnamods + uri_format: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?$1 +rnao: + biocontext: + is_identifiers: false + is_obo: true + prefix: RNAO + uri_format: http://purl.obolibrary.org/obo/RNAO_$1 + bioportal: + name: RNA Ontology + prefix: RNAO + example: '0000128' + fairsharing: + abbreviation: RNAO + description: RNAO is a controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure, and from base pairing and base stacking interactions to sophisticated motifs. + id: '65' + name: RNA Ontology + prefix: FAIRsharing.kqt2h2 + subjects: + - Biochemistry + - Life Science + mappings: + biocontext: RNAO + bioportal: RNAO + fairsharing: FAIRsharing.kqt2h2 + obofoundry: rnao + ols: rnao + ontobee: RNAO + prefixcommons: rnao + obofoundry: + contact: BatchelorC@rsc.org + contact.label: Colin Batchelor + contact.orcid: 0000-0001-5985-7429 + deprecated: true + description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. + download.obo: http://purl.obolibrary.org/obo/rnao.obo + download.owl: http://purl.obolibrary.org/obo/rnao.owl + homepage: https://github.com/bgsu-rna/rnao + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: RNA ontology + prefix: rnao + repository: https://github.com/BGSU-RNA/rnao + ols: + description: Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. + download: http://purl.obolibrary.org/obo/rnao.owl + homepage: https://github.com/bgsu-rna/rnao + name: 'The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data' + prefix: rnao + version: 2019-04-15 + ontobee: + library: Library + name: RNA ontology + prefix: RNAO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1500' + description: The central aim of the RNA Ontology Consortium (ROC) is to develop an ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs. + example: RNAO_0000112 + homepage: http://code.google.com/p/rnao/ + keywords: + - obo + name: RNA ontology + pattern: ^RNAO_\d{7}$ + prefix: rnao + uri_format: http://purl.obolibrary.org/obo/$1 +ro: + biocontext: + is_identifiers: false + is_obo: true + prefix: OBO_REL + uri_format: http://purl.obolibrary.org/obo/OBO_REL_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: RO + uri_format: http://purl.obolibrary.org/obo/RO_$1 + bioportal: + prefix: OBOREL + example: '0002533' + fairsharing: + abbreviation: OBOREL + description: Defines core relations used in all OBO ontologies. + id: '534' + name: Open Biological and Biomedical Ontologies Relationship Types + prefix: FAIRsharing.1vrrdh + subjects: [] + go: + description: A collection of relations used across OBO ontologies + name: OBO Relation Ontology Ontology + prefix: RO + mappings: + biocontext: OBO_REL + biolink: RO + bioportal: OBOREL + fairsharing: FAIRsharing.1vrrdh + go: RO + miriam: ro + n2t: ro + obofoundry: ro + ols: ro + ontobee: RO + prefixcommons: ro + miriam: + deprecated: false + description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. + homepage: http://obofoundry.org/ontology/ro.html + id: '00000120' + name: Relation Ontology + namespaceEmbeddedInLui: false + pattern: ^RO_\d{7}$ + prefix: ro + sampleId: RO_0002533 + uri_format: http://purl.obolibrary.org/obo/$1 + n2t: + description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. + example: RO_0002533 + homepage: http://obofoundry.org/ontology/ro.html + name: OBO Relation Ontology through OntoBee + namespaceEmbeddedInLui: false + pattern: ^RO_\d{7}$ + prefix: ro + uri_format: http://purl.obolibrary.org/obo/$1 + name: Relation Ontology + obofoundry: + appears_in: + - go + - agro + - aism + - cdno + - cl + - clao + - clyh + - colao + - cteno + - ecao + - ecocore + - ecto + - envo + - foodon + - fovt + - genepio + - hso + - lepao + - maxo + - ons + - ontoavida + - pcl + - pco + - plana + - planp + - poro + - psdo + - pso + - rbo + - xpo + - zp + - upa + contact: cjmungall@lbl.gov + contact.github: cmungall + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + deprecated: false + description: Relationship types shared across multiple ontologies + download.json: http://purl.obolibrary.org/obo/ro.json + download.obo: http://purl.obolibrary.org/obo/ro.obo + download.owl: http://purl.obolibrary.org/obo/ro.owl + homepage: https://oborel.github.io/ + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Relation Ontology + preferredPrefix: RO + prefix: ro + repository: https://github.com/oborel/obo-relations + ols: + description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. + download: http://purl.obolibrary.org/obo/ro.owl + homepage: ' https://github.com/oborel/obo-relations/' + name: OBO Relations Ontology + prefix: ro + version: 2022-05-23 + version.iri: http://purl.obolibrary.org/obo/ro/releases/2022-05-23/ro.owl + ontobee: + library: Library + name: Relation Ontology + prefix: RO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1042' + description: The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. + example: part_of + homepage: http://www.obofoundry.org/ro + keywords: + - obo + - relations + name: Relation Ontology + pattern: ^\w+$ + prefix: ro + pubmed_ids: + - '15892874' + synonyms: + - RO_proposed_relation + - obo_rel + - oborel + uri_format: http://purl.obolibrary.org/obo/RO_$1 + wikidata: + prefix: P3590 +rouge: + biocontext: + is_identifiers: true + is_obo: false + prefix: ROUGE + uri_format: http://identifiers.org/rouge/$1 + fairsharing: + abbreviation: ROUGE + description: The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs). + id: '1942' + name: ROdent Unidentified Gene-Encoded large proteins + prefix: FAIRsharing.vdbagq + subjects: + - Life Science + mappings: + biocontext: ROUGE + fairsharing: FAIRsharing.vdbagq + miriam: rouge + n2t: rouge + prefixcommons: rouge + uniprot: Rouge + miriam: + deprecated: false + description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. + homepage: http://www.kazusa.or.jp/rouge/ + id: '00000293' + name: Rouge + namespaceEmbeddedInLui: false + pattern: ^m\w+$ + prefix: rouge + sampleId: mKIAA4200 + uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1/ + n2t: + description: The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. + example: mKIAA4200 + homepage: http://www.kazusa.or.jp/rouge/ + name: Rouge at Kazusa DNA Research Institute + namespaceEmbeddedInLui: false + pattern: ^m\w+$ + prefix: rouge + uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1/ + name: Rodent Unidentified Gene-Encoded Large Proteins + prefixcommons: + description: The ROUGE protein database is a sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs). + example: mKIAA0701 + homepage: http://www.kazusa.or.jp/rouge/ + keywords: + - protein + - DNA + name: A Database of Rodent Unidentified Gene-Encoded Large Proteins Analyzed + pattern: ^mKIAA\d+$ + prefix: rouge + uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1/ + uniprot: + category: Organism-specific databases + identifier: '92' + name: Rodent Unidentified Gene-Encoded large proteins database + prefix: Rouge + uri_format: http://www.kazusa.or.jp/rouge/gfpage/$1 + uri_format: https://www.kazusa.or.jp/rouge/gfpage/$1 +rrid: + banana: RRID + biocontext: + is_identifiers: true + is_obo: false + prefix: RRID + uri_format: http://identifiers.org/rrid/$1 + fairsharing: + abbreviation: RRID + description: 'The Resource Identification Initiative (#RRID) is designed to help researchers sufficiently cite the key resources used to produce the scientific findings reported in the biomedical literature. In addition to being unique, RRID’s meet three key criteria, they are: - Machine readable - Free to generate and access - Consistent across publishers and journals' + id: '538' + name: Research Resource Identifiers + prefix: FAIRsharing.ATwSZG + subjects: + - Chemistry + - Life Science + - Biomedical Science + mappings: + biocontext: RRID + fairsharing: FAIRsharing.ATwSZG + miriam: rrid + n2t: rrid + miriam: + deprecated: false + description: "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch." + homepage: https://scicrunch.org/resolver + id: '00000558' + name: RRID + namespaceEmbeddedInLui: true + pattern: ^RRID:[a-zA-Z]+.+$ + prefix: rrid + sampleId: AB_262044 + uri_format: https://scicrunch.org/resolver/RRID:$1 + n2t: + description: 'The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.' + example: AB_262044 + homepage: https://scicrunch.org/resolver + name: RRID at SciCrunch + namespaceEmbeddedInLui: true + pattern: ^RRID:[A-Z_a-z-0-9]+$ + prefix: rrid + uri_format: https://scicrunch.org/resolver/RRID:$1 + name: Research Resource Identification + pattern: ^[a-zA-Z]+.+$ +rs: + biocontext: + is_identifiers: false + is_obo: true + prefix: RS + uri_format: http://purl.obolibrary.org/obo/RS_$1 + bioportal: + name: Rat Strain Ontology + prefix: RS + download_obo: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo + download_owl: https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl + example: '0001807' + fairsharing: + abbreviation: RS + description: This ontology defines the hierarchical display of the different rat strains as derived from the parental strains. + id: '428' + name: Rat Strain Ontology + prefix: FAIRsharing.vajn3f + subjects: + - Life Science + mappings: + biocontext: RS + bioportal: RS + fairsharing: FAIRsharing.vajn3f + obofoundry: rs + ols: rs + ontobee: RS + prefixcommons: rs + obofoundry: + contact: sjwang@mcw.edu + contact.github: shurjenw + contact.label: Shur-Jen Wang + contact.orcid: 0000-0001-5256-8683 + deprecated: false + description: Ontology of rat strains + download.obo: http://purl.obolibrary.org/obo/rs.obo + download.owl: http://purl.obolibrary.org/obo/rs.owl + homepage: http://rgd.mcw.edu/rgdweb/search/strains.html + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Rat Strain Ontology + preferredPrefix: RS + prefix: rs + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/24267899 + title: 'Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.' + repository: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology + ols: + description: Ontology of rat strains + download: http://purl.obolibrary.org/obo/rs.owl + homepage: http://rgd.mcw.edu/rgdweb/search/strains.html + name: Rat Strain Ontology + prefix: rs + version: 2019-12-13 + version.iri: http://purl.obolibrary.org/obo/rs/6.106/rs.owl + ontobee: + library: Library + name: Rat Strain Ontology + prefix: RS + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1150' + description: This ontology defines the hierarchical display of the different rat strains as derived from the parental strains + example: RS_0000271 + homepage: http://rgd.mcw.edu/ + keywords: + - obo + name: Rat Strain Ontology + pattern: ^RS_\d{7}$ + prefix: rs + uri_format: http://purl.obolibrary.org/obo/$1 +runbiosimulations: + mappings: + miriam: runbiosimulations + miriam: + deprecated: false + description: runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive. + homepage: https://icahn.mssm.edu/ + id: '00000897' + name: runBioSimulations + namespaceEmbeddedInLui: false + pattern: '[0-9a-z]{24,24}' + prefix: runbiosimulations + sampleId: 5fde96bdc5f1aa9ff0cce18a + uri_format: https://run.biosimulations.org/simulations/$1 +rxno: + biocontext: + is_identifiers: false + is_obo: true + prefix: RXNO + uri_format: http://purl.obolibrary.org/obo/RXNO_$1 + bioportal: + name: Name Reaction Ontology + prefix: RXNO + download_obo: https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo + example: '0000253' + fairsharing: + abbreviation: RXNO + description: The Name Reaction Ontology (RXNO) connects organic name reactions such as the Diels-Alder cyclization and the Cannizzaro reaction to their roles in organic synthesis. + id: '361' + name: Name Reaction Ontology + prefix: FAIRsharing.w4tncg + subjects: + - Molecular Chemistry + mappings: + biocontext: RXNO + bioportal: RXNO + fairsharing: FAIRsharing.w4tncg + obofoundry: rxno + ols: rxno + ontobee: RXNO + name: Name Reaction Ontology + obofoundry: + contact: batchelorc@rsc.org + contact.github: batchelorc + contact.label: Colin Batchelor + contact.orcid: 0000-0001-5985-7429 + deprecated: false + description: Connects organic name reactions to their roles in an organic synthesis and to processes in MOP + download.owl: http://purl.obolibrary.org/obo/rxno.owl + homepage: https://github.com/rsc-ontologies/rxno + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Name Reaction Ontology + preferredPrefix: RXNO + prefix: rxno + repository: https://github.com/rsc-ontologies/rxno + ols: + contact: chemistry-ontologies@googlegroups.com + description: RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization. + download: http://purl.obolibrary.org/obo/rxno.owl + homepage: https://github.com/rsc-ontologies/rxno + name: RXNO + prefix: rxno + version: 2021-12-16 + version.iri: http://purl.obolibrary.org/obo/rxno/releases/2021-12-16/rxno.owl + ontobee: + library: Library + name: Name Reaction Ontology + prefix: RXNO + pattern: ^\d{7}$ + wikidata: + prefix: P2106 +rxnorm: + biocontext: + is_identifiers: false + is_obo: false + prefix: RXCUI + uri_format: http://purl.bioontology.org/ontology/RXNORM/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: RXCUI + uri_format: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1 + bioportal: + name: RxNORM + prefix: RXNORM + description: RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. + example: '221058' + fairsharing: + abbreviation: RxNORM + description: RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, MediSpan, Gold Standard Drug Database, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. RxNorm now includes the National Drug File - Reference Terminology (NDF-RT) from the Veterans Health Administration. NDF-RT is a terminology used to code clinical drug properties, including mechanism of action, physiologic effect, and therapeutic category. + id: '187' + name: RxNORM + prefix: FAIRsharing.36pf8q + subjects: + - Biomedical Science + - Preclinical Studies + homepage: https://www.nlm.nih.gov/research/umls/rxnorm/ + mappings: + biocontext: RXCUI + biolink: RXCUI + bioportal: RXNORM + fairsharing: FAIRsharing.36pf8q + name: RxNorm + pattern: ^[0-9]{1,7}$ + synonyms: + - RXCUI + uri_format: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1 + wikidata: + database: Q7383767 + prefix: P3345 +sabiork.compound: + mappings: + miriam: sabiork.compound + n2t: sabiork.compound + miriam: + deprecated: false + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information. + homepage: http://sabiork.h-its.org/ + id: '00000688' + name: SABIO-RK Compound + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sabiork.compound + sampleId: '75' + uri_format: http://sabiork.h-its.org/newSearch?q=$1 + n2t: + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information. + example: '75' + homepage: http://sabiork.h-its.org/ + name: SABIO-RK Compound + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sabiork.compound + uri_format: http://sabiork.h-its.org/newSearch?q=$1 +sabiork.ec: + biocontext: + is_identifiers: true + is_obo: false + prefix: SABIORK.EC + uri_format: http://identifiers.org/sabiork.ec/$1 + mappings: + biocontext: SABIORK.EC + miriam: sabiork.ec + n2t: sabiork.ec + prefixcommons: sabiork.ec + miriam: + deprecated: false + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. + homepage: http://sabiork.h-its.org/ + id: '00000128' + name: SABIO-RK EC Record + namespaceEmbeddedInLui: false + pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ + prefix: sabiork.ec + sampleId: 2.7.1.1 + uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1 + n2t: + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. + example: 2.7.1.1 + homepage: http://sabiork.h-its.org/ + name: SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC) + namespaceEmbeddedInLui: false + pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ + prefix: sabiork.ec + uri_format: http://sabiork.h-its.org/newSearch?q=ecnumber:$1 + prefixcommons: + description: The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. + example: 2.7.1.1 + keywords: + - reaction + name: SABIO-RK EC Record + pattern: ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ + prefix: sabiork.ec + pubmed_ids: + - '17822389' + uri_format: http://sabiork.h-its.org/index2.jsp?EC=$1 + provides: eccode +sabiork.kineticrecord: + biocontext: + is_identifiers: true + is_obo: false + prefix: SABIORK.KINETICRECORD + uri_format: http://identifiers.org/sabiork.kineticrecord/$1 + go: + description: The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. + homepage: http://sabio.villa-bosch.de/ + name: SABIO Reaction Kinetics + prefix: SABIO-RK + uri_format: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=$1 + mappings: + biocontext: SABIORK.KINETICRECORD + go: SABIO-RK + miriam: sabiork.kineticrecord + n2t: sabiork.kineticrecord + miriam: + deprecated: false + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. + homepage: http://sabiork.h-its.org/ + id: '00000086' + name: SABIO-RK Kinetic Record + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sabiork.kineticrecord + sampleId: '5046' + uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1 + n2t: + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. + example: '5046' + homepage: http://sabiork.h-its.org/ + name: SABIO-RK Reaction Kinetics Database - Kinetic Dataset + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sabiork.kineticrecord + uri_format: http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1 +sabiork.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: SABIORK.REACTION + uri_format: http://identifiers.org/sabiork.reaction/$1 + fairsharing: + abbreviation: SABIO-RK + description: SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. + id: '1891' + name: SABIO-RK Biochemical Reaction Kinetics Database + prefix: FAIRsharing.cwx04e + subjects: + - Biochemistry + - Life Science + mappings: + biocontext: SABIORK.REACTION + fairsharing: FAIRsharing.cwx04e + miriam: sabiork.reaction + n2t: sabiork.reaction + prefixcommons: sabiork.reaction + uniprot: SABIO-RK + miriam: + deprecated: false + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. + homepage: http://sabiork.h-its.org/ + id: '00000038' + name: SABIO-RK Reaction + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sabiork.reaction + sampleId: '75' + uri_format: http://sabiork.h-its.org/newSearch?q=sabioreactionid:$1 + n2t: + description: SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. + example: '75' + homepage: http://sabiork.h-its.org/ + name: SABIO-RK reaction + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sabiork.reaction + uri_format: http://sabiork.h-its.org/newSearch?q=sabioreactionid:$1 + prefixcommons: + description: The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. + example: '75' + keywords: + - kinetics + - pathway + - reaction + name: SABIO-RK Reaction Record + pattern: ^\d+$ + prefix: sabiork.reaction + uri_format: http://sabiork.h-its.org/index2.jsp?reac=$1 + synonyms: + - SABIO-RK + uniprot: + category: Enzyme and pathway databases + identifier: '177' + link_is_explicit: 'true' + name: 'SABIO-RK: Biochemical Reaction Kinetics Database' + prefix: SABIO-RK + uri_format: http://sabiork.h-its.org/newSearch?q=UniProtKB_AC:$1 + uri_format: http://sabiork.h-its.org/reacdetails.jsp?reactid=$1 +sael: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + name: Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List + references: + - https://pubmed.ncbi.nlm.nih.gov/18629134/ +salk: + appears_in: + - efo + comment: spider stuff! + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Scientific research institute for neuroscience, genetics, immunology, plant biology and more. + example: '037727' + homepage: https://www.salk.edu/ + name: Salk Institute for Biological Studies + pattern: ^\d{6}$ + uri_format: https://abrc.osu.edu/stocks/number/SALK_$1 +sao: + biocontext: + is_identifiers: false + is_obo: true + prefix: SAO + uri_format: http://purl.obolibrary.org/obo/SAO_$1 + bioportal: + name: Subcellular Anatomy Ontology + prefix: SAO + mappings: + biocontext: SAO + bioportal: SAO + obofoundry: sao + prefixcommons: sao + name: Subcellular Anatomy Ontology + obofoundry: + contact: slarson@ncmir.ucsd.edu + contact.label: Stephen Larson + deprecated: true + homepage: http://ccdb.ucsd.edu/CCDBWebSite/sao.html + name: Subcellular anatomy ontology + prefix: sao + prefixcommons: + bioportal: '1068' + description: SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. + example: sao1289741256 + homepage: http://ccdb.ucsd.edu/SAO + keywords: + - owl + - biochemistry + name: Subcellular Anatomy Ontology (SAO) + pattern: ^sao\d+$ + prefix: sao + references: + - http://www.ontobee.org/ontology/SAO +sasbdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: SASBDB + uri_format: http://identifiers.org/sasbdb/$1 + fairsharing: + abbreviation: SASBDB + description: Curated repository for small angle scattering data and models. SASBDB contains X-ray (SAXS) and neutron (SANS) scattering data from biological macromolecules in solution. + id: '2607' + name: Small angle scattering biological data bank + prefix: FAIRsharing.i1F3Hb + subjects: + - Molecular biology + - Life Science + mappings: + biocontext: SASBDB + fairsharing: FAIRsharing.i1F3Hb + miriam: sasbdb + n2t: sasbdb + uniprot: SASBDB + miriam: + deprecated: false + description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. + homepage: http://www.sasbdb.org/ + id: '00000572' + name: SASBDB + namespaceEmbeddedInLui: false + pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ + prefix: sasbdb + sampleId: SASDAX8 + uri_format: http://www.sasbdb.org/data/$1 + n2t: + description: Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. + example: SASDAX8 + homepage: http://www.sasbdb.org/ + name: SASBDB at European Molecular Biology Laboratory + namespaceEmbeddedInLui: false + pattern: ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ + prefix: sasbdb + uri_format: http://www.sasbdb.org/data/$1 + name: Small Angle Scattering Biological Data Bank + uniprot: + category: 3D structure databases + identifier: '258' + link_is_explicit: 'true' + name: Small Angle Scattering Biological Data Bank + prefix: SASBDB + uri_format: https://www.sasbdb.org/uniprot/$1/ +sbo: + biocontext: + is_identifiers: false + is_obo: true + prefix: SBO + uri_format: http://purl.obolibrary.org/obo/SBO_$1 + bioportal: + name: Systems Biology Ontology + prefix: SBO + example: '0000485' + fairsharing: + abbreviation: SBO + description: 'The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles (e.g. "substrate"), quantitative parameters (e.g. "Michaelis constant"), classification of mathematical expressions describing the system (e.g. "mass action rate law"), modelling framework used (e.g. "logical framework"), the nature of the entity (e.g. "macromolecule"), the type of interaction (e.g. "process"), as well as a branch to define the different types of metadata that may be present within a model. Use of such terms introduces a layer of semantic information into the standard description of a model, facilitating its interpretation and efficient reuse.' + id: '1156' + name: Systems Biology Ontology + prefix: FAIRsharing.s19src + subjects: + - Systems Biology + mappings: + biocontext: SBO + bioportal: SBO + fairsharing: FAIRsharing.s19src + miriam: sbo + n2t: sbo + obofoundry: sbo + ols: sbo + ontobee: SBO + prefixcommons: sbo + miriam: + deprecated: false + description: The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. + homepage: https://www.ebi.ac.uk/sbo/ + id: '00000024' + name: Systems Biology Ontology + namespaceEmbeddedInLui: true + pattern: ^SBO:\d{7}$ + prefix: sbo + sampleId: '0000262' + uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1 + n2t: + description: The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. + example: '0000262' + homepage: https://www.ebi.ac.uk/sbo/ + name: SBO + namespaceEmbeddedInLui: true + pattern: ^SBO:\d{7}$ + prefix: sbo + uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1 + obofoundry: + appears_in: + - scdo + contact: sheriff@ebi.ac.uk + contact.github: rsmsheriff + contact.label: Rahuman Sheriff + contact.orcid: 0000-0003-0705-9809 + deprecated: false + description: Terms commonly used in Systems Biology, and in particular in computational modeling. + download.owl: http://purl.obolibrary.org/obo/sbo.owl + homepage: http://www.ebi.ac.uk/sbo/ + license: Artistic License 2.0 + license.url: http://opensource.org/licenses/Artistic-2.0 + name: Systems Biology Ontology + preferredPrefix: SBO + prefix: sbo + repository: https://github.com/EBI-BioModels/SBO + ols: + download: http://purl.obolibrary.org/obo/sbo.owl + name: Systems Biology Ontology + prefix: sbo + version: 2021-08-28 + ontobee: + library: Library + name: Systems Biology Ontology + prefix: SBO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1046' + description: The Systems Biology Ontology is a set of controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modelling. + example: SBO:0000262 + homepage: http://www.ebi.ac.uk/sbo/ + keywords: + - obo + - systems biology + name: Systems Biology Ontology + pattern: ^SBO:\d{7}$ + prefix: sbo + pubmed_ids: + - '17118155' + uri_format: http://www.ebi.ac.uk/sbo/main/$1 +scdo: + bioportal: + name: Sickle Cell Disease Ontology + prefix: SCDO + example: '0000728' + fairsharing: + abbreviation: SCDO + description: 'The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. Once complete, we anticipate that the ontology will: 1) be the most comprehensive collection of knowledge on SCD, 2) facilitate exploration of new scientific questions and ideas, 3) facilitate seamless data sharing and collaborations including meta-analysis within the SCD community, 4) support the building of databasing and clinical informatics in SCD.' + id: '888' + name: Sickle Cell Disease Ontology + prefix: FAIRsharing.kkq6pw + subjects: [] + mappings: + bioportal: SCDO + fairsharing: FAIRsharing.kkq6pw + obofoundry: scdo + ols: scdo + ontobee: SCDO + obofoundry: + contact: giant.plankton@gmail.com + contact.github: JadeHotchkiss + contact.label: Jade Hotchkiss + contact.orcid: 0000-0002-2193-0704 + depends_on: + - apollo_sv + - aro + - chebi + - chmo + - cmo + - doid + - dron + - duo + - envo + - eupath + - exo + - gaz + - gsso + - hp + - hsapdv + - ico + - ido + - idomal + - mp + - nbo + - ncit + - obi + - ogms + - opmi + - pr + - sbo + - stato + - symp + - uo + - vo + - vt + deprecated: false + description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. + download.obo: http://purl.obolibrary.org/obo/scdo.obo + download.owl: http://purl.obolibrary.org/obo/scdo.owl + homepage: https://scdontology.h3abionet.org/ + license: GPL-3.0 + license.url: https://www.gnu.org/licenses/gpl-3.0.en.html + name: Sickle Cell Disease Ontology + preferredPrefix: SCDO + prefix: scdo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/35363306 + title: 'The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.' + - id: https://www.ncbi.nlm.nih.gov/pubmed/33021900 + title: 'The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.' + - id: https://www.ncbi.nlm.nih.gov/pubmed/31769834 + title: 'The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.' + repository: https://github.com/scdodev/scdo-ontology + ols: + description: An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. + download: http://purl.obolibrary.org/obo/scdo.owl + homepage: https://scdontology.h3abionet.org/ + name: Sickle Cell Disease Ontology + prefix: scdo + version: 2021-04-15 + version.iri: http://purl.obolibrary.org/obo/scdo/releases/2021-04-15/scdo.owl + ontobee: + library: Library + name: Sickle Cell Disease Ontology + prefix: SCDO + pattern: ^\d{7}$ +schem: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Selventa legacy chemical namespace used with the Biological Expression Language + example: A0001 + homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets + name: Selventa Chemicals + pattern: ^A\d{4}$ +scholia.resource: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A frontend to Wikidata + example: doi + homepage: https://scholia.toolforge.org/ + name: Scholia Registry + uri_format: https://bioregistry.io/metaregistry/scholia/$1 +scomp: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Selventa legacy complex namespace used with the Biological Expression Language + example: C0001 + homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets + name: Selventa Complexes + pattern: ^C\d{4}$ +scop: + biocontext: + is_identifiers: true + is_obo: false + prefix: SCOP + uri_format: http://identifiers.org/scop/$1 + fairsharing: + abbreviation: SCOP + description: The SCOP database is a curated both manually and with the use of automated tools. This freely available resource aims to provide a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. + id: '1957' + name: Structural Classification Of Proteins + prefix: FAIRsharing.wjzty + subjects: + - Life Science + mappings: + biocontext: SCOP + fairsharing: FAIRsharing.wjzty + miriam: scop + n2t: scop + prefixcommons: scop + miriam: + deprecated: false + description: The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes. + homepage: http://scop.mrc-lmb.cam.ac.uk/scop/ + id: '00000371' + name: SCOP + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: scop + providers: + - code: CURATOR_REVIEW + description: SCOP at Berkeley + homepage: http://scop.berkeley.edu/ + name: SCOP at Berkeley + uri_format: http://scop.berkeley.edu/sunid=$1 + sampleId: '47419' + uri_format: http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1 + n2t: + description: The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes. + example: '47419' + homepage: http://scop.berkeley.edu/ + name: SCOP at Berkeley + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: scop + uri_format: http://scop.berkeley.edu/sunid=$1 + name: Structural Classification of Protein + prefixcommons: + description: The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. + example: '47419' + homepage: http://scop.mrc-lmb.cam.ac.uk/scop + keywords: + - protein + - structure + name: Structural Classification Of Proteins + pattern: ^\d+$ + prefix: scop +scopus: + biolink: + is_identifiers: false + is_obo: false + prefix: ScopusID + uri_format: https://www.scopus.com/authid/detail.uri?authorId=$1 + description: >- + Scopus is the largest abstract and citation database of peer-reviewed + literature: scientific journals, books and conference proceedings. + + Delivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts + + and humanities, Scopus features smart tools to track, analyze and visualize research. + example: '56305849200' + fairsharing: + abbreviation: Scopus + description: Scopus is an abstract and citation database of peer-reviewed literature across all research areas. It provides tools for visualization, tracking and analysis of its data. Non-subscribed users access Scopus through Scopus Preview, which allows the searching of authors and source material (e.g. journal) titles. + id: '3053' + name: Scopus + prefix: FAIRsharing.0a674c + subjects: + - Subject Agnostic + homepage: https://www.scopus.com + mappings: + biolink: ScopusID + fairsharing: FAIRsharing.0a674c + name: Scopus Researcher + pattern: ^\d+$ +scretf: + biocontext: + is_identifiers: true + is_obo: false + prefix: SCRETF + uri_format: http://identifiers.org/scretf/$1 + mappings: + biocontext: SCRETF + miriam: scretf + n2t: scretf + miriam: + deprecated: false + description: ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. + homepage: http://stormo.wustl.edu/ScerTF/ + id: '00000244' + name: ScerTF + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: scretf + sampleId: RSC3 + uri_format: http://stormo.wustl.edu/ScerTF/details/$1/ + n2t: + description: ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. + example: RSC3 + homepage: http://stormo.wustl.edu/ScerTF/ + name: ScerTF at Washington University + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: scretf + uri_format: http://stormo.wustl.edu/ScerTF/details/$1/ + uri_format: http://stormo.wustl.edu/ScerTF/details/$1 +sdbs: + biocontext: + is_identifiers: true + is_obo: false + prefix: SDBS + uri_format: http://identifiers.org/sdbs/$1 + mappings: + biocontext: SDBS + miriam: sdbs + n2t: sdbs + miriam: + deprecated: false + description: The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. + homepage: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi + id: '00000319' + name: Spectral Database for Organic Compounds + namespaceEmbeddedInLui: false + pattern: \d+$ + prefix: sdbs + sampleId: '4544' + uri_format: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1 + n2t: + description: The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. + example: '4544' + homepage: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi + name: SDBS at AIST + namespaceEmbeddedInLui: false + pattern: \d+$ + prefix: sdbs + uri_format: http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1 +sdgio: + download_owl: https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl + example: '00020134' + fairsharing: + abbreviation: SDGIO + description: The Sustainable Development Goals Interface Ontology (SDGIO) aims to provide a semantic bridge between 1) the Sustainable Development Goals, their targets, and indicators and 2) the large array of entities they refer to. SDGIO will reuse existing ontologies where appropriate. + id: '407' + name: Sustainable Development Goals Interface Ontology + prefix: FAIRsharing.d5ff6e + subjects: + - Environmental Science + mappings: + fairsharing: FAIRsharing.d5ff6e + ols: sdgio + ontobee: SDGIO + ols: + description: An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators. + download: http://purl.unep.org/sdg/sdgio.owl + homepage: https://github.com/SDG-InterfaceOntology/sdgio + name: Sustainable Development Goals Interface Ontology + prefix: sdgio + version: 2018-08-10 + version.iri: http://purl.unep.org/sdg/releases/2018-08-10/sdgio.owl + ontobee: + library: Not Specified/No + name: Sustainable Development Goals Interface Ontology + prefix: SDGIO + pattern: ^\d{8}$ + references: + - https://github.com/SDG-InterfaceOntology/sdgio/issues/233 + repository: https://github.com/SDG-InterfaceOntology/sdgio +sdis: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Selventa legacy disease namespace used with the Biological Expression Language + example: D0001 + homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets + name: Selventa Diseases + pattern: ^D\d{4}$ +sedml.format: + mappings: + miriam: sedml.format + miriam: + deprecated: false + description: Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). + homepage: http://sed-ml.org/ + id: '00000841' + name: SED-ML data format + namespaceEmbeddedInLui: false + pattern: ^[a-z]+(\..*?)?$ + prefix: sedml.format + sampleId: csv + uri_format: https://sed-ml.org/urns.html#format:$1 +sedml.language: + mappings: + miriam: sedml.language + miriam: + deprecated: false + description: Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML). + homepage: http://sed-ml.org/ + id: '00000843' + name: SED-ML model format + namespaceEmbeddedInLui: false + pattern: ^[a-z]+(\..*?)?$ + prefix: sedml.language + sampleId: sbml.level-3.version-2 + uri_format: https://sed-ml.org/urns.html#language:$1 +seed: + biocontext: + is_identifiers: true + is_obo: false + prefix: SEED + uri_format: http://identifiers.org/seed/$1 + go: + description: Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices + homepage: http://www.theseed.org + name: The SEED; + prefix: SEED + uri_format: http://www.theseed.org/linkin.cgi?id=$1 + mappings: + biocontext: SEED + go: SEED + miriam: seed + n2t: seed + ncbi: SEED + miriam: + deprecated: false + description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. + id: '00000552' + name: SEED Subsystem + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: seed + sampleId: Biotin_biosynthesis + n2t: + description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. + example: Biotin_biosynthesis + homepage: http://seed-viewer.theseed.org/seedviewer.cgi + name: SEED Subsystem at Argonne National Laboratory + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: seed + uri_format: http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1 + ncbi: + example: fig|83331.1.peg.1 + homepage: http://www.theseed.org + name: The SEED Database + prefix: SEED +seed.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: SEED.COMPOUND + uri_format: http://identifiers.org/seed.compound/$1 + mappings: + biocontext: SEED.COMPOUND + miriam: seed.compound + n2t: seed.compound + miriam: + deprecated: false + description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. + homepage: http://modelseed.org/ + id: '00000553' + name: SEED Compound + namespaceEmbeddedInLui: false + pattern: ^cpd\d+$ + prefix: seed.compound + sampleId: cpd15380 + uri_format: http://modelseed.org/biochem/compounds/$1 + n2t: + description: This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. + example: cpd15380 + homepage: http://modelseed.org/ + name: SEED Compound at Argonne National Laboratory + namespaceEmbeddedInLui: false + pattern: ^cpd\d+$ + prefix: seed.compound + uri_format: http://modelseed.org/biochem/compounds/$1 +seed.reaction: + biolink: + is_identifiers: false + is_obo: false + prefix: SEED.REACTION + uri_format: https://modelseed.org/biochem/reactions/$1 + mappings: + biolink: SEED.REACTION + miriam: seed.reaction + n2t: seed.reaction + miriam: + deprecated: false + description: ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions. + homepage: http://modelseed.org/biochem/reactions/ + id: '00000692' + name: SEED Reactions + namespaceEmbeddedInLui: false + pattern: ^rxn\d+$ + prefix: seed.reaction + sampleId: rxn00001 + uri_format: http://modelseed.org/biochem/reactions/$1 + n2t: + description: ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions. + example: rxn00001 + homepage: http://modelseed.org/biochem/reactions/ + name: SEED Reactions + namespaceEmbeddedInLui: false + pattern: ^rxn\d+$ + prefix: seed.reaction + uri_format: http://modelseed.org/biochem/reactions/$1 +sep: + biocontext: + is_identifiers: false + is_obo: true + prefix: SEP + uri_format: http://purl.obolibrary.org/obo/SEP_$1 + bioportal: + name: Sample Processing and Separation Techniques Ontology + prefix: SEP + download_obo: https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo + example: '00073' + homepage: https://psidev.info/sepcv + mappings: + biocontext: SEP + bioportal: SEP + obofoundry: sep + ontobee: SEP + prefixcommons: sep + obofoundry: + contact: psidev-gps-dev@lists.sourceforge.net + contact.label: SEP developers via the PSI and MSI mailing lists + deprecated: true + description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. + download.owl: http://purl.obolibrary.org/obo/sep.owl + homepage: http://psidev.info/index.php?q=node/312 + name: Sample processing and separation techniques + prefix: sep + ontobee: + library: Library + name: Sample processing and separation techniques + prefix: SEP + pattern: ^\d{5}$ + prefixcommons: + bioportal: '1044' + description: A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments, such as, and including, gel electrophoresis, column chromatography, capillary electrophoresis, centrifugation and so on. Developed jointly by the HUPO Proteomics Standards Initiative and The Metabolomics Standards Initiative. + example: sep_00005 + homepage: http://psidev.info/index.php?q=node/312 + keywords: + - obo + - protein + name: Sample processing and separation techniques + pattern: ^sep_\d+$ + prefix: sep +sepio: + biocontext: + is_identifiers: false + is_obo: true + prefix: SEPIO + uri_format: http://purl.obolibrary.org/obo/SEPIO_$1 + bioportal: + name: Scientific Evidence and Provenance Information Ontology + prefix: SEPIO + example: '0000048' + mappings: + biocontext: SEPIO + bioportal: SEPIO + obofoundry: sepio + ols: sepio + ontobee: SEPIO + obofoundry: + contact: mhb120@gmail.com + contact.github: mbrush + contact.label: Matthew Brush + contact.orcid: 0000-0002-1048-5019 + deprecated: false + description: An ontology for representing the provenance of scientific claims and the evidence that supports them. + download.owl: http://purl.obolibrary.org/obo/sepio.owl + homepage: https://github.com/monarch-initiative/SEPIO-ontology + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Scientific Evidence and Provenance Information Ontology + preferredPrefix: SEPIO + prefix: sepio + repository: https://github.com/monarch-initiative/SEPIO-ontology + ols: + description: An ontology for representing the provenance of scientific claims and the evidence that supports them. + download: http://purl.obolibrary.org/obo/sepio.owl + homepage: http://ifomis.org/bfo + name: Scientific Evidence and Provenance Information Ontology + prefix: sepio + version: $Revision$ + version.iri: http://purl.obolibrary.org/obo/sepio-v20170929.owl + ontobee: + library: Library + name: Scientific Evidence and Provenance Information Ontology + prefix: SEPIO + pattern: ^\d{7}$ +sfam: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Selventa legacy protein family namespace used with the Biological Expression Language + example: F0001 + homepage: https://raw.githubusercontent.com/OpenBEL/resource-generator/master/datasets + name: Selventa Families + pattern: ^F\d{4}$ +sgd: + biocontext: + is_identifiers: false + is_obo: false + prefix: SGD + uri_format: https://www.yeastgenome.org/locus/$1 + example: S000002493 + fairsharing: + abbreviation: SGD + description: The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms. + id: '1644' + name: Saccharomyces Genome Database + prefix: FAIRsharing.pzvw40 + subjects: + - Epigenetics + - Proteomics + - Life Science + - Transcriptomics + go: + homepage: http://www.yeastgenome.org/ + name: Saccharomyces Genome Database + prefix: SGD + synonyms: + - SGDID + uri_format: https://www.yeastgenome.org/locus/$1 + mappings: + biocontext: SGD + fairsharing: FAIRsharing.pzvw40 + go: SGD + miriam: sgd + n2t: sgd + ncbi: SGD + prefixcommons: sgd + uniprot: SGD + wikidata: P3406 + miriam: + deprecated: false + description: The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. + homepage: https://www.yeastgenome.org/ + id: '00000023' + name: SGD + namespaceEmbeddedInLui: false + pattern: ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ + prefix: sgd + providers: + - code: CURATOR_REVIEW + description: Bio2RDF + homepage: http://sgd.bio2rdf.org/fct + name: Bio2RDF + uri_format: http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$1 + - code: bioentitylink + description: SGD through BioEntity Link + homepage: https://bioentity.link/ + name: SGD through BioEntity Link + uri_format: https://bioentity.link/#/lexicon/public/$1 + - code: agr + description: SGD through the Alliance of Genome Resources + homepage: https://www.alliancegenome.org + name: SGD through the Alliance of Genome Resources + uri_format: https://www.alliancegenome.org/gene/SGD:$1 + sampleId: S000003909 + uri_format: https://www.yeastgenome.org/locus/$1 + n2t: + description: The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. + example: S000003909 + homepage: https://www.yeastgenome.org/ + name: SGD + namespaceEmbeddedInLui: false + pattern: ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ + prefix: sgd + uri_format: https://www.yeastgenome.org/locus/$1 + name: Saccharomyces Genome Database + ncbi: + example: L0000470 + homepage: http://www.yeastgenome.org/ + name: Saccharomyces Genome Database + prefix: SGD + prefixcommons: + description: The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it. + example: S000006169 + homepage: http://www.yeastgenome.org/ + keywords: + - eukaryotic + - genome + - nucleotide + name: Saccharomyces Genome Database + pattern: ^S\d+$ + prefix: sgd + pubmed_ids: + - '14681421' + uri_format: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=$1 + uniprot: + category: Organism-specific databases + identifier: '95' + link_is_explicit: 'true' + name: Saccharomyces Genome Database + prefix: SGD + uri_format: https://www.yeastgenome.org/locus/$1 + wikidata: + database: Q3460832 + database.homepage: http://www.yeastgenome.org + database.label: Saccharomyces Genome Database + homepage: http://www.yeastgenome.org + name: Saccharomyces Genome Database ID + pattern: S\d{9} + prefix: P3406 + uri_format: http://www.yeastgenome.org/locus/$1/overview +sgd.pathways: + biocontext: + is_identifiers: true + is_obo: false + prefix: SGD.PATHWAYS + uri_format: http://identifiers.org/sgd.pathways/$1 + mappings: + biocontext: SGD.PATHWAYS + miriam: sgd.pathways + n2t: sgd.pathways + prefixcommons: sgd.pathways + miriam: + deprecated: false + description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). + homepage: http://pathway.yeastgenome.org/ + id: '00000057' + name: Saccharomyces genome database pathways + namespaceEmbeddedInLui: false + pattern: ^PWY\w{2}\-\d{3}$ + prefix: sgd.pathways + sampleId: PWY3O-214 + uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1 + n2t: + description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). + example: PWY3O-214 + homepage: http://pathway.yeastgenome.org/ + name: Saccharomyces cerevisiae pathways at SGD. + namespaceEmbeddedInLui: false + pattern: ^PWY\w{2}\-\d{3}$ + prefix: sgd.pathways + uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1 + prefixcommons: + description: Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). + example: PWY3O-214 + homepage: http://www.yeastgenome.org/ + keywords: + - genome + - pathway + - sequence + name: Saccharomyces genome database pathways + pattern: ^PWY\w{2}\-\d{3}$ + prefix: sgd.pathways + pubmed_ids: + - '14681421' + uri_format: http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1 +sgn: + biocontext: + is_identifiers: true + is_obo: false + prefix: SGN + uri_format: http://identifiers.org/sgn/$1 + fairsharing: + abbreviation: SGN + description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant. + id: '1841' + name: Sol Genomics Network + prefix: FAIRsharing.3zqvaf + subjects: + - Botany + - Genomics + - Agriculture + - Comparative Genomics + go: + homepage: https://www.sgn.cornell.edu/ + name: Sol Genomics Network + prefix: SGN + synonyms: + - SGN_gene + uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 + mappings: + biocontext: SGN + fairsharing: FAIRsharing.3zqvaf + go: SGN + miriam: sgn + n2t: sgn + ncbi: SGN + prefixcommons: sgn + miriam: + deprecated: false + description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. + homepage: http://solgenomics.net/ + id: '00000185' + name: Sol Genomics Network + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sgn + sampleId: '0001' + uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 + n2t: + description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. + example: '0001' + homepage: http://solgenomics.net/ + name: Sol Genomics Network at Boyce Thompson Institute for Plant Research + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sgn + uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 + ncbi: + example: E553090 + homepage: http://www.sgn.cornell.edu + name: SOL Genomics Network + prefix: SGN + prefixcommons: + description: The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. + example: '1' + homepage: http://www.sgn.cornell.edu + keywords: + - pathway + - small molecule + - genome + - plant + name: Sol Genomics Network + pattern: ^\d+$ + prefix: sgn + pubmed_ids: + - '20935049' + uri_format: http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 +sheepqtldb: + biocontext: + is_identifiers: true + is_obo: false + prefix: SHEEPQTLDB + uri_format: http://identifiers.org/sheepqtldb/$1 + mappings: + biocontext: SHEEPQTLDB + miriam: sheepqtldb + n2t: sheepqtldb + prefixcommons: sheepqtldb + miriam: + deprecated: false + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. + homepage: https://www.animalgenome.org/QTLdb + id: '00000507' + name: Animal Genome Sheep QTL + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sheepqtldb + sampleId: '19803' + uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 + n2t: + description: The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. + example: '19803' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/OA/index + name: Animal QTL Sheep at Iowa State University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sheepqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1 + part_of: qtldb + prefixcommons: + description: This Sheep Quantitative Trait Locus (QTL) database (Sheep QTLdb) has gathered all sheep QTL data published during the past 10+ years. The database and its peripheral tools make it possible to compare, confirm and locate on sheep chromosomes the most feasible location for genes responsible for quantitative trait important to sheep production. + example: '66' + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/OA/index + keywords: + - DNA + - genome + name: Sheep Quantitative Trait Locus database + pattern: ^\d+$ + prefix: sheepqtldb + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$1 +sibo: + biocontext: + is_identifiers: false + is_obo: true + prefix: SIBO + uri_format: http://purl.obolibrary.org/obo/SIBO_$1 + bioportal: + name: Social Inset Behavior Ontology + prefix: SIBO + example: '0000509' + fairsharing: + abbreviation: SIBO + description: Social behavior in insects. + id: '596' + name: Social Inset Behavior Ontology + prefix: FAIRsharing.q09hck + subjects: [] + mappings: + biocontext: SIBO + bioportal: SIBO + fairsharing: FAIRsharing.q09hck + obofoundry: sibo + ols: sibo + ontobee: SIBO + obofoundry: + contact: cjmungall@lbl.gov + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + deprecated: true + description: Social Behavior in insects + download.obo: http://purl.obolibrary.org/obo/sibo.obo + download.owl: http://purl.obolibrary.org/obo/sibo.owl + homepage: https://github.com/obophenotype/sibo + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Social Insect Behavior Ontology + preferredPrefix: SIBO + prefix: sibo + repository: https://github.com/obophenotype/sibo + ols: + description: Social Behavior in insects + download: http://purl.obolibrary.org/obo/sibo.owl + homepage: https://github.com/obophenotype/sibo + name: Social Insect Behavior Ontology + prefix: sibo + version: 2015-06-15 + version.iri: http://purl.obolibrary.org/obo/sibo/releases/2015-06-15/sibo.owl + ontobee: + library: Library + name: Social Insect Behavior Ontology + prefix: SIBO + pattern: ^\d{7}$ +sider.drug: + biocontext: + is_identifiers: true + is_obo: false + prefix: SIDER.DRUG + uri_format: http://identifiers.org/sider.drug/$1 + mappings: + biocontext: SIDER.DRUG + miriam: sider.drug + n2t: sider.drug + miriam: + deprecated: false + description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. + homepage: http://sideeffects.embl.de/ + id: '00000435' + name: SIDER Drug + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sider.drug + sampleId: '2244' + uri_format: http://sideeffects.embl.de/drugs/$1/ + n2t: + description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. + example: '2244' + homepage: http://sideeffects.embl.de/ + name: SIDER Drug v2 at EMBL (Heidelberg) + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sider.drug + uri_format: http://sideeffects.embl.de/drugs/$1/ + uri_format: http://sideeffects.embl.de/drugs/$1 +sider.effect: + biocontext: + is_identifiers: true + is_obo: false + prefix: SIDER.EFFECT + uri_format: http://identifiers.org/sider.effect/$1 + mappings: + biocontext: SIDER.EFFECT + miriam: sider.effect + n2t: sider.effect + miriam: + deprecated: false + description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. + homepage: http://sideeffects.embl.de/ + id: '00000436' + name: SIDER Side Effect + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: sider.effect + sampleId: C0017565 + uri_format: http://sideeffects.embl.de/se/$1/ + n2t: + description: SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. + example: C0017565 + homepage: http://sideeffects.embl.de/ + name: SIDER Side Effect v2 at EMBL (Heidelberg) + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: sider.effect + uri_format: http://sideeffects.embl.de/se/$1/ + provides: umls + uri_format: http://sideeffects.embl.de/se/$1 +sigmaaldirch: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Sigma Aldrich is a life sciences supply vendor. + example: HPA000698 + homepage: https://www.sigmaaldrich.com + name: Sigma Aldrich + uri_format: https://www.sigmaaldrich.com/US/en/product/sigma/$1 +signaling-gateway: + biocontext: + is_identifiers: true + is_obo: false + prefix: SIGNALING-GATEWAY + uri_format: http://identifiers.org/signaling-gateway/$1 + mappings: + biocontext: SIGNALING-GATEWAY + miriam: signaling-gateway + n2t: signaling-gateway + prefixcommons: signaling-gateway + miriam: + deprecated: false + description: The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. + homepage: http://www.signaling-gateway.org/molecule + id: '00000045' + name: Signaling Gateway + namespaceEmbeddedInLui: false + pattern: A\d{6}$ + prefix: signaling-gateway + sampleId: A001094 + uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1 + n2t: + description: The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. + example: A001094 + homepage: http://www.signaling-gateway.org/molecule + name: Signaling Gateway Molecule Pages + namespaceEmbeddedInLui: false + pattern: A\d{6}$ + prefix: signaling-gateway + uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1 + prefixcommons: + description: The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. + example: A001094 + homepage: http://www.signaling-gateway.org/molecule/ + keywords: + - pathway + - protein + - small molecule + name: The Signaling Gateway + pattern: ^A\d{6}$ + prefix: signaling-gateway + pubmed_ids: + - '17965093' + - '12478304' + - '21505029' + uri_format: http://www.signaling-gateway.org/molecule/query?afcsid=$1 +signor: + example: SIGNOR-C41 + fairsharing: + abbreviation: SIGNOR + description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms. + id: '2224' + name: SIGnaling Network Open Resource + prefix: FAIRsharing.ss78t4 + subjects: + - Biology + mappings: + fairsharing: FAIRsharing.ss78t4 + miriam: signor + uniprot: SIGNOR + miriam: + deprecated: false + description: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. + homepage: https://signor.uniroma2.it/ + id: '00000808' + name: SIGNOR + namespaceEmbeddedInLui: false + pattern: ^SIGNOR\-[A-Z]+\d+$ + prefix: signor + sampleId: SIGNOR-C2 + uri_format: https://signor.uniroma2.it/relation_result.php?id=$1 + name: Signaling Network Open Resource + synonyms: + - SIGNOR + uniprot: + category: Enzyme and pathway databases + identifier: '206' + link_is_explicit: 'true' + name: SIGNOR Signaling Network Open Resource + prefix: SIGNOR + uri_format: https://signor.uniroma2.it/relation_result.php?id=$1 +signor.relation: + comment: Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern + contributor: + email: benjamin_gyori@hms.harvard.edu + github: bgyori + name: Benjamin M. Gyori + orcid: 0000-0001-9439-5346 + description: Identifiers for relationships between proteins and complexes, along with their type and provenance + example: SIGNOR-252737 + homepage: https://signor.uniroma2.it + name: SIGNOR Relation + part_of: signor + pattern: ^SIGNOR-\d+$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 +sio: + biocontext: + is_identifiers: false + is_obo: false + prefix: SIO + uri_format: http://semanticscience.org/resource/SIO_$1 + biolink: + is_identifiers: false + is_obo: false + prefix: SIO + uri_format: http://semanticscience.org/resource/SIO_$1 + bioportal: + name: Semanticscience Integrated Ontology + prefix: SIO + example: '000912' + fairsharing: + abbreviation: SIO + description: The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. + id: '1286' + name: Semanticscience Integrated Ontology + prefix: FAIRsharing.dpkb5f + subjects: + - Natural Science + - Subject Agnostic + mappings: + biocontext: SIO + biolink: SIO + bioportal: SIO + fairsharing: FAIRsharing.dpkb5f + miriam: sio + ols: sio + ontobee: SIO + miriam: + deprecated: false + description: The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. + homepage: https://www.ebi.ac.uk + id: '00000851' + name: Semanticscience Integrated Ontology + namespaceEmbeddedInLui: false + pattern: ^SIO_\d{6,6}$ + prefix: sio + sampleId: SIO_000276 + uri_format: https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1 + ols: + contact: sio-ontology@googlegroups.com + description: The Semanticscience Integrated Ontology (SIO) provides a simple, integrated ontology of types and relations for rich description of objects, processes and their attributes. + download: https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl + homepage: https://github.com/micheldumontier/semanticscience + name: Semanticscience Integrated Ontology + prefix: sio + version: '1.53' + version.iri: http://semanticscience.org/ontology/sio/v1.53/sio-release.owl + ontobee: + library: Not Specified/No + name: Semanticscience Integrated Ontology + prefix: SIO + pattern: ^\d{6}$ + repository: https://github.com/micheldumontier/semanticscience +sisu: + biocontext: + is_identifiers: true + is_obo: false + prefix: SISU + uri_format: http://identifiers.org/sisu/$1 + fairsharing: + abbreviation: SISu + description: The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in the Finnish population. It provides valuable summary data for researchers and clinicians as well as other researchers with an interest in genetics in Finland. With SISu, you can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map. The SISu project is an international collaboration between multiple research groups aiming to build tools for genomic medicine. + id: '2383' + name: Sequencing Initiative Suomi + prefix: FAIRsharing.t1a232 + subjects: + - Medicine + - Genomics + - Biomedical Science + - Epidemiology + - Preclinical Studies + mappings: + biocontext: SISU + fairsharing: FAIRsharing.t1a232 + miriam: sisu + n2t: sisu + miriam: + deprecated: false + description: The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies. + homepage: http://www.sisuproject.fi/ + id: '00000624' + name: SISu + namespaceEmbeddedInLui: false + pattern: ^[0-9]+:[0-9]+$ + prefix: sisu + sampleId: 17:41223048 + uri_format: http://search.sisuproject.fi/#/variant/$1 + n2t: + description: The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies. + example: 17:41223048 + homepage: http://www.sisuproject.fi/ + name: SISu + namespaceEmbeddedInLui: false + pattern: ^[0-9]+:[0-9]+$ + prefix: sisu + uri_format: http://search.sisuproject.fi/#/variant/$1 + name: Sequencing Initiative Suomi +sitex: + biocontext: + is_identifiers: true + is_obo: false + prefix: SITEX + uri_format: http://identifiers.org/sitex/$1 + fairsharing: + abbreviation: SitEx + description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. + id: '1672' + name: SitEx database of eukaryotic protein functional sites + prefix: FAIRsharing.5mr9c5 + subjects: + - Life Science + mappings: + biocontext: SITEX + fairsharing: FAIRsharing.5mr9c5 + miriam: sitex + n2t: sitex + prefixcommons: sitex + miriam: + deprecated: false + description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. + homepage: http://www-bionet.sscc.ru/sitex/ + id: '00000252' + name: SitEx + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sitex + sampleId: '1000' + uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1 + n2t: + description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. + example: '1000' + homepage: http://www-bionet.sscc.ru/sitex/ + name: SitEx at Novosibirsk State University + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: sitex + uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1 + prefixcommons: + description: SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. + example: '1000' + homepage: http://www-bionet.sscc.ru/sitex/ + keywords: + - domain + - eukaryotic + - sequence + - structure + name: SitEx database of eukaryotic protein functional sites + pattern: ^\d+$ + prefix: sitex + pubmed_ids: + - '22139920' + uri_format: http://www-bionet.sscc.ru/sitex/index.php?siteid=$1 +skip: + cellosaurus: + category: Cell line databases/resources + homepage: https://www.skip.stemcellinformatics.org/en/ + name: Stemcell Knowledge and Information Portal + prefix: SKIP + uri_format: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1 + description: SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine. + example: SKIP001214 + homepage: https://skip.stemcellinformatics.org/en/ + mappings: + cellosaurus: SKIP + name: Stemcell Knowledge and Information Portal + uri_format: https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1 +skos: + biocontext: + is_identifiers: false + is_obo: false + prefix: skos + uri_format: http://www.w3.org/2004/02/skos/core#$1 + description: SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web + example: prefLabel + homepage: https://www.w3.org/2004/02/skos/ + mappings: + biocontext: skos + name: Simple Knowledge Organization System + uri_format: http://www.w3.org/2004/02/skos/core#$1 +slkbase: + cellosaurus: + category: Cell line databases/resources + homepage: https://sumlineknowledgebase.com/ + name: SUM Breast Cancer Cell Line Knowledge Base + prefix: SLKBase + uri_format: https://sumlineknowledgebase.com/?page_id=$1 + example: '3618' + mappings: + cellosaurus: SLKBase + pattern: ^\d+$ +smart: + biocontext: + is_identifiers: true + is_obo: false + prefix: SMART + uri_format: http://identifiers.org/smart/$1 + fairsharing: + abbreviation: SMART + description: SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa. + id: '1645' + name: Simple Modular Architecture Research Tool + prefix: FAIRsharing.hsbpq3 + subjects: + - Life Science + go: + homepage: http://smart.embl-heidelberg.de/ + name: Simple Modular Architecture Research Tool + prefix: SMART + uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=$1 + mappings: + biocontext: SMART + fairsharing: FAIRsharing.hsbpq3 + go: SMART + miriam: smart + n2t: smart + prefixcommons: smart + uniprot: SMART + miriam: + deprecated: false + description: The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. + homepage: http://smart.embl-heidelberg.de/ + id: '00000118' + name: SMART + namespaceEmbeddedInLui: false + pattern: ^SM\d{5}$ + prefix: smart + sampleId: SM00015 + uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1 + n2t: + description: The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. + example: SM00015 + homepage: http://smart.embl-heidelberg.de/ + name: SMART (Simple Modular Architecture Research Tool) + namespaceEmbeddedInLui: false + pattern: ^SM\d{5}$ + prefix: smart + uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1 + prefixcommons: + description: The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. + example: SM00015 + homepage: http://smart.embl.de/ + keywords: + - domain + - protein + - structure + name: Simple Modular Architecture Research Tool; a protein domain database + pattern: ^SM\d{5}$ + prefix: smart + pubmed_ids: + - '9847187' + uri_format: http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1 + uniprot: + category: Family and domain databases + identifier: '97' + link_is_explicit: 'true' + name: Simple Modular Architecture Research Tool; a protein domain database + prefix: SMART + uri_format: http://smart.embl.de/smart/do_annotation.pl?DOMAIN=$1 +smid: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. ' + example: '137' + homepage: https://smid-db.org/ + name: C. elegans Small Molecule Identifier Database + pattern: ^\d+$ + synonyms: + - SMID-DB + uri_format: https://smid-db.org/smid/$1 +smiles: + description: Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. + example: COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1 + fairsharing: + abbreviation: SMILES + description: This format is an open specification version of the SMILES language, a typographical line notation for specifying chemical structure. It is hosted under the banner of the Blue Obelisk project, with the intent to solicit contributions and comments from the entire computational chemistry community. + id: '140' + name: Simplified Molecular Input Line Entry Specification Format + prefix: FAIRsharing.qv4b3c + subjects: + - Chemistry + - Life Science + homepage: https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html + mappings: + fairsharing: FAIRsharing.qv4b3c + name: Simplified molecular-input line-entry system + wikidata: + prefix: P233 +smpdb: + biocontext: + is_identifiers: false + is_obo: false + prefix: SMPDB + uri_format: http://smpdb.ca/view/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: PathWhiz + uri_format: http://smpdb.ca/pathways/#$1 + example: SMP0000219 + fairsharing: + abbreviation: SMPDB + description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. + id: '1887' + name: Small Molecule Pathway Database + prefix: FAIRsharing.y1zyaq + subjects: + - Life Science + mappings: + biocontext: SMPDB + biolink: PathWhiz + fairsharing: FAIRsharing.y1zyaq + miriam: smpdb + n2t: smpdb + prefixcommons: smpdb + miriam: + deprecated: false + description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. + homepage: https://smpdb.ca/ + id: '00000104' + name: Small Molecule Pathway Database + namespaceEmbeddedInLui: false + pattern: ^SMP\d+$ + prefix: smpdb + sampleId: SMP00001 + uri_format: http://smpdb.ca/view/$1 + n2t: + description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. + example: SMP00001 + homepage: http://www.smpdb.ca/pathways + name: Small Molecule Pathway Database + namespaceEmbeddedInLui: false + pattern: ^SMP\d+$ + prefix: smpdb + uri_format: http://smpdb.ca/view/$1 + name: Small Molecule Pathway Database + pattern: ^SMP\d+$ + prefixcommons: + description: The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. + example: SMP00001 + homepage: http://www.smpdb.ca/ + keywords: + - chemical + - human + - metabolite + - pathway + name: Small Molecule Pathway Database + pattern: ^SMP\d{5}$ + prefix: smpdb + uri_format: http://pathman.smpdb.ca/pathways/$1/pathway + synonyms: + - SMP + uri_format: https://smpdb.ca/view/$1 +snap: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality. + example: Quality + homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf + mappings: + prefixcommons: snap + name: Snapshot + prefixcommons: + description: Snap is a sequence analysis tool providing a simple but detailed analysis of human genes and their variations. For each gene, a gene-gene relationship network can be generated based on protein-protein interaction data, metabolic pathway connections and extended through phylogenetic relations. + example: ENSG00000187634 + homepage: http://snap.humgen.au.dk + keywords: + - gene + - protein + - interaction + - pathway + name: 'SNAP: a SNP Annotation Platform' + pattern: ^ENSG\d+$ + prefix: snap + uri_format: http://snap.humgen.au.dk/views/geneview.cgi?gene=$1 +snomedct: + biocontext: + is_identifiers: false + is_obo: true + prefix: SNOMED + uri_format: http://purl.obolibrary.org/obo/SNOMED_$1 + biolink: + is_identifiers: false + is_obo: false + prefix: SNOMEDCT + uri_format: http://www.snomedbrowser.com/Codes/Details/$1 + bioportal: + name: SNOMED CT + prefix: SNOMEDCT + fairsharing: + abbreviation: SNOMEDCT + description: The Systematized Nomenclature of Medicine Clinical Terms is a reference terminology that can be used to cross-map standardized healthcare languages across healthcare disciplines. + id: '609' + name: Systematized Nomenclature of Medicine-Clinical Terms + prefix: FAIRsharing.d88s6e + subjects: + - Medicine + - Health Science + - Biomedical Science + - Preclinical Studies + mappings: + biocontext: SNOMED + biolink: SNOMEDCT + bioportal: SNOMEDCT + fairsharing: FAIRsharing.d88s6e + miriam: snomedct + n2t: snomedct + ols: snomed + prefixcommons: snomedct + miriam: + deprecated: false + description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. + homepage: http://www.snomedbrowser.com/ + id: '00000269' + name: SNOMED CT + namespaceEmbeddedInLui: false + pattern: ^(\w+)?\d+$ + prefix: snomedct + sampleId: '284196006' + uri_format: http://www.snomedbrowser.com/Codes/Details/$1 + n2t: + description: SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. + example: '284196006' + homepage: http://www.snomedbrowser.com/ + name: SNOMED-CT at The National Pathology Exchange + namespaceEmbeddedInLui: false + pattern: ^(\w+)?\d+$ + prefix: snomedct + uri_format: http://www.snomedbrowser.com/Codes/Details/$1 + ols: + description: > + SNOMED CT or SNOMED Clinical Terms is a systematically organized computer + processable collection of medical terms providing codes, terms, synonyms + and definitions used in clinical documentation and reporting. + download: file:///nfs/spot/data/test/ols/snomed.owl + name: SNOMED CT (International Edition) + prefix: snomed + version: 2020-01-31 + version.iri: http://snomed.info/sct/900000000000207008/version/20200131 + prefixcommons: + bioportal: '1353' + description: SNOMED Clinical Terms + example: '284196006' + homepage: http://ihtsdo.org + name: Systematized Nomenclature of Medicine - Clinical Terms + pattern: ^(\w+)?\d+$ + prefix: snomedct + synonyms: + - SCTID + - SCTID_2010_1_31 + - SNOMECT + - SNOMED + - SNOMEDCT + - SNOMEDCTCT + - SNOMEDCTCT_2018_03_01 + - SNOMEDCTCT_2019_03_01 + - SNOMEDCT_2005_07_31 + - SNOMEDCT_2010_1_31 + - SNOMEDCT_2020_03_01 + - SNOMEDCT_US + - SNOMEDCT_US_2015_03_01 + - SNOMEDCT_US_2016_03_01 + - SNOMEDCT_US_2018_03_01 + - SNOMEDCT_US_2018_09_01 + - SNOMEDCT_US_2019_03_01 + - SNOMEDCT_US_2019_09_01 + - SNOMEDCT_US_2020_03_01 + - SNOMEDCT_US_2020_09_01 + - SNOMEDCT_US_2021_03_01 + - SNOMEDCT_US_2021_07_31 + - SNOMEDCT_US_2021_09_01 + - SNOMED_CT + - SNOMED_CT_US_2018_03_01 + - SNOWMEDCT + - SNOWMEDCT_US + - SNOWMEDCT_US_2018_03_01 + wikidata: + database: Q1753883 + database.label: SNOMED CT + homepage: http://snomed.info/ + name: SNOMED CT identifier + pattern: ^[0-9]*$ + prefix: P5806 + uri_format: http://snomed.info/id/$1 +snornabase: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: |- + A comprehensive database of + + human H/ACA and C/D box snoRNAs. + example: SR0000178 + homepage: https://www-snorna.biotoul.fr/ + name: snoRNABase + wikidata: + paper: Q24675417 +snp2tfbs: + mappings: + miriam: snp2tfbs + miriam: + deprecated: false + description: SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome. + homepage: https://ccg.epfl.ch/snp2tfbs/ + id: '00000766' + name: SNP2TFBS + namespaceEmbeddedInLui: false + pattern: ^rs[0-9]+$ + prefix: snp2tfbs + sampleId: rs11603840 + uri_format: https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 + name: SNP to Transcription Factor Binding Sites + provides: dbsnp +so: + biocontext: + is_identifiers: false + is_obo: true + prefix: SO + uri_format: http://purl.obolibrary.org/obo/SO_$1 + bioportal: + name: Sequence Types and Features Ontology + prefix: SO + download_obo: https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo + example: '0001157' + fairsharing: + abbreviation: SO + description: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence. + id: '238' + name: Sequence Ontology + prefix: FAIRsharing.6bc7h9 + subjects: + - Bioinformatics + - Life Science + - Biology + go: + homepage: http://www.sequenceontology.org/ + name: Sequence Ontology + prefix: SO + mappings: + biocontext: SO + bioportal: SO + fairsharing: FAIRsharing.6bc7h9 + go: SO + miriam: so + n2t: so + obofoundry: so + ols: so + ontobee: SO + prefixcommons: so + miriam: + deprecated: false + description: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. + homepage: http://www.sequenceontology.org/ + id: '00000081' + name: Sequence Ontology + namespaceEmbeddedInLui: true + pattern: ^SO:\d{7}$ + prefix: so + sampleId: '0000704' + uri_format: http://www.sequenceontology.org/miso/current_release/term/SO:$1 + n2t: + description: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. + example: '0000704' + homepage: http://bioportal.bioontology.org/ontologies/SO + name: Sequence Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^SO:\d{7}$ + prefix: so + uri_format: http://purl.bioontology.org/ontology/SO/SO:$1 + obofoundry: + appears_in: + - pcl + contact: keilbeck@genetics.utah.edu + contact.github: keilbeck + contact.label: Karen Eilbeck + contact.orcid: 0000-0002-0831-6427 + deprecated: false + description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. + download.obo: http://purl.obolibrary.org/obo/so.obo + download.owl: http://purl.obolibrary.org/obo/so.owl + homepage: http://www.sequenceontology.org/ + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Sequence types and features ontology + preferredPrefix: SO + prefix: so + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/15892872 + title: 'The Sequence Ontology: a tool for the unification of genome annotations.' + - id: https://www.ncbi.nlm.nih.gov/pubmed/20226267 + title: Evolution of the Sequence Ontology terms and relationships. + repository: https://github.com/The-Sequence-Ontology/SO-Ontologies + ols: + description: A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. + download: http://purl.obolibrary.org/obo/so.owl + homepage: http://www.sequenceontology.org/ + name: Sequence types and features ontology + prefix: so + version: 2021-11-22 + version.iri: http://purl.obolibrary.org/obo/so/2021-11-22/so.owl + ontobee: + library: Library + name: Sequence types and features ontology + prefix: SO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1109' + description: The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence. + example: SO:0000704 + homepage: http://www.sequenceontology.org/ + keywords: + - obo + - ontology + - DNA + - RNA + - structure + name: Sequence Ontology + pattern: ^SO:\d{7}$ + prefix: so + pubmed_ids: + - '15892872' + uri_format: http://www.sequenceontology.org/miso/current_release/term/$1 +sopharm: + biocontext: + is_identifiers: false + is_obo: true + prefix: SOPHARM + uri_format: http://purl.obolibrary.org/obo/SOPHARM_$1 + bioportal: + name: Suggested Ontology for Pharmacogenomics + prefix: SOPHARM + mappings: + biocontext: SOPHARM + bioportal: SOPHARM + obofoundry: sopharm + obofoundry: + contact: Adrien.Coulet@loria.fr + contact.label: Adrien Coulet + deprecated: true + homepage: http://www.loria.fr/~coulet/sopharm2.0_description.php + name: Suggested Ontology for Pharmacogenomics + prefix: sopharm +soybase: + biocontext: + is_identifiers: true + is_obo: false + prefix: SOYBASE + uri_format: http://identifiers.org/soybase/$1 + fairsharing: + abbreviation: SoyBase + description: SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies. + id: '1934' + name: SoyBase + prefix: FAIRsharing.z4agsr + subjects: + - Plant Breeding + - Agriculture + - Life Science + - Comparative Genomics + mappings: + biocontext: SOYBASE + fairsharing: FAIRsharing.z4agsr + miriam: soybase + n2t: soybase + ncbi: SoyBase + miriam: + deprecated: false + description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean. + homepage: http://soybase.org/ + id: '00000291' + name: SoyBase + namespaceEmbeddedInLui: false + pattern: ^\w+(\-)?\w+(\-)?\w+$ + prefix: soybase + sampleId: BARC-013845-01256 + uri_format: http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1 + n2t: + description: SoyBase is a repository for curated genetics, genomics and related data resources for soybean. + example: BARC-013845-01256 + homepage: http://soybase.org/ + name: SoyBase at Iowa State University + namespaceEmbeddedInLui: false + pattern: ^\w+(\-)?\w+(\-)?\w+$ + prefix: soybase + uri_format: http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1 + ncbi: + example: Satt005 + homepage: http://soybase.org + name: Glycine max Genome Database + prefix: SoyBase +span: + comment: see also snap. This ontology only exists in description in the paper and does not have an associated web resource + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality. + homepage: http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf + name: Span +spd: + biocontext: + is_identifiers: false + is_obo: true + prefix: SPD + uri_format: http://purl.obolibrary.org/obo/SPD_$1 + bioportal: + name: Spider Anatomy Ontology + prefix: SPD + example: '0000001' + fairsharing: + abbreviation: SPD + description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). + id: '7' + name: Spider Anatomy Ontology + prefix: FAIRsharing.yecp83 + subjects: + - Anatomy + - Life Science + mappings: + biocontext: SPD + bioportal: SPD + fairsharing: FAIRsharing.yecp83 + obofoundry: spd + ols: spd + ontobee: SPD + prefixcommons: spd + obofoundry: + contact: ramirez@macn.gov.ar + contact.github: martinjramirez + contact.label: Martin Ramirez + contact.orcid: 0000-0002-0358-0130 + deprecated: false + description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). + download.owl: http://purl.obolibrary.org/obo/spd.owl + homepage: http://research.amnh.org/atol/files/ + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Spider Ontology + preferredPrefix: SPD + prefix: spd + publications: + - id: https://doi.org/10.3390/d11100202 + title: The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data + repository: https://github.com/obophenotype/spider-ontology + ols: + description: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). + download: http://purl.obolibrary.org/obo/spd.owl + homepage: http://research.amnh.org/atol/files/ + name: Spider Ontology + prefix: spd + version: 2019-02-27 + version.iri: http://purl.obolibrary.org/obo/spd/1.0/spd.owl + ontobee: + library: Library + name: Spider Ontology + prefix: SPD + pattern: ^\d{7}$ + prefixcommons: + description: A collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq. + example: Q9UK53 + homepage: http://spd.cbi.pku.edu.cn + keywords: + - protein + - structure + name: Secreted Protein Database + pattern: ^[A-Z]\d+$ + prefix: spd + uri_format: http://spd.cbi.pku.edu.cn/spd_pro.php?id=$1 + wikidata: + prefix: P4537 +spdx: + homepage: https://spdx.org/licenses + mappings: + miriam: spdx + n2t: spdx + miriam: + deprecated: false + description: The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception. + homepage: https://spdx.org + id: '00000687' + name: SPDX License List + namespaceEmbeddedInLui: false + pattern: ^[0-9A-Za-z\-.]+$ + prefix: spdx + sampleId: CC-BY-1.0 + uri_format: https://spdx.org/licenses/$1 + n2t: + description: The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception. + example: CC-BY-1.0 + homepage: https://spdx.org + name: SPDX License List + namespaceEmbeddedInLui: false + pattern: ^[0-9A-Za-z\-.]+$ + prefix: spdx + uri_format: https://spdx.org/licenses/$1 + name: Software Package Data Exchange License +spike.map: + biocontext: + is_identifiers: true + is_obo: false + prefix: SPIKE.MAP + uri_format: http://identifiers.org/spike.map/$1 + mappings: + biocontext: SPIKE.MAP + miriam: spike.map + n2t: spike.map + miriam: + deprecated: false + description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. + homepage: http://www.cs.tau.ac.il/~spike/ + id: '00000321' + name: SPIKE Map + namespaceEmbeddedInLui: false + pattern: ^spike\d{5}$ + prefix: spike.map + sampleId: spike00001 + uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html + n2t: + description: SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. + example: spike00001 + homepage: http://www.cs.tau.ac.il/~spike/ + name: SPIKE database at Tel Aviv University + namespaceEmbeddedInLui: false + pattern: ^spike\d{5}$ + prefix: spike.map + uri_format: http://www.cs.tau.ac.il/~spike/maps/$1.html +splash: + biocontext: + is_identifiers: true + is_obo: false + prefix: SPLASH + uri_format: http://identifiers.org/splash/$1 + mappings: + biocontext: SPLASH + miriam: splash + n2t: splash + miriam: + deprecated: false + description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. + homepage: http://mona.fiehnlab.ucdavis.edu/ + id: '00000566' + name: SPLASH + namespaceEmbeddedInLui: false + pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ + prefix: splash + sampleId: splash10-0zq2000000-77302b0326a418630a84 + uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1 + n2t: + description: The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. + example: splash10-0zq2000000-77302b0326a418630a84 + homepage: http://mona.fiehnlab.ucdavis.edu/ + name: Mass Bank of North America (MoNA) + namespaceEmbeddedInLui: false + pattern: ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ + prefix: splash + uri_format: http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1 + name: Spectra Hash Code +spp: + fairsharing: + abbreviation: SPP + description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways. + id: '2773' + name: Signaling Pathways Project + prefix: FAIRsharing.WxI96O + subjects: + - Transcriptomics + - Omics + mappings: + fairsharing: FAIRsharing.WxI96O + miriam: spp + miriam: + deprecated: false + description: The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways. + homepage: https://www.signalingpathways.org/index.jsf + id: '00000726' + name: Signaling Pathways Project + namespaceEmbeddedInLui: false + pattern: ^10.\w{4}/\w{10}$ + prefix: spp + sampleId: 10.1621/vwN2g2HaX3 + uri_format: https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1 +sprint: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database. PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints. + example: PR00001 + homepage: http://130.88.97.239/dbbrowser/sprint/ + mappings: + prefixcommons: sprint + name: Search PRINTS-S + pattern: ^PR\d{5}$ + prefixcommons: + description: SPRINT provides search access to the data bank of protein family fingerprints (PRINTS). + example: PR00001 + homepage: http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ + keywords: + - domain + - protein + name: SPRINT + pattern: ^PR\d{5}$ + prefix: sprint + pubmed_ids: + - '10592232' + uri_format: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off + uri_format: 130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1 +srao: + download_owl: https://raw.githubusercontent.com/FAIRsharing/subject-ontology/master/releases/SRAO.owl + example: '0000400' + fairsharing: + abbreviation: SRAO + description: The Subject Resource Application Ontology (SRAO) is an application ontology describing subject areas / academic disciplines used within FAIRsharing records by curators and the user community. It is built in conjunction with the Domain Resource Application Ontology (DRAO), which contains more specific domain terms and other descriptors. All classes within SRAO come from publicly-available ontologies and controlled vocabularies. + id: '1405' + name: Subject Resource Application Ontology + prefix: FAIRsharing.b1xD9f + subjects: + - Environmental Science + - Humanities + - Natural Science + - Earth Science + - Agriculture + - Life Science + - Computer Science + - Biomedical Science + mappings: + fairsharing: FAIRsharing.b1xD9f + ols: srao + name: FAIRsharing Subject Ontology + ols: + contact: contact@fairsharing.org + description: The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies. + download: https://github.com/FAIRsharing/subject-ontology/raw/master/releases/SRAO.owl + homepage: https://github.com/FAIRsharing/subject-ontology + name: FAIRsharing Subject Ontology (SRAO) + prefix: srao + version: 0.3.0 + version.iri: http://www.fairsharing.org/ontology/subject/SRAO.owl/0.3.0 + pattern: ^\d{7}$ + repository: https://github.com/FAIRsharing/subject-ontology +ssbd.dataset: + description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. + example: '1' + fairsharing: + abbreviation: SSBD + description: SSBD is a database that collects and shares quantitative biological dynamics data, microscopy images, and software tools. SSBD provides a rich set of resources for analyzing quantitative biological data, such as single-molecule, cell, and gene expression nuclei. Quantitative biological data are collected from a variety of species, sources and methods. These include data obtained from both experiment and computational simulation. + id: '2310' + name: 'SSBD: Systems Science of Biological Dynamics' + prefix: FAIRsharing.we2r5a + subjects: + - Molecular Dynamics + - Developmental Biology + - Cell Biology + homepage: https://ssbd.riken.jp + mappings: + fairsharing: FAIRsharing.we2r5a + name: System Science of Biological Dynamics dataset + pattern: ^\d+$ + uri_format: https://ssbd.riken.jp/database/dataset/$1 +ssbd.project: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. + example: '1' + homepage: https://ssbd.riken.jp + name: System Science of Biological Dynamics project + pattern: ^\d+$ + uri_format: https://ssbd.riken.jp/database/project/$1 +stap: + biocontext: + is_identifiers: true + is_obo: false + prefix: STAP + uri_format: http://identifiers.org/stap/$1 + fairsharing: + abbreviation: STAP + description: The STAP database contains refined versions of the NMR structures deposited in PDB. These refinements have been performed using statistical torsion angle potential and structurally- or experimentally- derived distance potential. The refined structures have a significantly improved structural quality compared to their initial NMR structure. + id: '1647' + name: Statistical Torsional Angles Potentials of NMR Refinement Database + prefix: FAIRsharing.ja9cdq + subjects: + - Statistics + - Life Science + mappings: + biocontext: STAP + fairsharing: FAIRsharing.ja9cdq + miriam: stap + n2t: stap + miriam: + deprecated: false + description: STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). + homepage: http://psb.kobic.re.kr/STAP/refinement/ + id: '00000399' + name: STAP + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: stap + sampleId: 1a24 + uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1 + n2t: + description: STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). + example: 1a24 + homepage: http://psb.kobic.re.kr/STAP/refinement/ + name: STAP at Korean Bioinformation Center + namespaceEmbeddedInLui: false + pattern: ^[0-9][A-Za-z0-9]{3}$ + prefix: stap + uri_format: http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1 + name: Statistical Torsional Angles Potentials +stato: + biocontext: + is_identifiers: false + is_obo: true + prefix: STATO + uri_format: http://purl.obolibrary.org/obo/STATO_$1 + bioportal: + name: Statistics Ontology + prefix: STATO + example: '0000288' + fairsharing: + abbreviation: STATO + description: STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of applications, and information needed or resulting from statistical methods, such as probability distributions, variable, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results. + id: '1169' + name: Statistics Ontology + prefix: FAIRsharing.na5xp + subjects: + - Statistics + - Data Visualization + mappings: + biocontext: STATO + bioportal: STATO + fairsharing: FAIRsharing.na5xp + obofoundry: stato + ols: stato + ontobee: STATO + obofoundry: + appears_in: + - ontoavida + - psdo + - scdo + contact: alejandra.gonzalez.beltran@gmail.com + contact.github: agbeltran + contact.label: Alejandra Gonzalez-Beltran + contact.orcid: 0000-0003-3499-8262 + deprecated: false + description: STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions of application, and information needed or resulting from statistical methods, such as probability distributions, variables, spread and variation metrics. STATO also covers aspects of experimental design and description of plots and graphical representations commonly used to provide visual cues of data distribution or layout and to assist review of the results. + download.owl: http://purl.obolibrary.org/obo/stato.owl + homepage: http://stato-ontology.org/ + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: The Statistical Methods Ontology + preferredPrefix: STATO + prefix: stato + repository: https://github.com/ISA-tools/stato + ols: + contact: stat-ontology@googlegroups.com + description: STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. + download: http://purl.obolibrary.org/obo/stato.owl + homepage: http://stato-ontology.org/ + name: 'STATO: the statistical methods ontology' + prefix: stato + version: '1.4' + ontobee: + library: Library + name: The Statistical Methods Ontology + prefix: STATO + pattern: ^\d{7}$ +stitch: + biocontext: + is_identifiers: true + is_obo: false + prefix: STITCH + uri_format: http://identifiers.org/stitch/$1 + fairsharing: + abbreviation: STITCH + description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. + id: '1648' + name: Search Tool for Interactions of Chemicals + prefix: FAIRsharing.zhwa8x + subjects: + - Life Science + mappings: + biocontext: STITCH + fairsharing: FAIRsharing.zhwa8x + miriam: stitch + n2t: stitch + prefixcommons: stitch + miriam: + deprecated: false + description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. + homepage: http://stitch.embl.de/ + id: '00000266' + name: STITCH + namespaceEmbeddedInLui: false + pattern: ^\w{14}$ + prefix: stitch + sampleId: BQJCRHHNABKAKU + uri_format: http://stitch.embl.de/interactions/$1 + n2t: + description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. + example: BQJCRHHNABKAKU + homepage: http://stitch.embl.de/ + name: STITCH + namespaceEmbeddedInLui: false + pattern: ^\w{14}$ + prefix: stitch + uri_format: http://stitch.embl.de/interactions/$1 + name: Search Tool for Interactions of Chemicals + prefixcommons: + description: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. + example: ICXJVZHDZFXYQC + homepage: http://stitch.embl.de + keywords: + - interaction + - protein + - small molecule + name: 'STITCH: Chemical-Protein Interactions' + pattern: ^\w{14}$ + prefix: stitch + pubmed_ids: + - '18084021' +storedb: + banana: STOREDB + biocontext: + is_identifiers: true + is_obo: false + prefix: STOREDB + uri_format: http://identifiers.org/storedb/$1 + example: STUDY1040 + fairsharing: + abbreviation: STOREDB + description: STOREDB provides infrastructure for sharing data and resources in radiation biology and epidemiology. It is a platform for the archiving and sharing of primary data and outputs of all kinds, including epidemiological and experimental data, from research on the effects of radiation. It also provides a directory of bioresources and databases containing information and materials that investigators are willing to share. STORE supports the creation of a radiation research commons. + id: '2362' + name: STOREDB + prefix: FAIRsharing.6h8d2r + subjects: + - Ecology + - Life Science + - Biomedical Science + - Epidemiology + - Preclinical Studies + mappings: + biocontext: STOREDB + fairsharing: FAIRsharing.6h8d2r + miriam: storedb + n2t: storedb + miriam: + deprecated: false + description: STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. + homepage: https://www.storedb.org/ + id: '00000577' + name: STOREDB + namespaceEmbeddedInLui: false + pattern: ^STOREDB:(STUDY|FILE|DATASET)\d+$ + prefix: storedb + sampleId: STOREDB:STUDY1040 + uri_format: https://www.storedb.org/?$1 + n2t: + description: STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. + example: STOREDB:STUDY1040 + homepage: https://www.storedb.org/ + name: STOREDB at University of Cambridge + namespaceEmbeddedInLui: false + pattern: ^STOREDB:(STUDY|FILE|DATASET)\d+$ + prefix: storedb + uri_format: https://www.storedb.org/?$1 + name: Store DB + pattern: ^(STUDY|FILE|DATASET)\d+$ +string: + biocontext: + is_identifiers: true + is_obo: false + prefix: STRING + uri_format: http://identifiers.org/string/$1 + fairsharing: + abbreviation: STRING + description: STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations. + id: '1875' + name: STRING + prefix: FAIRsharing.9b7wvk + subjects: + - Life Science + - Biology + mappings: + biocontext: STRING + fairsharing: FAIRsharing.9b7wvk + miriam: string + n2t: string + prefixcommons: string + uniprot: STRING + miriam: + deprecated: false + description: "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable." + homepage: http://string.embl.de/ + id: '00000265' + name: STRING + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ + prefix: string + providers: + - code: CURATOR_REVIEW + description: STRING Mirror at Heidelberg + homepage: http://string-db.org/ + name: STRING Mirror at Heidelberg + uri_format: http://string-db.org/interactions/$1 + sampleId: P53350 + uri_format: http://string.embl.de/interactions/$1 + n2t: + description: STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. + example: P53350 + homepage: http://string-db.org/ + name: STRING Mirror at Heidelberg + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ + prefix: string + uri_format: http://string-db.org/interactions/$1 + name: Search Tool for Retrieval of Interacting Genes/Proteins + prefixcommons: + description: STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations + example: P53350 + homepage: http://string-db.org + keywords: + - protein + - interaction + name: 'STRING: functional protein association networks' + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$ + prefix: string + pubmed_ids: + - '18940858' + provides: uniprot + uniprot: + category: Protein-protein interaction databases + identifier: '141' + link_is_explicit: 'true' + name: 'STRING: functional protein association networks' + prefix: STRING + uri_format: https://string-db.org/network/$1 +sty: + biolink: + is_identifiers: false + is_obo: false + prefix: STY + uri_format: http://purl.bioontology.org/ontology/STY/$1 + bioportal: + name: Semantic Types Ontology + prefix: STY + description: UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types. + example: T039 + homepage: https://lhncbc.nlm.nih.gov/semanticnetwork/ + mappings: + biolink: STY + bioportal: STY + name: Semantic Types Ontology + pattern: ^T\d{3}$ + uri_format: http://purl.bioontology.org/ontology/STY/$1 +subtilist: + biocontext: + is_identifiers: true + is_obo: false + prefix: SUBTILIST + uri_format: http://identifiers.org/subtilist/$1 + fairsharing: + abbreviation: SubtiList + description: Its purpose is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments + id: '1924' + name: Bacillus subtilis strain 168 genome + prefix: FAIRsharing.40j2vd + subjects: [] + mappings: + biocontext: SUBTILIST + fairsharing: FAIRsharing.40j2vd + miriam: subtilist + n2t: subtilist + ncbi: SubtiList + prefixcommons: subtilist + miriam: + deprecated: false + description: "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments." + homepage: http://genolist.pasteur.fr/SubtiList/ + id: '00000433' + name: SubtiList + namespaceEmbeddedInLui: false + pattern: ^BG\d+$ + prefix: subtilist + sampleId: BG11523 + uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1 + n2t: + description: SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments. + example: BG11523 + homepage: http://genolist.pasteur.fr/SubtiList/ + name: SubtiList at Pasteur Institute + namespaceEmbeddedInLui: false + pattern: ^BG\d+$ + prefix: subtilist + uri_format: http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1 + ncbi: + example: BG10001 + homepage: http://genolist.pasteur.fr/SubtiList/ + name: Bacillus subtilis genome sequencing project + prefix: SubtiList + prefixcommons: + description: Its purpose is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments + example: BG11523 + homepage: http://genolist.pasteur.fr/SubtiList/ + keywords: + - genome + - DNA + - protein + name: Bacillus subtilis strain 168 genome database + pattern: ^BG\d+$ + prefix: subtilist +subtiwiki: + biocontext: + is_identifiers: true + is_obo: false + prefix: SUBTIWIKI + uri_format: http://identifiers.org/subtiwiki/$1 + fairsharing: + abbreviation: SubtiWiki + description: Collaborative resource for the Bacillus community. + id: '1690' + name: SubtiWiki + prefix: FAIRsharing.2ck3st + subjects: + - Life Science + mappings: + biocontext: SUBTIWIKI + fairsharing: FAIRsharing.2ck3st + miriam: subtiwiki + n2t: subtiwiki + prefixcommons: subtiwiki + miriam: + deprecated: false + description: "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon." + homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page + id: '00000132' + name: SubtiWiki + namespaceEmbeddedInLui: false + pattern: ^BSU\d{5}$ + prefix: subtiwiki + sampleId: BSU29180 + uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1 + n2t: + description: 'SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.' + example: BSU29180 + homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page + name: SubtiWiki website + namespaceEmbeddedInLui: false + pattern: ^BSU\d{5}$ + prefix: subtiwiki + uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1 + prefixcommons: + description: 'SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.' + example: BSU29180 + homepage: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page + keywords: + - gene + - protein + - RNA + - DNA + name: SubtiWiki + pattern: ^BSU\d{5}$ + prefix: subtiwiki + pubmed_ids: + - '19959575' + - '20157485' + uri_format: http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1 +sugarbind: + biocontext: + is_identifiers: true + is_obo: false + prefix: SUGARBIND + uri_format: http://identifiers.org/sugarbind/$1 + fairsharing: + abbreviation: SugarBind + description: The SugarBind Database (SugarBindDB) was created in 2002 as part of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture technology based on the binding of viral, bacterial and biotoxin lectins to specific glycans (aka, sugars, carbohydrates) displayed on glycoprotein films. The database content results from compiling publicly available information. In 2010, the 2008 version of the database was migrated from MITRE Corporation to the SIB Swiss Institute of Bioinformatics in Geneva, Switzerland. From then, substantial changes in the database design and usage were undertaken and previous content was significantly extended. + id: '2397' + name: SugarBind + prefix: FAIRsharing.d064y6 + subjects: + - Glycomics + - Biomedical Science + mappings: + biocontext: SUGARBIND + fairsharing: FAIRsharing.d064y6 + miriam: sugarbind + n2t: sugarbind + miriam: + deprecated: false + description: The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands. + homepage: http://sugarbind.expasy.org/ + id: '00000629' + name: SugarBind + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+\/[0-9]+$ + prefix: sugarbind + sampleId: lectins/172 + uri_format: http://sugarbind.expasy.org/$1 + n2t: + description: The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands. + example: lectins/172 + homepage: http://sugarbind.expasy.org/ + name: SugarBind + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z]+\/[0-9]+$ + prefix: sugarbind + uri_format: http://sugarbind.expasy.org/$1 +supfam: + biocontext: + is_identifiers: true + is_obo: false + prefix: SUPFAM + uri_format: http://identifiers.org/supfam/$1 + mappings: + biocontext: SUPFAM + miriam: supfam + n2t: supfam + uniprot: SUPFAM + miriam: + deprecated: false + description: SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. + homepage: http://supfam.org/SUPERFAMILY/ + id: '00000357' + name: SUPFAM + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: supfam + sampleId: SSF57615 + uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1 + n2t: + description: SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. + example: SSF57615 + homepage: http://supfam.org/SUPERFAMILY/ + name: SUPFAM at MRC and University of Bristol + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: supfam + uri_format: http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1 + name: SUPERFAMILY + uniprot: + category: Family and domain databases + identifier: '155' + link_is_explicit: 'true' + name: Superfamily database of structural and functional annotation + prefix: SUPFAM + uri_format: https://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1 +sweetrealm: + bioportal: + name: Semantic Web for Earth and Environment Technology Ontology + prefix: SWEET + description: The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). + download_obo: https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo + example: ANOVA + homepage: https://bioportal.bioontology.org/ontologies/SWEET + mappings: + bioportal: SWEET + name: Semantic Web for Earth and Environment Technology Ontology +swh: + banana: swh + biocontext: + is_identifiers: true + is_obo: false + prefix: SWH + uri_format: http://identifiers.org/swh/$1 + mappings: + biocontext: SWH + miriam: swh + n2t: swh + miriam: + deprecated: false + description: Software Heritage is the universal archive of software source code. + homepage: https://archive.softwareheritage.org + id: '00000655' + name: Software Heritage + namespaceEmbeddedInLui: true + pattern: ^swh:[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$ + prefix: swh + sampleId: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d + uri_format: https://archive.softwareheritage.org/browse/swh:$1 + n2t: + description: Software Heritage is the universal archive of software source code. + example: 1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d + homepage: https://archive.softwareheritage.org + name: Software Heritage + namespaceEmbeddedInLui: true + pattern: ^swh:[1-9]:[a-z][a-z][a-z]:[a-f0-9]+$ + prefix: swh + uri_format: https://archive.softwareheritage.org/browse/swh:$1 + pattern: ^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$ +swiss-model: + biocontext: + is_identifiers: true + is_obo: false + prefix: SWISS-MODEL + uri_format: http://identifiers.org/swiss-model/$1 + fairsharing: + abbreviation: SWISS-MODEL + description: The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms. + id: '2061' + name: SWISS-MODEL Repository of 3D protein structure models + prefix: FAIRsharing.vxz9pn + subjects: + - Proteomics + - Life Science + mappings: + biocontext: SWISS-MODEL + fairsharing: FAIRsharing.vxz9pn + miriam: swiss-model + n2t: swiss-model + prefixcommons: swissmodel + miriam: + deprecated: false + description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences. + homepage: https://swissmodel.expasy.org + id: '00000231' + name: SWISS-MODEL Repository + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: swiss-model + sampleId: P23298 + uri_format: https://swissmodel.expasy.org/repository/uniprot/$1 + n2t: + description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences. + example: P23298 + homepage: https://swissmodel.expasy.org + name: SWISS-MODEL at SIB Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: swiss-model + uri_format: https://swissmodel.expasy.org/repository/uniprot/$1 + prefixcommons: + description: The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for sequences registered is SWISS-PROT. + example: P23298 + homepage: http://swissmodel.expasy.org/ + keywords: + - protein + - structure + name: SWISS-MODEL repository of 3D protein structure models + pattern: ^\w+$ + prefix: swissmodel + pubmed_ids: + - '18931379' + uri_format: http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$1 + provides: uniprot +swisslipid: + banana: SLM + biocontext: + is_identifiers: true + is_obo: false + prefix: SWISSLIPID + uri_format: http://identifiers.org/swisslipid/$1 + example: '000000341' + fairsharing: + abbreviation: SwissLipids + description: SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily. + id: '2259' + name: SwissLipids + prefix: FAIRsharing.pxr7x2 + subjects: + - Life Science + - Metabolomics + mappings: + biocontext: SWISSLIPID + fairsharing: FAIRsharing.pxr7x2 + miriam: slm + n2t: swisslipid + uniprot: SwissLipids + wikidata: P8691 + miriam: + deprecated: false + description: SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. + homepage: http://www.swisslipids.org/#/ + id: '00000550' + name: SwissLipids + namespaceEmbeddedInLui: true + pattern: ^SLM:\d+$ + prefix: slm + sampleId: '000048885' + uri_format: http://www.swisslipids.org/#/entity/SLM:$1/ + n2t: + description: SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. + example: '000048885' + homepage: http://www.swisslipids.org/#/ + name: SwissLipids at Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: true + pattern: ^SLM:\d+$ + prefix: swisslipid + uri_format: http://www.swisslipids.org/#/entity/SLM:$1/ + name: SwissLipid + pattern: ^\d+$ + synonyms: + - slm + - swisslipids + uniprot: + category: Chemistry databases + identifier: '197' + link_is_explicit: 'true' + name: SwissLipids knowledge resource for lipid biology + prefix: SwissLipids + uri_format: https://www.swisslipids.org/#/entity/$1/ + uri_format: https://www.swisslipids.org/#/entity/SLM:$1 + wikidata: + database: Q41165322 + database.homepage: http://www.swisslipids.org/ + database.label: SwissLipids + homepage: https://www.swisslipids.org/#/ + name: SwissLipids identifier + prefix: P8691 + uri_format: https://www.swisslipids.org/#/entity/$1/ +swissregulon: + biocontext: + is_identifiers: true + is_obo: false + prefix: SWISSREGULON + uri_format: http://identifiers.org/swissregulon/$1 + fairsharing: + abbreviation: SwissRegulon + description: The Swissregulon Database contains genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including i) Experimentally determined binding sites reported in the literature, ii) Known sequence-specificities of transcription factors, iii) ChIP-chip and ChIP-seq data, iiii) Alignments of orthologous non-coding regions. + id: '2398' + name: SwissRegulon + prefix: FAIRsharing.7fnx38 + subjects: + - Life Science + mappings: + biocontext: SWISSREGULON + fairsharing: FAIRsharing.7fnx38 + miriam: swissregulon + n2t: swissregulon + miriam: + deprecated: false + description: A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. + homepage: http://swissregulon.unibas.ch + id: '00000632' + name: SwissRegulon + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: swissregulon + sampleId: AHR + uri_format: http://swissregulon.unibas.ch/query/$1 + n2t: + description: A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. + example: AHR + homepage: http://swissregulon.unibas.ch + name: SwissRegulon + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9]+$ + prefix: swissregulon + uri_format: http://swissregulon.unibas.ch/query/$1 +swo: + biocontext: + is_identifiers: false + is_obo: true + prefix: SWO + uri_format: http://purl.obolibrary.org/obo/SWO_$1 + bioportal: + name: Software Ontology + prefix: SWO + download_owl: https://github.com/allysonlister/swo/raw/master/release/swo.owl + example: '0000144' + fairsharing: + abbreviation: SWO + description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. SWO also covers software manufacturer, input and output data types and the uses (i.e. objectives) to which the software can be put. + id: '1195' + name: SoftWare Ontology + prefix: FAIRsharing.sp3szt + subjects: + - Computer Science + mappings: + biocontext: SWO + bioportal: SWO + fairsharing: FAIRsharing.sp3szt + obofoundry: swo + ols: swo + ontobee: SWO + prefixcommons: swo + obofoundry: + contact: allyson.lister@oerc.ox.ac.uk + contact.github: allysonlister + contact.label: Allyson Lister + contact.orcid: 0000-0002-7702-4495 + deprecated: false + description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. + download.owl: http://purl.obolibrary.org/obo/swo.owl + homepage: https://github.com/allysonlister/swo + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Software ontology + preferredPrefix: SWO + prefix: swo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/25068035 + title: 'The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation' + repository: https://github.com/allysonlister/swo + ols: + description: The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. + download: http://purl.obolibrary.org/obo/swo.owl + homepage: https://github.com/allysonlister/swo + name: SWO (The Software Ontology) + prefix: swo + version: '1.7' + version.iri: http://www.ebi.ac.uk/swo/swo.owl/1.7 + ontobee: + library: Library + name: Software ontology + prefix: SWO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1413' + description: 'The Software Ontology (SWO) has the scope of describing types of software used in Bioinformatics. The SWO covers areas such as the software type, the manufacturer of the software, the input and output data types and the uses (i.e. objectives) the software can be put to. The SWO intends to use BFO as an upper level ontolgoy and subclasses types from the Ontology of Biomedical Investigations. Contact James Malone for info: malone@ebi.ac.uk' + example: SWO_0000396 + homepage: http://theswo.sourceforge.net + name: Software Ontology + pattern: ^SWO_\d{7}$ + prefix: swo +symp: + biocontext: + is_identifiers: false + is_obo: true + prefix: SYMP + uri_format: http://purl.obolibrary.org/obo/SYMP_$1 + bioportal: + name: Symptom Ontology + prefix: SYMP + example: '0019171' + fairsharing: + abbreviation: SYMP + description: 'The symptom ontology was designed around the guiding concept of a symptom being: "A perceived change in function, sensation or appearance reported by a patient indicative of a disease". There is a close relationship between Signs and Symptoms, where Signs are the objective observation of an illness. The Symptom Ontology will work to broaden its scope to capture and document in a more robust manor these two sets of terms. At times, the same term may be both a Sign and a Symptom.' + id: '85' + name: Symptom Ontology + prefix: FAIRsharing.ay74mj + subjects: + - Life Science + - Biomedical Science + - Pain Medicine + mappings: + biocontext: SYMP + bioportal: SYMP + fairsharing: FAIRsharing.ay74mj + obofoundry: symp + ols: symp + ontobee: SYMP + obofoundry: + appears_in: + - scdo + contact: lynn.schriml@gmail.com + contact.github: lschriml + contact.label: Lynn Schriml + contact.orcid: 0000-0001-8910-9851 + deprecated: false + description: An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease. + download.obo: http://purl.obolibrary.org/obo/symp.obo + download.owl: http://purl.obolibrary.org/obo/symp.owl + homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Symptom Ontology + preferredPrefix: SYMP + prefix: symp + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/19850722 + title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database + - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 + title: The Human Disease Ontology 2022 update + repository: https://github.com/DiseaseOntology/SymptomOntology + ols: + description: The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases. + download: http://purl.obolibrary.org/obo/symp.owl + homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page + name: Symptom Ontology + prefix: symp + version: 2022-04-05 + version.iri: http://purl.obolibrary.org/obo/symp/releases/2022-04-05/symp.owl + ontobee: + library: Library + name: Symptom Ontology + prefix: SYMP + pattern: ^\d{7}$ + synonyms: + - SYMP + wikidata: + prefix: P8656 +syoid: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + name: Gemina Symptom Ontology + references: + - https://github.com/DiseaseOntology/SymptomOntology/issues/7#event-4223716562 +t3db: + biocontext: + is_identifiers: true + is_obo: false + prefix: T3DB + uri_format: http://identifiers.org/t3db/$1 + fairsharing: + abbreviation: T3DB + description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. + id: '2085' + name: Toxin and Toxin Target Database + prefix: FAIRsharing.psn0h2 + subjects: + - Life Science + - Biomedical Science + mappings: + biocontext: T3DB + fairsharing: FAIRsharing.psn0h2 + miriam: t3db + n2t: t3db + prefixcommons: t3db + miriam: + deprecated: false + description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. + homepage: http://www.t3db.org/ + id: '00000103' + name: T3DB + namespaceEmbeddedInLui: false + pattern: ^T3D\d+$ + prefix: t3db + sampleId: T3D0001 + uri_format: http://www.t3db.org/toxins/$1 + n2t: + description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. + example: T3D0001 + homepage: http://www.t3db.org/ + name: Toxin and Toxin Target Database + namespaceEmbeddedInLui: false + pattern: ^T3D\d+$ + prefix: t3db + uri_format: http://www.t3db.org/toxins/$1 + name: Toxin and Toxin Target Database + prefixcommons: + description: Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. + example: T3D0001 + homepage: http://www.t3db.org/ + keywords: + - protein + - molecule + name: Toxin and Toxin Target Database + pattern: ^T3D\d+$ + prefix: t3db + uri_format: http://www.t3db.org/toxins/$1 +tads: + biocontext: + is_identifiers: false + is_obo: true + prefix: TADS + uri_format: http://purl.obolibrary.org/obo/TADS_$1 + bioportal: + name: Tick Gross Anatomy Ontology + prefix: TADS + download_obo: http://purl.obolibrary.org/obo/tads.obo + example: '0000547' + fairsharing: + abbreviation: TADS + description: This ontology covers all the terms relevant for the gross anatomy of the tick (family Ixodida). + id: '222' + name: Tick Gross Anatomy + prefix: FAIRsharing.8wm364 + subjects: + - Anatomy + - Life Science + mappings: + biocontext: TADS + bioportal: TADS + fairsharing: FAIRsharing.8wm364 + obofoundry: tads + ols: tads + ontobee: TADS + obofoundry: + contact: dsonensh@odu.edu + contact.label: Daniel Sonenshine + deprecated: true + description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae' + download.obo: http://purl.obolibrary.org/obo/tads.obo + download.owl: http://purl.obolibrary.org/obo/tads.owl + homepage: https://www.vectorbase.org/ontology-browser + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Tick Anatomy Ontology + prefix: tads + repository: https://github.com/VEuPathDB-ontology/TADS + ols: + description: 'The anatomy of the Tick, Families: Ixodidae, Argassidae' + download: http://purl.obolibrary.org/obo/tads.owl + homepage: https://www.vectorbase.org/ontology-browser + name: Tick Anatomy Ontology + prefix: tads + version: 2015-08-20 + version.iri: http://purl.obolibrary.org/obo/tads/2015-08-20/tads.owl + ontobee: + library: Library + name: Tick Anatomy Ontology + prefix: TADS + pattern: ^\d{7}$ +tahe: + biocontext: + is_identifiers: false + is_obo: true + prefix: TAHE + uri_format: http://purl.obolibrary.org/obo/TAHE_$1 + mappings: + biocontext: TAHE + obofoundry: tahe + obofoundry: + contact: pierre.sprumont@unifr.ch + contact.label: Pierre Sprumont + deprecated: true + name: Terminology of Anatomy of Human Embryology + prefix: tahe +tahh: + biocontext: + is_identifiers: false + is_obo: true + prefix: TAHH + uri_format: http://purl.obolibrary.org/obo/TAHH_$1 + mappings: + biocontext: TAHH + obofoundry: tahh + obofoundry: + contact: pierre.sprumont@unifr.ch + contact.label: Pierre Sprumont + deprecated: true + name: Terminology of Anatomy of Human Histology + prefix: tahh +tair.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: TAIR.GENE + uri_format: http://identifiers.org/tair.gene/$1 + example: '2200934' + mappings: + biocontext: TAIR.GENE + miriam: tair.gene + n2t: tair.gene + prefixcommons: tair.gene + miriam: + deprecated: false + description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus. + homepage: http://arabidopsis.org/index.jsp + id: '00000049' + name: TAIR Gene + namespaceEmbeddedInLui: false + pattern: ^Gene:\d{7}$ + prefix: tair.gene + sampleId: Gene:2200934 + uri_format: http://arabidopsis.org/servlets/TairObject?accession=$1 + n2t: + description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus. + example: Gene:2200934 + homepage: http://arabidopsis.org/index.jsp + name: The Arabidopsis Information Resource (TAIR) Gene + namespaceEmbeddedInLui: false + pattern: ^Gene:\d{7}$ + prefix: tair.gene + uri_format: http://arabidopsis.org/servlets/TairObject?accession=$1 + pattern: ^\d{7}$ + prefixcommons: + description: The reference gene model for a given locus + example: Gene:2200934 + keywords: + - gene + name: TAIR-Gene + pattern: ^Gene:\d{7}$ + prefix: tair.gene + pubmed_ids: + - '12444417' + uri_format: http://arabidopsis.org/servlets/TairObject?accession=$1 + uri_format: http://arabidopsis.org/servlets/TairObject?accession=Gene:$1 +tair.locus: + biocontext: + is_identifiers: true + is_obo: false + prefix: TAIR.LOCUS + uri_format: http://identifiers.org/tair.locus/$1 + contributor_extras: + - email: benjamin_gyori@hms.harvard.edu + github: bgyori + name: Benjamin M. Gyori + orcid: 0000-0001-9439-5346 + go: + homepage: http://www.arabidopsis.org/ + name: The Arabidopsis Information Resource + prefix: TAIR + mappings: + biocontext: TAIR.LOCUS + go: TAIR + miriam: tair.locus + n2t: tair.locus + ncbi: TAIR + prefixcommons: tair.locus + miriam: + deprecated: false + description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. + homepage: http://arabidopsis.org/index.jsp + id: '00000050' + name: TAIR Locus + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: tair.locus + sampleId: '2200950' + uri_format: http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1 + n2t: + description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. + example: '2200950' + homepage: http://arabidopsis.org/index.jsp + name: The Arabidopsis Information Resource (TAIR) Locus + namespaceEmbeddedInLui: false + pattern: ^\d{7}$ + prefix: tair.locus + uri_format: http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1 + ncbi: + example: AT1F51370 + homepage: http://www.arabidopsis.org/servlets/Search?type=gene&action=new_search + name: Arabidopsis IR + prefix: TAIR + pattern: ^\d+$ + prefixcommons: + description: The locus name + example: AT1G01030 + keywords: + - genome + name: TAIR-Locus + pattern: ^AT[1-5]G\d{5}$ + prefix: tair.locus + pubmed_ids: + - '12444417' + uri_format: http://arabidopsis.org/servlets/TairObject?type=locus&name=$1 +tair.protein: + biocontext: + is_identifiers: true + is_obo: false + prefix: TAIR.PROTEIN + uri_format: http://identifiers.org/tair.protein/$1 + example: '1009107926' + mappings: + biocontext: TAIR.PROTEIN + miriam: tair.protein + n2t: tair.protein + prefixcommons: tair.protein + miriam: + deprecated: false + description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept + homepage: http://arabidopsis.org/index.jsp + id: '00000048' + name: TAIR Protein + namespaceEmbeddedInLui: false + pattern: ^AASequence:\d{10}$ + prefix: tair.protein + sampleId: AASequence:1009107926 + uri_format: http://arabidopsis.org/servlets/TairObject?accession=$1 + n2t: + description: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept + example: AASequence:1009107926 + homepage: http://arabidopsis.org/index.jsp + name: The Arabidopsis Information Resource (TAIR) Protein + namespaceEmbeddedInLui: false + pattern: ^AASequence:\d{10}$ + prefix: tair.protein + uri_format: http://arabidopsis.org/servlets/TairObject?accession=$1 + pattern: ^\d{10}$ + prefixcommons: + description: The protein entry + example: AASequence:1009107926 + keywords: + - protein + name: TAIR-Protein + pattern: ^AASequence:\d{10}$ + prefix: tair.protein + pubmed_ids: + - '12444417' + uri_format: http://arabidopsis.org/servlets/TairObject?accession=$1 + uri_format: http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1 +tao: + biocontext: + is_identifiers: false + is_obo: true + prefix: TAO + uri_format: http://purl.obolibrary.org/obo/TAO_$1 + bioportal: + name: Teleost Anatomy Ontology + prefix: TAO + example: '0000086' + mappings: + biocontext: TAO + bioportal: TAO + obofoundry: tao + prefixcommons: tao + name: Teleost Anatomy Ontology + obofoundry: + contact: wasila.dahdul@usd.edu + contact.label: Wasila Dahdul + contact.orcid: 0000-0003-3162-7490 + deprecated: true + description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa + download.owl: http://purl.obolibrary.org/obo/tao.owl + homepage: http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Teleost Anatomy Ontology + prefix: tao + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/20547776 + title: 'The teleost anatomy ontology: anatomical representation for the genomics age' + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1110' + description: Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa + example: TAO_0000297 + homepage: https://www.nescent.org/phenoscape/Main_Page + keywords: + - obo + - classification + - anatomy + name: Teleost Anatomy Ontology + pattern: ^TAO_\d{7}$ + prefix: tao + uri_format: http://purl.obolibrary.org/obo/$1 + synonyms: + - TAO_RETIRED +tarbase: + biocontext: + is_identifiers: true + is_obo: false + prefix: TARBASE + uri_format: http://identifiers.org/tarbase/$1 + fairsharing: + abbreviation: TarBase + description: DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBase is supported by information on methodologies, cell types/tissues and experimental conditions. + id: '1674' + name: TarBase + prefix: FAIRsharing.a0k4cd + subjects: + - Life Science + - Biomedical Science + mappings: + biocontext: TARBASE + fairsharing: FAIRsharing.a0k4cd + miriam: tarbase + n2t: tarbase + miriam: + deprecated: false + description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. + homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index + id: '00000340' + name: TarBase + namespaceEmbeddedInLui: false + pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)? + prefix: tarbase + sampleId: hsa-let-7a-2-3p + uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1 + n2t: + description: TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. + example: hsa-let-7a-2-3p + homepage: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index + name: TarBase v7 at University of Thessaly + namespaceEmbeddedInLui: false + pattern: ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)? + prefix: tarbase + uri_format: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1 +taxrank: + biocontext: + is_identifiers: false + is_obo: true + prefix: TAXRANK + uri_format: http://purl.obolibrary.org/obo/TAXRANK_$1 + bioportal: + name: Taxonomic Rank Vocabulary + prefix: TAXRANK + example: '0000001' + fairsharing: + abbreviation: TAXRANK + description: This is a vocabulary of taxonomic ranks intended to replace the sets of rank terms found in the Teleost Taxonomy Ontology, the OBO translation of the NCBI taxonomy and similar OBO taxonomy ontologies. It provides terms for taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. Each term contains cross reference links to the resources that use the terms. Consistent with its intended use as a vocabulary, there is no relation specifying an ordering of the rank terms. Likewise, all terms are directly descended from the term 'taxonomic rank' (TAXRANK:0000000). + id: '356' + name: Taxonomic Rank Vocabulary + prefix: FAIRsharing.p1sejz + subjects: + - Taxonomy + - Life Science + mappings: + biocontext: TAXRANK + bioportal: TAXRANK + fairsharing: FAIRsharing.p1sejz + obofoundry: taxrank + ols: taxrank + ontobee: TAXRANK + prefixcommons: taxrank + obofoundry: + contact: balhoff@renci.org + contact.github: balhoff + contact.label: Jim Balhoff + contact.orcid: 0000-0002-8688-6599 + deprecated: false + description: A vocabulary of taxonomic ranks (species, family, phylum, etc) + download.obo: http://purl.obolibrary.org/obo/taxrank.obo + download.owl: http://purl.obolibrary.org/obo/taxrank.owl + homepage: https://github.com/phenoscape/taxrank + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Taxonomic rank vocabulary + preferredPrefix: TAXRANK + prefix: taxrank + publications: + - id: https://doi.org/10.1186/2041-1480-4-34 + title: 'The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes' + repository: https://github.com/phenoscape/taxrank + ols: + description: A vocabulary of taxonomic ranks (species, family, phylum, etc) + download: http://purl.obolibrary.org/obo/taxrank.owl + homepage: https://github.com/phenoscape/taxrank + name: Taxonomic rank vocabulary + prefix: taxrank + version: 2016-04-15 + version.iri: http://purl.obolibrary.org/obo/taxrank/releases/2016-04-15/taxrank.owl + ontobee: + library: Library + name: Taxonomic rank vocabulary + prefix: TAXRANK + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1419' + description: Taxonomic ranks drawn from both the NCBI taxonomy database and from a rank vocabulary developed for the TDWG biodiversity information standards group. + example: TAXRANK:0000001 + homepage: https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary + keywords: + - obo + name: Taxonomic rank vocabulary + pattern: ^TAXRANK:\d+$ + prefix: taxrank + uri_format: http://purl.obolibrary.org/obo/$1 +tcb: + cellosaurus: + category: Cell line collections + homepage: https://www.pirbright.ac.uk/tick-cell-lines-views-page + name: Tick Cell Biobank + prefix: TCB + uri_format: https://www.pirbright.ac.uk/node/$1 + example: '2966' + mappings: + cellosaurus: TCB + pattern: ^\d+$ +tcdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: TCDB + uri_format: http://identifiers.org/tcdb/$1 + fairsharing: + abbreviation: TCDB + description: This freely accessible database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information for organisms of all types. As of April. 1, 2021, TCDB consists of 21,114 proteins classified in 16,558 non-redundant transport systems with 1,605 tabulated 3D structures, 19,196 reference citations describing 1,586 transporter families, of which 26% are members of 83 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. The most recent update of the database contents and features include (1) adoption of a chemical ontology for substrates of transporters, (2) inclusion of new superfamilies, (3) a domain-based characterization of transporter families (tcDoms) for the identification of new members as well as functional and evolutionary relationships between families, (4) development of novel software to facilitate curation and use of the database, (5) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators, and (6) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers. + id: '2022' + name: Transporter Classification Database + prefix: FAIRsharing.p3bzqb + subjects: + - Knowledge and Information Systems + - Phylogenetics + - Computational Biology + - Life Science + - Cell Biology + go: + homepage: http://www.tcdb.org/ + name: Transport Protein Database + prefix: TC + uri_format: http://www.tcdb.org/tcdb/index.php?tc=$1 + homepage: https://www.tcdb.org + mappings: + biocontext: TCDB + fairsharing: FAIRsharing.p3bzqb + go: TC + miriam: tcdb + n2t: tcdb + prefixcommons: tcdb + uniprot: TCDB + wikidata: P7260 + miriam: + deprecated: false + description: The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. + homepage: http://www.tcdb.org/ + id: '00000040' + name: Transport Classification Database + namespaceEmbeddedInLui: false + pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$ + prefix: tcdb + sampleId: 5.A.1.1.1 + uri_format: http://www.tcdb.org/search/result.php?tc=$1 + n2t: + description: The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. + example: 5.A.1.1.1 + homepage: http://www.tcdb.org/ + name: TCDB + namespaceEmbeddedInLui: false + pattern: ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$ + prefix: tcdb + uri_format: http://www.tcdb.org/search/result.php?tc=$1 + name: Transporter Classification Database + prefixcommons: + description: TCDB is a curated database of factual information from over 10,000 published references; it contains about 5,600 unique protein sequences that are classified into over 600 transporter families based on the TC-system. + example: 5.A.1.1.1 + homepage: http://www.tcdb.org/ + keywords: + - protein + - structure + name: Transport Classification Database + pattern: ^\d+\.[A-Z]\.\d+\.\d+\.\d+$ + prefix: tcdb + pubmed_ids: + - '16381841' + uri_format: http://www.tcdb.org/search/result.php?tc=$1 + synonyms: + - TC + uniprot: + category: Protein family/group databases + identifier: '135' + link_is_explicit: 'true' + name: Transport Classification Database + prefix: TCDB + uri_format: http://www.tcdb.org/search/result.php?tc=$1 + wikidata: + database: Q142667 + database.homepage: http://www.tcdb.org/ + database.label: Transporter Classification database + homepage: https://www.tcdb.org + name: Transporter Classification Database ID + pattern: \d|(\d\.[A-Z](\.(\d{1,3}){0,3})) + prefix: P7260 + uri_format: http://www.tcdb.org/search/result.php?tc=$1 +te: + description: The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia] + example: E5.11.2.0.0.0.4 + homepage: https://ifaa.unifr.ch/ + name: Terminologia Embryologica + references: + - https://en.wikipedia.org/wiki/Terminologia_Embryologica + wikidata: + prefix: P1693 +tfclass: + description: TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.. + example: 2.1.1 + fairsharing: + abbreviation: TFClass + description: TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains. Combining information from different resources, manually checking the retrieved mammalian TF sequences and applying extensive phylogenetic analyses, >39,000 TFs from up to 41 mammalian species were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass. TFClass provides corresponding sequence collections in FASTA format; sequence logos and phylogenetic trees at different classification levels; predicted TF binding sites for human, mouse, dog and cow genomes; and links to several external databases. + id: '1207' + name: Transcription Factor Class + prefix: FAIRsharing.XykycZ + subjects: + - Bioinformatics + - Phylogenetics + - Transcriptomics + go: + homepage: http://tfclass.bioinf.med.uni-goettingen.de/ + name: TFClass is a resource for the classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains + prefix: TFClass + synonyms: + - TFCLASS_FAMILY + - tfclass + uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1 + homepage: http://tfclass.bioinf.med.uni-goettingen.de + mappings: + fairsharing: FAIRsharing.XykycZ + go: TFClass + name: Classification of Transcription Factors in Mammalia + uri_format: http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1 +tgd: + biocontext: + is_identifiers: true + is_obo: false + prefix: TGD + uri_format: http://identifiers.org/tgd/$1 + go: + homepage: http://www.ciliate.org/ + name: Tetrahymena Genome Database + prefix: TGD + mappings: + biocontext: TGD + go: TGD + miriam: tgd + n2t: tgd + prefixcommons: tgd + miriam: + deprecated: false + description: The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. + homepage: http://ciliate.org/index.php/ + id: '00000313' + name: Tetrahymena Genome Database + namespaceEmbeddedInLui: false + pattern: ^TTHERM\_\d+$ + prefix: tgd + sampleId: TTHERM_00648910 + uri_format: http://ciliate.org/index.php/feature/details/$1 + n2t: + description: The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. + example: TTHERM_00648910 + homepage: http://ciliate.org/index.php/ + name: TGD at Stanford University + namespaceEmbeddedInLui: false + pattern: ^TTHERM\_\d+$ + prefix: tgd + uri_format: http://ciliate.org/index.php/feature/details/$1 + prefixcommons: + description: Pages with links to phage information are also available, including a T4 genetic map reference figure, RB69, RB49, and Aeh1 Map figures, electron micrographs, annotation tables, sequence files, and links to NCBI T4 and Integrated Genomics RB69 annotation sites are available. + example: RB51 + homepage: http://phage.bioc.tulane.edu + keywords: + - genome + name: T4-like genome database + pattern: ^[A-Z,0-9]+$ + prefix: tgd + uri_format: http://phage.bioc.tulane.edu/cgi-bin/gbrowse/$1?name=$1 +tgma: + biocontext: + is_identifiers: false + is_obo: true + prefix: TGMA + uri_format: http://purl.obolibrary.org/obo/TGMA_$1 + bioportal: + name: Mosquito Gross Anatomy Ontology + prefix: TGMA + download_obo: http://purl.obolibrary.org/obo/tgma.obo + example: '0000984' + fairsharing: + abbreviation: TGMA + description: A structured controlled vocabulary of the anatomy of mosquitoes. + id: '15' + name: Mosquito gross anatomy + prefix: FAIRsharing.dqnfkg + subjects: + - Anatomy + - Life Science + mappings: + biocontext: TGMA + bioportal: TGMA + fairsharing: FAIRsharing.dqnfkg + obofoundry: tgma + ols: tgma + ontobee: TGMA + prefixcommons: tgma + obofoundry: + contact: topalis@imbb.forth.gr + contact.label: Pantelis Topalis + deprecated: true + description: A structured controlled vocabulary of the anatomy of mosquitoes. + download.obo: http://purl.obolibrary.org/obo/tgma.obo + download.owl: http://purl.obolibrary.org/obo/tgma.owl + homepage: https://www.vectorbase.org/ontology-browser + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Mosquito gross anatomy ontology + prefix: tgma + repository: https://github.com/VEuPathDB-ontology/TGMA + ols: + description: A structured controlled vocabulary of the anatomy of mosquitoes. + download: http://purl.obolibrary.org/obo/tgma.owl + homepage: https://www.vectorbase.org/ontology-browser + name: Mosquito gross anatomy ontology + prefix: tgma + version: 2013-06-03 + version.iri: http://purl.obolibrary.org/obo/tgma/releases/2013-06-03/tgma.owl + ontobee: + library: Library + name: Mosquito gross anatomy ontology + prefix: TGMA + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1030' + description: A structured controlled vocabulary of the anatomy of mosquitoes. + example: TGMA_0001525 + homepage: http://www.anobase.org + keywords: + - obo + - anatomy + - mosquito + name: Mosquito gross anatomy + pattern: ^TGMA_\d{7}$ + prefix: tgma +tgn: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + example: '1023371' + homepage: https://www.getty.edu/research/tools/vocabularies/tgn/ + name: Getty Thesaurus of Geographic Names + pattern: ^\d+$ + references: + - https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200 + uri_format: http://vocab.getty.edu/page/tgn/$1 +th: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia] + example: H3.03.00.0.00007 + homepage: https://ifaa.unifr.ch/ + name: Terminologia Histologica + references: + - https://en.wikipedia.org/wiki/Terminologia_Histologica +thermofisher: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: ThermoFisher is a life sciences supply vendor. + example: OSR00185W + homepage: https://www.thermofisher.com + name: Thermo Fisher Scientific + uri_format: https://www.thermofisher.com/antibody/product/$1 +tigrfam: + biocontext: + is_identifiers: true + is_obo: false + prefix: TIGRFAM + uri_format: http://identifiers.org/tigrfam/$1 + contributor_extras: + - email: cjmungall@lbl.gov + github: cmungall + name: Chris Mungall + orcid: 0000-0002-6601-2165 + mappings: + biocontext: TIGRFAM + miriam: tigrfam + n2t: tigrfam + ncbi: TIGRFAM + miriam: + deprecated: false + description: TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. + homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi + id: '00000315' + name: TIGRFAMS + namespaceEmbeddedInLui: false + pattern: ^TIGR\d+$ + prefix: tigrfam + sampleId: TIGR00010 + uri_format: http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1 + n2t: + description: TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. + example: TIGR00010 + homepage: http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi + name: TIGRFAM at JCVI + namespaceEmbeddedInLui: false + pattern: ^TIGR\d+$ + prefix: tigrfam + uri_format: http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$1 + ncbi: + example: TIGR00094 + homepage: http://www.tigr.org/TIGRFAMs/index.shtml + name: TIGR protein families + prefix: TIGRFAM + references: + - https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt + - https://github.com/biopragmatics/bioregistry/issues/366 + uri_format: https://www.ncbi.nlm.nih.gov/cdd?term=$1 +tkg: + cellosaurus: + category: Cell line collections + homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/ + name: Tohoku University cell line catalog + prefix: TKG + uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvo10%n/$1.html + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. + example: '0221' + homepage: http://www2.idac.tohoku.ac.jp/dep/ccr/ + mappings: + cellosaurus: TKG + name: Tohoku University cell line catalog + pattern: ^\d+$ + uri_format: http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html +tngb: + cellosaurus: + category: Cell line collections + homepage: http://biobanknetwork.telethon.it/ + name: Telethon Network of Genetic Biobanks + prefix: TNGB + uri_format: http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 + example: '67035' + mappings: + cellosaurus: TNGB + pattern: ^\d+$ +to: + biocontext: + is_identifiers: false + is_obo: true + prefix: TO + uri_format: http://purl.obolibrary.org/obo/TO_$1 + bioportal: + name: Plant Trait Ontology + prefix: PTO + example: '0000630' + fairsharing: + abbreviation: TO + description: A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part. The TO is part of the Planteome Project. + id: '613' + name: Plant Trait Ontology + prefix: FAIRsharing.w69t6r + subjects: + - Botany + mappings: + biocontext: TO + bioportal: PTO + fairsharing: FAIRsharing.w69t6r + obofoundry: to + ols: to + ontobee: TO + obofoundry: + appears_in: + - agro + contact: jaiswalp@science.oregonstate.edu + contact.github: jaiswalp + contact.label: Pankaj Jaiswal + contact.orcid: 0000-0002-1005-8383 + deprecated: false + description: A controlled vocabulary to describe phenotypic traits in plants. + download.obo: http://purl.obolibrary.org/obo/to.obo + download.owl: http://purl.obolibrary.org/obo/to.owl + homepage: http://browser.planteome.org/amigo + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Plant Trait Ontology + preferredPrefix: TO + prefix: to + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/29186578 + title: 'The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.' + repository: https://github.com/Planteome/plant-trait-ontology + ols: + description: A controlled vocabulary to describe phenotypic traits in plants. + download: http://purl.obolibrary.org/obo/to.owl + homepage: http://browser.planteome.org/amigo + name: Plant Trait Ontology + prefix: to + version: 2022-04-13 + version.iri: http://purl.obolibrary.org/obo/to/releases/2022-04-13/to.owl + ontobee: + library: Library + name: Plant Trait Ontology + prefix: TO + pattern: ^\d{7}$ +tokue: + cellosaurus: + category: Cell line databases/resources + homepage: http://cell-lines.toku-e.com + name: TOKU-E Cell-culture Database + prefix: TOKU-E + uri_format: http://cell-lines.toku-e.com/Cell-Lines_$1.html + deprecated: true + mappings: + cellosaurus: TOKU-E +tol: + biocontext: + is_identifiers: true + is_obo: false + prefix: TOL + uri_format: http://identifiers.org/tol/$1 + mappings: + biocontext: TOL + miriam: tol + n2t: tol + miriam: + deprecated: false + description: "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things." + homepage: http://tolweb.org/tree/ + id: '00000405' + name: Tree of Life + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: tol + sampleId: '98034' + uri_format: http://tolweb.org/$1 + n2t: + description: The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things. + example: '98034' + homepage: http://tolweb.org/tree/ + name: Tree of Life Web + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: tol + uri_format: http://tolweb.org/$1 +topdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: TOPDB + uri_format: http://identifiers.org/topdb/$1 + mappings: + biocontext: TOPDB + miriam: topdb + n2t: topdb + prefixcommons: topdb + miriam: + deprecated: false + description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. + homepage: http://topdb.enzim.hu/ + id: '00000503' + name: TOPDB + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: topdb + sampleId: AP00378 + uri_format: http://topdb.enzim.hu/?m=show&id=$1 + n2t: + description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. + example: AP00378 + homepage: http://topdb.enzim.hu/ + name: TOPDB at Hungarian Academy of Sciences + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: topdb + uri_format: http://topdb.enzim.hu/?m=show&id=$1 + name: Topology Data Bank of Transmembrane Proteins + prefixcommons: + description: The Topology Data Bank of Transmembrane Proteins (TOPDB) is currently the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information. + example: AB00979 + homepage: http://topdb.enzim.hu + keywords: + - protein + name: The Topology Databank + pattern: ^[A-Z]+\d+$ + prefix: topdb + uri_format: http://topdb.enzim.hu/?m=show&id=$1 +topfind: + biocontext: + is_identifiers: true + is_obo: false + prefix: TOPFIND + uri_format: http://identifiers.org/topfind/$1 + fairsharing: + abbreviation: TopFIND + description: The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases. + id: '1693' + name: Termini-Oriented Protein Function INferred Database + prefix: FAIRsharing.rkpmhn + subjects: + - Life Science + homepage: https://topfind.clip.msl.ubc.ca + mappings: + biocontext: TOPFIND + fairsharing: FAIRsharing.rkpmhn + miriam: topfind + n2t: topfind + miriam: + deprecated: false + description: 'TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.' + homepage: http://clipserve.clip.ubc.ca/topfind + id: '00000255' + name: TopFind + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: topfind + sampleId: Q9UKQ2 + uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1 + n2t: + description: 'TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.' + example: Q9UKQ2 + homepage: http://clipserve.clip.ubc.ca/topfind + name: TopFind at University of British Columbia + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ + prefix: topfind + uri_format: http://clipserve.clip.ubc.ca/topfind/proteins/$1 + provides: uniprot +toxoplasma: + biocontext: + is_identifiers: true + is_obo: false + prefix: TOXOPLASMA + uri_format: http://identifiers.org/toxoplasma/$1 + mappings: + biocontext: TOXOPLASMA + miriam: toxoplasma + n2t: toxoplasma + miriam: + deprecated: false + description: ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: http://toxodb.org/toxo/ + id: '00000153' + name: ToxoDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: toxoplasma + sampleId: TGME49_053730 + uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + n2t: + description: ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: TGME49_053730 + homepage: http://toxodb.org/toxo/ + name: ToxoDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: toxoplasma + uri_format: http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +trans: + biocontext: + is_identifiers: false + is_obo: true + prefix: TRANS + uri_format: http://purl.obolibrary.org/obo/TRANS_$1 + bioportal: + name: Nurse Transitional + prefix: TRANS + example: '0000024' + fairsharing: + abbreviation: TRANS + description: This is an ontology of a transitional care nurse's process domain + id: '954' + name: Nurse Transitional + prefix: FAIRsharing.nygmp7 + subjects: [] + mappings: + biocontext: TRANS + bioportal: TRANS + fairsharing: FAIRsharing.nygmp7 + obofoundry: trans + ols: trans + ontobee: TRANS + obofoundry: + contact: lynn.schriml@gmail.com + contact.github: lschriml + contact.label: Lynn Schriml + contact.orcid: 0000-0001-8910-9851 + deprecated: false + description: An ontology representing the disease transmission process during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. + download.obo: http://purl.obolibrary.org/obo/trans.obo + download.owl: http://purl.obolibrary.org/obo/trans.owl + homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Pathogen Transmission Ontology + preferredPrefix: TRANS + prefix: trans + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/19850722 + title: GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database + - id: https://www.ncbi.nlm.nih.gov/pubmed/34755882 + title: The Human Disease Ontology 2022 update + repository: https://github.com/DiseaseOntology/PathogenTransmissionOntology + ols: + description: The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. + download: http://purl.obolibrary.org/obo/trans.owl + homepage: https://github.com/DiseaseOntology/PathogenTransmissionOntology + name: Pathogen Transmission Ontology + prefix: trans + version: 2020-08-04 + version.iri: http://purl.obolibrary.org/obo/trans/releases/2020-08-04/trans.owl + ontobee: + library: Library + name: Pathogen Transmission Ontology + prefix: TRANS + pattern: ^\d{7}$ +transyt: + mappings: + miriam: transyt + miriam: + deprecated: false + description: The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes. + homepage: https://www.bio.di.uminho.pt/ + id: '00000736' + name: TranSyT + namespaceEmbeddedInLui: false + pattern: T[A-Z]\d{7} + prefix: transyt + sampleId: TR0000001 + uri_format: https://transyt.bio.di.uminho.pt/reactions/$1 + name: Transport Systems Tracker +treebase: + biocontext: + is_identifiers: true + is_obo: false + prefix: TREEBASE + uri_format: http://identifiers.org/treebase/$1 + fairsharing: + abbreviation: TreeBase + description: TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. + id: '2072' + name: TreeBase + prefix: FAIRsharing.zcn4w4 + subjects: + - Phylogenetics + - Phylogenomics + mappings: + biocontext: TREEBASE + fairsharing: FAIRsharing.zcn4w4 + miriam: treebase + n2t: treebase + prefixcommons: treebase + miriam: + deprecated: false + description: TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. + homepage: http://treebase.org/ + id: '00000312' + name: TreeBASE + namespaceEmbeddedInLui: false + pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$ + prefix: treebase + sampleId: TB2:S1000 + uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html + n2t: + description: TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. + example: TB2:S1000 + homepage: http://treebase.org/ + name: TreeBASE (hosted at National Evolutionary Synthesis Center) + namespaceEmbeddedInLui: false + pattern: ^TB[1,2]?:[A-Z][a-z]?\d+$ + prefix: treebase + uri_format: http://purl.org/phylo/treebase/phylows/study/$1?format=html + prefixcommons: + description: TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. + example: '1245' + homepage: http://www.treebase.org/ + keywords: + - classification + name: TreeBase + pattern: ^\d+$ + prefix: treebase + uri_format: http://www.treebase.org/treebase-web/search/study/summary.html?id=$1 +treefam: + biocontext: + is_identifiers: true + is_obo: false + prefix: TREEFAM + uri_format: http://identifiers.org/treefam/$1 + mappings: + biocontext: TREEFAM + miriam: treefam + n2t: treefam + prefixcommons: treefam + uniprot: TreeFam + miriam: + deprecated: false + description: TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. + homepage: http://www.treefam.org/ + id: '00000395' + name: TreeFam + namespaceEmbeddedInLui: false + pattern: ^\w{1,2}\d+$ + prefix: treefam + sampleId: TF101014 + uri_format: http://www.treefam.org/family/$1 + n2t: + description: TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. + example: TF101014 + homepage: http://www.treefam.org/ + name: TreeFam database + namespaceEmbeddedInLui: false + pattern: ^\w{1,2}\d+$ + prefix: treefam + uri_format: http://www.treefam.org/family/$1 + prefixcommons: + description: TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. + example: TF101142 + homepage: http://www.treefam.org + keywords: + - gene + - classification + name: TreeFam + pattern: ^TF\d+$ + prefix: treefam + uri_format: http://www.treefam.org/cgi-bin/TFinfo.pl?ac=$1 + uniprot: + category: Phylogenomic databases + identifier: '185' + link_is_explicit: 'true' + name: TreeFam database of animal gene trees + prefix: TreeFam + uri_format: http://www.treefam.org/family/$1 +trichdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: TRICHDB + uri_format: http://identifiers.org/trichdb/$1 + fairsharing: + abbreviation: TrichDB + description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: '1884' + name: TrichDB + prefix: FAIRsharing.pv0ezt + subjects: + - Life Science + mappings: + biocontext: TRICHDB + fairsharing: FAIRsharing.pv0ezt + miriam: trichdb + n2t: trichdb + miriam: + deprecated: false + description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: http://trichdb.org/trichdb/ + id: '00000154' + name: TrichDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: trichdb + sampleId: TVAG_386080 + uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + n2t: + description: TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: TVAG_386080 + homepage: http://trichdb.org/trichdb/ + name: TrichDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: trichdb + uri_format: http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +tritrypdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: TRITRYPDB + uri_format: http://identifiers.org/tritrypdb/$1 + fairsharing: + abbreviation: TriTrypDB + description: TriTrypDB is one of the databases that can be accessed through the VEuPathDB portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the VEuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + id: '1885' + name: TriTrypDB + prefix: FAIRsharing.fs1z27 + subjects: + - Genomics + - Infectious Disease Medicine + - Comparative Genomics + go: + homepage: https://tritrypdb.org/ + name: TriTrypDB + prefix: TriTrypDB + uri_format: https://tritrypdb.org/tritrypdb/app/record/gene/$1 + mappings: + biocontext: TRITRYPDB + fairsharing: FAIRsharing.fs1z27 + go: TriTrypDB + miriam: tritrypdb + n2t: tritrypdb + miriam: + deprecated: false + description: TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + homepage: http://tritrypdb.org/tritrypdb/ + id: '00000155' + name: TriTrypDB + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?\w+(\.)?\w+ + prefix: tritrypdb + sampleId: Tb927.8.620 + uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 + n2t: + description: TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. + example: Tb927.8.620 + homepage: http://tritrypdb.org/tritrypdb/ + name: TriTrypDB at EuPathDB + namespaceEmbeddedInLui: false + pattern: ^\w+(\.)?\w+(\.)?\w+ + prefix: tritrypdb + uri_format: http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +ttd.drug: + biocontext: + is_identifiers: true + is_obo: false + prefix: TTD.DRUG + uri_format: http://identifiers.org/ttd.drug/$1 + mappings: + biocontext: TTD.DRUG + miriam: ttd.drug + n2t: ttd.drug + miriam: + deprecated: false + description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. + homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp + id: '00000092' + name: TTD Drug + namespaceEmbeddedInLui: false + pattern: ^DAP\d+$ + prefix: ttd.drug + sampleId: DAP000773 + uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1 + n2t: + description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. + example: DAP000773 + homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp + name: Therapeutic Target Database Drug + namespaceEmbeddedInLui: false + pattern: ^DAP\d+$ + prefix: ttd.drug + uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1 +ttd.target: + biocontext: + is_identifiers: true + is_obo: false + prefix: TTD.TARGET + uri_format: http://identifiers.org/ttd.target/$1 + mappings: + biocontext: TTD.TARGET + miriam: ttd.target + n2t: ttd.target + miriam: + deprecated: false + description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. + homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp + id: '00000093' + name: TTD Target + namespaceEmbeddedInLui: false + pattern: ^TTDS\d+$ + prefix: ttd.target + sampleId: TTDS00056 + uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1 + n2t: + description: The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. + example: TTDS00056 + homepage: http://bidd.nus.edu.sg/group/ttd/ttd.asp + name: Therapeutic Target Database Target + namespaceEmbeddedInLui: false + pattern: ^TTDS\d+$ + prefix: ttd.target + uri_format: http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1 +tto: + biocontext: + is_identifiers: false + is_obo: true + prefix: TTO + uri_format: http://purl.obolibrary.org/obo/TTO_$1 + bioportal: + name: Teleost Taxonomy Ontology + prefix: TTO + example: '1058367' + fairsharing: + abbreviation: TTO + description: This is an ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish. + id: '82' + name: Teleost Taxonomy Ontology + prefix: FAIRsharing.1rj558 + subjects: + - Life Science + mappings: + biocontext: TTO + bioportal: TTO + fairsharing: FAIRsharing.1rj558 + obofoundry: tto + ols: tto + ontobee: TTO + prefixcommons: tto + obofoundry: + contact: balhoff@renci.org + contact.github: balhoff + contact.label: Jim Balhoff + contact.orcid: 0000-0002-8688-6599 + deprecated: false + description: An ontology covering the taxonomy of teleosts (bony fish) + download.obo: http://purl.obolibrary.org/obo/tto.obo + download.owl: http://purl.obolibrary.org/obo/tto.owl + homepage: https://github.com/phenoscape/teleost-taxonomy-ontology + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Teleost taxonomy ontology + preferredPrefix: TTO + prefix: tto + publications: + - id: https://doi.org/10.1038/npre.2010.4629.1 + title: The Teleost Taxonomy Ontology + repository: https://github.com/phenoscape/teleost-taxonomy-ontology + ols: + description: An ontology covering the taxonomy of teleosts (bony fish) + download: http://purl.obolibrary.org/obo/tto.owl + homepage: https://github.com/phenoscape/teleost-taxonomy-ontology + name: Teleost taxonomy ontology + prefix: tto + version: 2018-03-26 + version.iri: http://purl.obolibrary.org/obo/tto/2012-05-18/tto.owl + ontobee: + library: Library + name: Teleost taxonomy ontology + prefix: TTO + pattern: ^\d+$ + prefixcommons: + bioportal: '1081' + description: The Teleost taxonomy ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. + example: TTO_2 + homepage: https://www.nescent.org/phenoscape/Main_Page + keywords: + - obo + - phenotype + - fish + name: Teleost taxonomy Ontology + pattern: ^TTO_\d$ + prefix: tto + uri_format: http://purl.obolibrary.org/obo/$1 + wikidata: + database: Q81661821 +txpo: + bioportal: + name: Toxic Process Ontology + prefix: TXPO + example: '0002066' + mappings: + bioportal: TXPO + obofoundry: txpo + ols: txpo + ontobee: TXPO + obofoundry: + contact: yuki.yamagata@riken.jp + contact.github: yuki-yamagata + contact.label: Yuki Yamagata + contact.orcid: 0000-0002-9673-1283 + deprecated: false + description: TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. + download.owl: http://purl.obolibrary.org/obo/txpo.owl + homepage: https://toxpilot.nibiohn.go.jp/ + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: Toxic Process Ontology + preferredPrefix: TXPO + prefix: txpo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/32883995 + title: Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management + repository: https://github.com/txpo-ontology/TXPO + ols: + description: >- + Elucidating the mechanism of toxicity is crucial in drug safety + evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of + terms involving toxicity courses and processes. The first version of TXPO + focuses on liver toxicity. + + + The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. + + + In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp + download: http://purl.obolibrary.org/obo/txpo.owl + homepage: https://toxpilot.nibiohn.go.jp/ + name: TOXic Process Ontology (TXPO) + prefix: txpo + version: 2020-07-09 + version.iri: http://purl.obolibrary.org/obo/txpo/releases/2020-03-03/txpo.owl + ontobee: + library: Library + name: Toxic Process Ontology + prefix: TXPO + pattern: ^\d{7}$ +uberon: + biocontext: + is_identifiers: false + is_obo: true + prefix: UBERON + uri_format: http://purl.obolibrary.org/obo/UBERON_$1 + bioportal: + name: Uber Anatomy Ontology + prefix: UBERON + cellosaurus: + category: Anatomy/cell type resources + homepage: https://uberon.github.io/ + name: Uber-anatomy ontology + prefix: UBERON + uri_format: https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1 + download_obo: http://purl.obolibrary.org/obo/uberon/basic.obo + example: '2005080' + fairsharing: + abbreviation: UBERON + description: Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. It represents a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. + id: '1197' + name: UBER anatomy ONtology + prefix: FAIRsharing.4c0b6b + subjects: + - Anatomy + - Taxonomy + - Developmental Biology + - Life Science + go: + description: A multi-species anatomy ontology + homepage: http://uberon.org + name: Uber-anatomy ontology + prefix: UBERON + mappings: + biocontext: UBERON + bioportal: UBERON + cellosaurus: UBERON + fairsharing: FAIRsharing.4c0b6b + go: UBERON + miriam: uberon + n2t: uberon + obofoundry: uberon + ols: uberon + ontobee: UBERON + miriam: + deprecated: false + description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. + homepage: http://bioportal.bioontology.org/ontologies/UBERON + id: '00000446' + name: UBERON + namespaceEmbeddedInLui: true + pattern: ^UBERON:\d+$ + prefix: uberon + sampleId: '0008203' + uri_format: http://purl.bioontology.org/ontology/UBERON/UBERON:$1 + n2t: + description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. + example: '0008203' + homepage: http://bioportal.bioontology.org/ontologies/UBERON + name: UBERON through bioPortal + namespaceEmbeddedInLui: true + pattern: ^UBERON\:\d+$ + prefix: uberon + uri_format: http://purl.bioontology.org/ontology/UBERON/UBERON:$1 + name: Uber Anatomy Ontology + obofoundry: + appears_in: + - go + - aism + - amphx + - chiro + - cl + - clo + - clyh + - colao + - cteno + - ecao + - ecocore + - ecto + - envo + - foodon + - fovt + - genepio + - hso + - lepao + - maxo + - mco + - mfmo + - ons + - pcl + - plana + - poro + - zp + contact: cjmungall@lbl.gov + contact.github: cmungall + contact.label: Chris Mungall + contact.orcid: 0000-0002-6601-2165 + depends_on: + - chebi + - cl + - go + - pr + deprecated: false + description: An integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies + download.owl: http://purl.obolibrary.org/obo/uberon.owl + homepage: http://uberon.org + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Uberon multi-species anatomy ontology + preferredPrefix: UBERON + prefix: uberon + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22293552 + title: Uberon, an integrative multi-species anatomy ontology + - id: https://www.ncbi.nlm.nih.gov/pubmed/25009735 + title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon + repository: https://github.com/obophenotype/uberon + twitter: uberanat + ols: + description: Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. + download: http://purl.obolibrary.org/obo/uberon.owl + homepage: http://uberon.org + name: Uber-anatomy ontology + prefix: uberon + version: 2022-04-18 + version.iri: http://purl.obolibrary.org/obo/uberon/releases/2022-04-18/uberon.owl + ontobee: + library: Library + name: Uberon multi-species anatomy ontology + prefix: UBERON + pattern: ^\d+$ + synonyms: + - UBERON + - Uber-anatomy ontology + - Uberon + wikidata: + prefix: P1554 +ubio.namebank: + biocontext: + is_identifiers: true + is_obo: false + prefix: UBIO.NAMEBANK + uri_format: http://identifiers.org/ubio.namebank/$1 + mappings: + biocontext: UBIO.NAMEBANK + miriam: ubio.namebank + n2t: ubio.namebank + miriam: + deprecated: false + description: NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. + homepage: http://www.ubio.org + id: '00000338' + name: uBio NameBank + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ubio.namebank + sampleId: '2555646' + uri_format: http://www.ubio.org/browser/details.php?namebankID=$1 + n2t: + description: NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. + example: '2555646' + homepage: http://www.ubio.org + name: uBio NameBank at The Marine Biological Laboratory + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: ubio.namebank + uri_format: http://www.ubio.org/browser/details.php?namebankID=$1 +ubprop: + comment: All of these are typedefs in uberon now + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + name: Uberon Property +ucsc: + biocontext: + is_identifiers: false + is_obo: false + prefix: UCSC + uri_format: ftp://hgdownload.cse.ucsc.edu/goldenPath/$1 + description: The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. + example: uc001rvw.5 + homepage: https://genome.ucsc.edu/ + mappings: + biocontext: UCSC + uniprot: UCSC + name: UCSC Genome Browser + uniprot: + category: Genome annotation databases + identifier: '139' + link_is_explicit: 'true' + name: UCSC genome browser + prefix: UCSC + uri_format: https://genome.ucsc.edu/cgi-bin/hgLinkIn?resource=uniprot&id=$1 + wikidata: + prefix: P2576 +umbbd.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: UMBBD.COMPOUND + uri_format: http://identifiers.org/umbbd.compound/$1 + mappings: + biocontext: UMBBD.COMPOUND + miriam: umbbd.compound + n2t: umbbd.compound + miriam: + deprecated: false + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information. + homepage: http://umbbd.ethz.ch/ + id: '00000276' + name: UM-BBD Compound + namespaceEmbeddedInLui: false + pattern: ^c\d+$ + prefix: umbbd.compound + sampleId: c0001 + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1 + n2t: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information. + example: c0001 + homepage: http://umbbd.ethz.ch/ + name: Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich + namespaceEmbeddedInLui: false + pattern: ^c\d+$ + prefix: umbbd.compound + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1 + part_of: umbbd + synonyms: + - UM-BBD_compID + uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1 + wikidata: + prefix: P8121 +umbbd.enzyme: + biocontext: + is_identifiers: true + is_obo: false + prefix: UMBBD.ENZYME + uri_format: http://identifiers.org/umbbd.enzyme/$1 + go: + homepage: http://eawag-bbd.ethz.ch/ + name: EAWAG Biocatalysis/Biodegradation Database + prefix: UM-BBD_enzymeID + uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1 + mappings: + biocontext: UMBBD.ENZYME + go: UM-BBD_enzymeID + miriam: umbbd.enzyme + n2t: umbbd.enzyme + miriam: + deprecated: false + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information. + homepage: http://umbbd.ethz.ch/ + id: '00000326' + name: UM-BBD Enzyme + namespaceEmbeddedInLui: false + pattern: ^e\d+$ + prefix: umbbd.enzyme + sampleId: e0333 + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1 + n2t: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information. + example: e0333 + homepage: http://umbbd.ethz.ch/ + name: Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich + namespaceEmbeddedInLui: false + pattern: ^e\d+$ + prefix: umbbd.enzyme + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1 + part_of: umbbd + synonyms: + - UM-BBD_enzymeID + uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1 +umbbd.pathway: + biocontext: + is_identifiers: true + is_obo: false + prefix: UMBBD.PATHWAY + uri_format: http://identifiers.org/umbbd.pathway/$1 + go: + homepage: http://eawag-bbd.ethz.ch/ + name: EAWAG Biocatalysis/Biodegradation Database + prefix: UM-BBD_pathwayID + uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html + mappings: + biocontext: UMBBD.PATHWAY + go: UM-BBD_pathwayID + miriam: umbbd.pathway + n2t: umbbd.pathway + miriam: + deprecated: false + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information. + homepage: http://umbbd.ethz.ch/ + id: '00000327' + name: UM-BBD Pathway + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: umbbd.pathway + sampleId: ala + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1 + n2t: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information. + example: ala + homepage: http://umbbd.ethz.ch/ + name: Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: umbbd.pathway + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1 + part_of: umbbd + synonyms: + - UM-BBD_pathwayID + uri_format: http://eawag-bbd.ethz.ch/$1/$1_map.html +umbbd.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: UMBBD.REACTION + uri_format: http://identifiers.org/umbbd.reaction/$1 + go: + homepage: http://eawag-bbd.ethz.ch/ + name: EAWAG Biocatalysis/Biodegradation Database + prefix: UM-BBD_reactionID + uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1 + mappings: + biocontext: UMBBD.REACTION + go: UM-BBD_reactionID + miriam: umbbd.reaction + n2t: umbbd.reaction + miriam: + deprecated: false + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. + homepage: http://umbbd.ethz.ch/ + id: '00000325' + name: UM-BBD Reaction + namespaceEmbeddedInLui: false + pattern: ^r\d+$ + prefix: umbbd.reaction + sampleId: r0001 + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1 + n2t: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. + example: r0001 + homepage: http://umbbd.ethz.ch/ + name: Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich + namespaceEmbeddedInLui: false + pattern: ^r\d+$ + prefix: umbbd.reaction + uri_format: http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1 + part_of: umbbd + synonyms: + - UM-BBD_reactionID + uri_format: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1 + wikidata: + database: Q24188985 +umbbd.rule: + biocontext: + is_identifiers: true + is_obo: false + prefix: UMBBD.RULE + uri_format: http://identifiers.org/umbbd.rule/$1 + go: + homepage: http://eawag-bbd.ethz.ch/ + name: EAWAG Biocatalysis/Biodegradation Database + prefix: UM-BBD_ruleID + uri_format: http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=$1 + mappings: + biocontext: UMBBD.RULE + go: UM-BBD_ruleID + miriam: umbbd.rule + n2t: umbbd.rule + miriam: + deprecated: false + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules. + homepage: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules + id: '00000328' + name: UM-BBD Biotransformation Rule + namespaceEmbeddedInLui: false + pattern: ^bt\d+$ + prefix: umbbd.rule + sampleId: bt0001 + uri_format: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1 + n2t: + description: The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules. + example: bt0001 + homepage: http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules + name: Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at ETH Zurich + namespaceEmbeddedInLui: false + pattern: ^bt\d+$ + prefix: umbbd.rule + uri_format: http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1 + part_of: umbbd + synonyms: + - UM-BBD_ruleID +umls: + biocontext: + is_identifiers: false + is_obo: false + prefix: UMLS + uri_format: http://linkedlifedata.com/resource/umls/id/$1 + example: C2584994 + homepage: https://www.nlm.nih.gov/research/umls + mappings: + biocontext: UMLS + miriam: umls + n2t: umls + miriam: + deprecated: false + description: The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. + homepage: http://linkedlifedata.com/ + id: '00000559' + name: UMLS + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: umls + sampleId: C0021390 + uri_format: http://linkedlifedata.com/resource/umls/id/$1 + n2t: + description: The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. + example: C0021390 + homepage: http://linkedlifedata.com/ + name: Unified Medical Language System at LinkedLifeData + namespaceEmbeddedInLui: false + pattern: ^C\d+$ + prefix: umls + uri_format: http://linkedlifedata.com/resource/umls/id/$1 + name: Unified Medical Language System Concept Unique Identifier + synonyms: + - UMLS + - UMLS CUI + - UMLS_CUI + - umls.cui + wikidata: + prefix: P2892 +umls.aui: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus. + example: A0118748 + homepage: https://www.nlm.nih.gov/research/umls + name: Unified Medical Language System Atomic Unique Identifier + pattern: ^A\d+$ + synonyms: + - UMLS_ICD9CM_2005_AUI +unigene: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNIGENE + uri_format: http://identifiers.org/unigene/$1 + fairsharing: + abbreviation: UniGene + description: Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + id: '1993' + name: UniGene gene-oriented nucleotide sequence clusters + prefix: FAIRsharing.ge1c3p + subjects: + - Life Science + mappings: + biocontext: UNIGENE + fairsharing: FAIRsharing.ge1c3p + miriam: unigene + n2t: unigene + prefixcommons: unigene + miriam: + deprecated: false + description: A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + homepage: http://www.ncbi.nlm.nih.gov/unigene + id: '00000346' + name: UniGene + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unigene + sampleId: '4900' + uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1 + n2t: + description: A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + example: '4900' + homepage: http://www.ncbi.nlm.nih.gov/unigene + name: UniGene at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unigene + uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1 + prefixcommons: + description: Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + example: '4900' + homepage: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene + keywords: + - DNA + - gene + - gene expression + - protein + name: UniGene gene-oriented nucleotide sequence clusters + pattern: ^\d+$ + prefix: unigene + uri_format: http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1 +unii: + biocontext: + is_identifiers: false + is_obo: false + prefix: UNII + uri_format: http://fdasis.nlm.nih.gov/srs/unii/$1 + cheminf: + description: Identifier used by the USA Food and Drug Administration. + name: Unique Ingredient Identifier + obsolete: false + prefix: '000563' + mappings: + biocontext: UNII + cheminf: '000563' + miriam: unii + n2t: unii + miriam: + deprecated: false + description: The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information. + homepage: http://fdasis.nlm.nih.gov/srs/ + id: '00000531' + name: UNII + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: unii + sampleId: 3G6A5W338E + uri_format: http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1 + n2t: + description: The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information. + example: 3G6A5W338E + homepage: http://fdasis.nlm.nih.gov/srs/ + name: UNII at U.S. Food and Drug Administration + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: unii + uri_format: http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1 + name: Unique Ingredient Identifier + wikidata: + prefix: P652 +unimod: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNIMOD + uri_format: http://identifiers.org/unimod/$1 + fairsharing: + abbreviation: Unimod + description: Unimod is a community-supported, comprehensive database of protein modifications for mass spectrometry applications. The aim is to provide accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). + id: '2796' + name: Unimod + prefix: FAIRsharing.zZHCUQ + subjects: + - Bioinformatics + mappings: + biocontext: UNIMOD + fairsharing: FAIRsharing.zZHCUQ + miriam: unimod + n2t: unimod + ols: unimod + miriam: + deprecated: false + description: Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). + homepage: http://www.unimod.org/ + id: '00000447' + name: Unimod + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unimod + sampleId: '1200' + uri_format: http://www.unimod.org/modifications_view.php?editid1=$1 + n2t: + description: Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). + example: '1200' + homepage: http://www.unimod.org/ + name: Unimod at Matrix Sciences Ltd. + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unimod + uri_format: http://www.unimod.org/modifications_view.php?editid1=$1 + ols: + contact: psidev-ms-vocab@lists.sourceforge.net + description: Unimod is a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, an d site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). + download: http://www.unimod.org/obo/unimod.obo + homepage: http://www.unimod.org/ + name: Unimod protein modification database for mass spectrometry + prefix: unimod +uniparc: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNIPARC + uri_format: http://identifiers.org/uniparc/$1 + go: + description: A non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office + homepage: https://www.uniprot.org/uniparc/ + name: UniProt Archive + prefix: UniParc + uri_format: https://www.uniprot.org/uniparc/$1 + mappings: + biocontext: UNIPARC + go: UniParc + miriam: uniparc + n2t: uniparc + prefixcommons: uniparc + miriam: + deprecated: false + description: The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. + homepage: https://www.ebi.ac.uk/uniparc/ + id: '00000041' + name: UniParc + namespaceEmbeddedInLui: false + pattern: ^UPI[A-F0-9]{10}$ + prefix: uniparc + providers: + - code: CURATOR_REVIEW + description: UniParc through UniProt + homepage: http://www.uniprot.org/uniparc/ + name: UniParc through UniProt + uri_format: https://www.uniprot.org/uniparc/$1 + sampleId: UPI000000000A + uri_format: https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1 + n2t: + description: The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. + example: UPI000000000A + homepage: http://www.uniprot.org/uniparc/ + name: UniParc through UniProt + namespaceEmbeddedInLui: false + pattern: ^UPI[A-F0-9]{10}$ + prefix: uniparc + uri_format: http://www.uniprot.org/uniparc/$1 + prefixcommons: + description: The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. + example: UPI000000000A + homepage: http://www.ebi.ac.uk/uniparc/ + keywords: + - protein + - structure + name: UniProt Archive + pattern: ^UPI[A-F0-9]{10}$ + prefix: uniparc + pubmed_ids: + - '14681372' + uri_format: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1 +unipathway.compound: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNIPATHWAY.COMPOUND + uri_format: http://identifiers.org/unipathway.compound/$1 + mappings: + biocontext: UNIPATHWAY.COMPOUND + miriam: unipathway.compound + n2t: unipathway.compound + miriam: + deprecated: false + description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds. + id: '00000551' + name: UniPathway Compound + namespaceEmbeddedInLui: false + pattern: ^UPC\d{5}$ + prefix: unipathway.compound + sampleId: UPC04349 + n2t: + description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds. + example: UPC04349 + homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway + name: UniPathway Compound at Swiss Institute of Bioinformatics (SIB) + namespaceEmbeddedInLui: false + pattern: ^UPC\d{5}$ + prefix: unipathway.compound + uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1 +unipathway.reaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNIPATHWAY.REACTION + uri_format: http://identifiers.org/unipathway.reaction/$1 + mappings: + biocontext: UNIPATHWAY.REACTION + miriam: unipathway.reaction + n2t: unipathway.reaction + miriam: + deprecated: false + description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions. + id: '00000570' + name: UniPathway Reaction + namespaceEmbeddedInLui: false + pattern: ^UCR\d{5}$ + prefix: unipathway.reaction + sampleId: UCR00226 + n2t: + description: UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions. + example: UCR00226 + homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway + name: UniPathway Reaction at Swiss Institute of Bioinformatics (SIB) + namespaceEmbeddedInLui: false + pattern: ^UCR\d{5}$ + prefix: unipathway.reaction + uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1 +uniprot: + biocontext: + is_identifiers: true + is_obo: false + prefix: UniProtKB + uri_format: http://identifiers.org/uniprot/$1 + cellosaurus: + category: Sequence databases + name: UniProt knowledgebase + prefix: UniProtKB + uri_format: https://www.uniprot.org/uniprot/$1 + fairsharing: + abbreviation: UniProtKB + description: 'The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").' + id: '2077' + name: UniProt Knowledgebase + prefix: FAIRsharing.s1ne3g + subjects: + - Functional Genomics + - Life Science + go: + description: A central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR database + homepage: http://www.uniprot.org + name: Universal Protein Knowledgebase + prefix: UniProtKB + uri_format: https://www.uniprot.org/uniprot/$1 + homepage: http://www.uniprot.org + mappings: + biocontext: UniProtKB + cellosaurus: UniProtKB + fairsharing: FAIRsharing.s1ne3g + go: UniProtKB + miriam: uniprot + n2t: uniprot + ncbi: UniProt + prefixcommons: uniprot + scholia: uniprot + wikidata: P352 + miriam: + deprecated: false + description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. + homepage: https://www.uniprot.org/ + id: '00000005' + name: UniProt Knowledgebase + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ + prefix: uniprot + providers: + - code: ncbi + description: UniProt through NCBI + homepage: https://www.ncbi.nlm.nih.gov/protein/ + name: UniProt through NCBI + uri_format: https://www.ncbi.nlm.nih.gov/protein/$1 + sampleId: P0DP23 + uri_format: http://purl.uniprot.org/uniprot/$1 + n2t: + description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. + example: P0DP23 + homepage: https://www.uniprot.org/ + name: Universal Protein Resource using Persistent URL system + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ + prefix: uniprot + uri_format: https://purl.uniprot.org/uniprot/$1 + name: UniProt Protein + ncbi: + example: P12345 + homepage: http://www.uniprot.org + name: section of the UniProt Knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature + prefix: UniProt + prefixcommons: + description: UniProtKB consists of the manually annotated and reviewed Swiss-Prot, the automatically annotated TrEMBL, and the PIR protein databases. + example: P62158 + homepage: http://www.uniprot.org/ + keywords: + - protein + name: UniProt Knowledgebase + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ + prefix: uniprot + pubmed_ids: + - '16381842' + uri_format: http://www.uniprot.org/uniprot/$1 + providers: + - code: omnipath + description: Molecular interations endpoint from OmniPathDB + homepage: https://omnipathdb.org/ + name: OmniPathDB + uri_format: https://omnipathdb.org/interactions/?fields=sources,references&partners=$1 + - code: iptmnet + description: Protein post translational modification information + homepage: https://research.bioinformatics.udel.edu/iptmnet + name: iPTMnet + uri_format: https://research.bioinformatics.udel.edu/iptmnet/entry/$1 + - code: indra + description: A large scale database of biomedical statements. + homepage: https://db.indra.bio + name: INDRA Database + uri_format: https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@UP + synonyms: + - SwissProt + - UP + - UniProt + - UniProtKB + - Uniprot ID + - uniprot/swiss-prot + wikidata: + database: Q905695 + database.homepage: http://www.uniprot.org/ + database.label: UniProt + format.rdf: http://purl.uniprot.org/uniprot/$1 + homepage: http://mygene.info + name: UniProt protein ID + pattern: ([OPQ][0-9][A-Z0-9]|[A-NR-Z][0-9][A-Z])[A-Z0-9][A-Z0-9][0-9]([A-Z][A-Z0-9][A-Z0-9][0-9])? + prefix: P352 + uri_format: https://www.uniprot.org/uniprot/$1 +uniprot.chain: + mappings: + miriam: uniprot.chain + miriam: + deprecated: false + description: This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein. + homepage: https://www.uniprot.org + id: '00000739' + name: UniProt Chain + namespaceEmbeddedInLui: false + pattern: ^PRO_[0-9]{10}$ + prefix: uniprot.chain + sampleId: PRO_0000016681 + uri_format: http://purl.uniprot.org/annotation/$1 + part_of: uniprot + synonyms: + - UPPRO +uniprot.disease: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary. + download_obo: https://www.uniprot.org/diseases/?query=*&format=obo + example: '04240' + homepage: https://www.uniprot.org/diseases/ + name: UniProt Diseases + part_of: uniprot + pattern: ^\d{5}$ + synonyms: + - DI + - SP_DI + uri_format: https://www.uniprot.org/diseases/DI-$1 +uniprot.isoform: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNIPROT.ISOFORM + uri_format: http://identifiers.org/uniprot.isoform/$1 + mappings: + biocontext: UNIPROT.ISOFORM + miriam: uniprot.isoform + n2t: uniprot.isoform + miriam: + deprecated: false + description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. + homepage: http://www.uniprot.org/ + id: '00000388' + name: UniProt Isoform + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ + prefix: uniprot.isoform + providers: + - code: CURATOR_REVIEW + description: UniProt Isoform through Universal Protein Resource using Persistent URL system + homepage: http://purl.uniprot.org/ + name: UniProt Isoform through Universal Protein Resource using Persistent URL system + uri_format: http://purl.uniprot.org/uniprot/$1 + - code: CURATOR_REVIEW + description: UniProt Isoform through UniParc + homepage: http://www.uniprot.org/uniparc/ + name: UniProt Isoform through UniParc + uri_format: http://www.uniprot.org/uniparc/?query=$1 + sampleId: Q5BJF6-3 + uri_format: http://www.uniprot.org/uniprot/$1 + n2t: + description: The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. + example: Q5BJF6-3 + homepage: http://www.uniprot.org/uniparc/ + name: UniProt Isoform through UniParc + namespaceEmbeddedInLui: false + pattern: ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ + prefix: uniprot.isoform + uri_format: http://www.uniprot.org/uniparc/?query=$1 + part_of: uniprot + synonyms: + - UPISO +uniprot.keyword: + description: UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. + download_obo: https://www.uniprot.org/keywords/?format=obo + example: '1273' + go: + homepage: http://www.uniprot.org/keywords/ + name: UniProt Knowledgebase keywords + prefix: UniProtKB-KW + synonyms: + - SP_KW + uri_format: https://www.uniprot.org/keywords/$1 + mappings: + go: UniProtKB-KW + name: UniProt Keywords + part_of: uniprot + pattern: ^\d{4}$ + synonyms: + - SP_KW + - UniProtKB-KW + - uniprot.keyword + uri_format: https://www.uniprot.org/keywords/KW-$1 +uniprot.location: + description: The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms. + download_obo: https://www.uniprot.org/locations/?query=*&format=obo + example: '0002' + go: + homepage: https://www.uniprot.org/locations/ + name: UniProt Knowledgebase Subcellular Location vocabulary + prefix: UniProtKB-SubCell + synonyms: + - SP_SL + uri_format: http://www.uniprot.org/locations/$1 + homepage: https://www.uniprot.org/locations/ + mappings: + go: UniProtKB-SubCell + name: UniProt Subcellular Locations + part_of: uniprot + pattern: ^\d+$ + synonyms: + - SP_SL + - UPLOC + - UniProtKB-SubCell + uri_format: https://www.uniprot.org/locations/SL-$1 +uniprot.ptm: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format + example: '0450' + homepage: https://www.uniprot.org/docs/ptmlist + name: UniProt Post-Translational Modification + part_of: uniprot + pattern: ^\d{4}$ + references: + - https://twitter.com/cthoyt/status/1510570256619778053 + - https://www.uniprot.org/docs/ptmlist.txt + synonyms: + - PTM +uniprot.resource: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources. + example: '0174' + homepage: https://www.uniprot.org/database/ + name: UniProt Resource + part_of: uniprot + pattern: ^\d{4}$ + uri_format: https://www.uniprot.org/database/DB-$1 +uniprot.tissue: + biocontext: + is_identifiers: true + is_obo: false + prefix: TISSUELIST + uri_format: http://identifiers.org/tissuelist/$1 + example: '0285' + mappings: + biocontext: TISSUELIST + miriam: tissuelist + n2t: tissuelist + miriam: + deprecated: false + description: The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified. + homepage: https://www.uniprot.org/docs/tisslist.txt + id: '00000360' + name: Tissue List + namespaceEmbeddedInLui: false + pattern: ^TS-\d{4}$ + prefix: tissuelist + sampleId: TS-0285 + uri_format: https://www.uniprot.org/tissues/$1 + n2t: + description: The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified. + example: TS-0285 + homepage: https://www.uniprot.org/docs/tisslist.txt + name: Tissue List at Swiss Institute of Bioinformatics + namespaceEmbeddedInLui: false + pattern: ^TS-\d{4}$ + prefix: tissuelist + uri_format: https://www.uniprot.org/tissues/$1 + part_of: uniprot + pattern: ^\d{4}$ + uri_format: https://www.uniprot.org/tissues/TS-$1 +uniprot.var: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.' + example: '068078' + homepage: https://web.expasy.org/variant_pages + name: UniProt Variants + part_of: uniprot + pattern: ^\d+$ + synonyms: + - SP_VAR + - UPVAR + - UniProtKB_VAR + uri_format: https://web.expasy.org/variant_pages/VAR_$1.html +uniref: + mappings: + miriam: uniref + miriam: + deprecated: false + description: The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view. + homepage: https://www.uniprot.org/ + id: '00000878' + name: UniRef + namespaceEmbeddedInLui: false + pattern: ^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$ + prefix: uniref + sampleId: UniRef90_P00750 + uri_format: https://www.uniprot.org/uniref/$1 +unirule: + description: Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites. + example: UR000124451 + go: + homepage: https://www.uniprot.org/unirule/ + name: Manually curated rules for automatic annotation of UniProtKB unreviewed entries + prefix: UniRule + uri_format: https://www.uniprot.org/unirule/$1 + homepage: https://www.uniprot.org/unirule/ + mappings: + go: UniRule + name: UniRule + uri_format: https://www.uniprot.org/unirule/$1 +unists: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNISTS + uri_format: http://identifiers.org/unists/$1 + mappings: + biocontext: UNISTS + miriam: unists + n2t: unists + ncbi: UniSTS + prefixcommons: unists + miriam: + deprecated: false + description: UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists + id: '00000162' + name: UniSTS + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unists + sampleId: '456789' + uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1 + n2t: + description: UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. + example: '456789' + homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists + name: UniSTS at NCBI + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: unists + uri_format: https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1 + ncbi: + example: '486599' + name: Database of Sequence Tagged Sites + prefix: UniSTS + prefixcommons: + description: UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. + example: '456789' + homepage: http://www.ncbi.nlm.nih.gov/unists + keywords: + - gene + - protein + name: NCBI UniSTS + pattern: ^\d+$ + prefix: unists + uri_format: http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=[?id] +unite: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNITE + uri_format: http://identifiers.org/unite/$1 + fairsharing: + abbreviation: + description: 'UNITE is a database and sequence management environment centered on the eukaryotic nuclear ribosomal ITS region. All eukaryotic ITS sequences from the International Nucleotide Sequence Database Collaboration are clustered to approximately the species level (distance between species in steps of 0.5%), and all such species hypotheses are given a DOI to facilitate unambiguous scientific communication and data assembly. The user can interact with these species hypotheses (e.g., SH1566366.08FU) in various ways, and third-party sequence and metadata annotation are supported. Registration is needed to access the more powerful features of the accompanying PlutoF workbench. A range of search and query options are available, and precompiled reference datasets for local sequence similarity searches and HTS pipelines are available for download. Owing to the mycological roots of UNITE, two versions of the release files are available: all eukaryotes (including fungi), and fungi only. UNITE is a community effort that relies on the scientific expertise of its users – please consider contributing by, e.g., annotating sequences of your taxa of expertise.' + id: '2110' + name: UNITE + prefix: FAIRsharing.cnwx8c + subjects: + - Metagenomics + - Genomics + - Bioinformatics + - Taxonomy + - Ecology + - Biodiversity + mappings: + biocontext: UNITE + fairsharing: FAIRsharing.cnwx8c + miriam: unite + n2t: unite + ncbi: UNITE + prefixcommons: unite + miriam: + deprecated: false + description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. + homepage: http://unite.ut.ee/ + id: '00000352' + name: Unite + namespaceEmbeddedInLui: false + pattern: ^UDB\d{6}$ + prefix: unite + sampleId: UDB000691 + uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1 + n2t: + description: UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. + example: UDB000691 + homepage: http://unite.ut.ee/ + name: Unite at University of Tartu + namespaceEmbeddedInLui: false + pattern: ^UDB\d{6}$ + prefix: unite + uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1 + ncbi: + example: UDB000157 + homepage: http://unite.ut.ee/index.php + name: Molecular database for the identification of fungi + prefix: UNITE + prefixcommons: + description: The UNITE is primarily a fungal rDNA ITS sequence database, although we also welcome additional genes and genetic markers. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. + example: UDB000691 + homepage: http://unite.ut.ee/index.php + keywords: + - DNA + name: Molecular database for the identification of fungi + pattern: ^UDB\d{6}$ + prefix: unite + pubmed_ids: + - '20409185' + uri_format: http://unite.ut.ee/bl_forw.php?nimi=$1 +unpd: + comment: The website is dead, there are no places to get the source information except inside https://oolonek.github.io/ISDB/. + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + homepage: http://pkuxxj.pku.edu.cn/UNPD/ + name: Universal Natural Products Database + references: + - http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database + - https://pharmacognosy.in/the-universal-natural-products-database-unpd/ + - https://pubs.acs.org/doi/abs/10.1021/acs.jnatprod.6b01093 + - https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062839 + - https://oolonek.github.io/ISDB/ +uo: + biocontext: + is_identifiers: false + is_obo: true + prefix: UO + uri_format: http://purl.obolibrary.org/obo/UO_$1 + bioportal: + name: Units of Measurement Ontology + prefix: UO + fairsharing: + abbreviation: UO + description: The Units Ontology (UO) models metrical units for use in conjunction with PATO. Units are basic scientific tools that render meaning to numerical data. Their standardization and formalization caters for the report, exchange, process, reproducibility and integration of quantitative measurements. The Units Ontology is an ontology currently being used for the standardized description of units of measurements. + id: '960' + name: Units Ontology + prefix: FAIRsharing.mjnypw + subjects: + - Mathematics + - Life Science + mappings: + biocontext: UO + bioportal: UO + fairsharing: FAIRsharing.mjnypw + miriam: uo + n2t: uo + obofoundry: uo + ols: uo + ontobee: UO + prefixcommons: uo + miriam: + deprecated: false + description: Ontology of standardized units + homepage: https://www.ebi.ac.uk/ols/ontologies/uo + id: '00000136' + name: Unit Ontology + namespaceEmbeddedInLui: true + pattern: ^UO:\d{7}? + prefix: uo + sampleId: '0000080' + uri_format: https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1 + n2t: + description: Ontology of standardized units + example: '0000080' + homepage: http://bioportal.bioontology.org/ontologies/UO + name: Unit Ontology through BioPortal + namespaceEmbeddedInLui: true + pattern: ^UO:\d{7}? + prefix: uo + uri_format: http://purl.bioontology.org/ontology/UO/UO:$1 + obofoundry: + appears_in: + - agro + - ms + - rbo + - scdo + contact: g.gkoutos@gmail.com + contact.github: gkoutos + contact.label: George Gkoutos + contact.orcid: 0000-0002-2061-091X + deprecated: false + description: Metrical units for use in conjunction with PATO + download.obo: http://purl.obolibrary.org/obo/uo.obo + download.owl: http://purl.obolibrary.org/obo/uo.owl + homepage: https://github.com/bio-ontology-research-group/unit-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Units of measurement ontology + preferredPrefix: UO + prefix: uo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/23060432 + title: 'The Units Ontology: a tool for integrating units of measurement in science' + repository: https://github.com/bio-ontology-research-group/unit-ontology + ols: + description: Metrical units for use in conjunction with PATO + download: http://purl.obolibrary.org/obo/uo.owl + homepage: https://github.com/bio-ontology-research-group/unit-ontology + name: Units of measurement ontology + prefix: uo + version: 2020-03-10 + version.iri: http://purl.obolibrary.org/obo/uo/releases/2020-03-10/uo.owl + ontobee: + library: Library + name: Units of measurement ontology + prefix: UO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1112' + description: Ontology of standardized units in conjunction with PATO + example: UO:0000080 + homepage: http://code.google.com/p/unit-ontology/ + keywords: + - obo + - ontology + name: Unit Ontology + pattern: ^UO:\d{7}?$ + prefix: uo + uri_format: http://www.ebi.ac.uk/ontology-lookup/?termId=$1 +upa: + biocontext: + is_identifiers: true + is_obo: false + prefix: UNIPATHWAY + uri_format: http://identifiers.org/unipathway/$1 + bioportal: + name: Unipathway + prefix: UPA + deprecated: true + download_obo: https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo + example: UCR00513 + go: + description: UniPathway is a a metabolic door to UniProtKB/Swiss-Prot, a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. + homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway + name: UniPathway + prefix: UniPathway + uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1 + mappings: + biocontext: UNIPATHWAY + bioportal: UPA + go: UniPathway + obofoundry: upa + ols: upa + ontobee: UPA + prefixcommons: unipathway + uniprot: UniPathway + obofoundry: + contact: Anne.Morgat@sib.swiss + contact.github: amorgat + contact.label: Anne Morgat + contact.orcid: 0000-0002-1216-2969 + depends_on: + - ro + deprecated: true + description: A manually curated resource for the representation and annotation of metabolic pathways + download.obo: http://purl.obolibrary.org/obo/upa.obo + download.owl: http://purl.obolibrary.org/obo/upa.owl + homepage: https://github.com/geneontology/unipathway + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Unipathway + prefix: upa + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22102589 + title: 'UniPathway: a resource for the exploration and annotation of metabolic pathways' + repository: https://github.com/geneontology/unipathway + ols: + description: A manually curated resource for the representation and annotation of metabolic pathways + download: http://purl.obolibrary.org/obo/upa.owl + homepage: https://github.com/geneontology/unipathway + name: Unipathway + prefix: upa + version: 2018-12-12 + version.iri: http://purl.obolibrary.org/obo/upa/releases/2018-12-12/upa.owl + ontobee: + library: Library + name: Unipathway + prefix: UPA + pattern: ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$ + prefixcommons: + description: UniPathway is a manually curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway. + example: UPA00206 + homepage: http://www.grenoble.prabi.fr/obiwarehouse/unipathway + keywords: + - pathway + name: UniPathway, a metabolic door to UniProtKB/Swiss-Prot + pattern: ^UPA\d{5}$ + prefix: unipathway + uri_format: http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1 + synonyms: + - UPa + - unipathway + - unipathway.pathway + uniprot: + category: Enzyme and pathway databases + identifier: '170' + link_is_explicit: 'true' + name: 'UniPathway: a resource for the exploration and annotation of metabolic pathways' + prefix: UniPathway + uri_format: http://www.unipathway.org?upid=%s&entryac=%u + wikidata: + database: Q85719315 +upheno: + biocontext: + is_identifiers: false + is_obo: true + prefix: UPHENO + uri_format: http://purl.obolibrary.org/obo/UPHENO_$1 + bioportal: + name: Combined Phenotype Ontology + prefix: UPHENO + download_owl: https://github.com/obophenotype/upheno/blob/master/upheno.owl + fairsharing: + abbreviation: UPHENO + description: Combined phenotype ontology + id: '303' + name: Combined Phenotype Ontology + prefix: FAIRsharing.r41qhx + subjects: [] + mappings: + biocontext: UPHENO + bioportal: UPHENO + fairsharing: FAIRsharing.r41qhx + obofoundry: upheno + ols: upheno + ontobee: UPHENO + name: Unified Phenotype Ontology + no_own_terms: true + obofoundry: + contact: vasilevs@ohsu.edu + contact.github: nicolevasilevsky + contact.label: Nicole Vasilevsky + contact.orcid: 0000-0001-5208-3432 + deprecated: false + description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. + download.owl: http://purl.obolibrary.org/obo/upheno.owl + homepage: https://github.com/obophenotype/upheno + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Unified phenotype ontology (uPheno) + preferredPrefix: UPHENO + prefix: upheno + publications: + - id: https://zenodo.org/record/2382757 + title: Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species + - id: https://zenodo.org/record/3352149 + title: 'Phenotype Ontologies Traversing All The Organisms (POTATO) workshop: 2nd edition' + repository: https://github.com/obophenotype/upheno + ols: + description: The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. + download: http://purl.obolibrary.org/obo/upheno.owl + homepage: https://github.com/obophenotype/upheno + name: Unified phenotype ontology (uPheno) + prefix: upheno + version: 2017-10-31 + ontobee: + library: Library + name: Unified phenotype ontology (uPheno) + prefix: UPHENO +uspto: + biocontext: + is_identifiers: true + is_obo: false + prefix: USPTO + uri_format: http://identifiers.org/uspto/$1 + mappings: + biocontext: USPTO + miriam: uspto + n2t: uspto + miriam: + deprecated: false + description: The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. + homepage: http://patft.uspto.gov/netahtml/PTO/index.html + id: '00000538' + name: USPTO + namespaceEmbeddedInLui: false + pattern: ^(D|PP|R|T|H|X|AI)?\d+$ + prefix: uspto + sampleId: '4145692' + uri_format: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1 + n2t: + description: The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. + example: '4145692' + homepage: http://patft.uspto.gov/netahtml/PTO/index.html + name: USPTO patents at USPTO + namespaceEmbeddedInLui: false + pattern: ^(D|PP|R|T|H|X|AI)?\d+$ + prefix: uspto + uri_format: http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1 + name: United States Patent and Trademark Office +validatordb: + biocontext: + is_identifiers: true + is_obo: false + prefix: VALIDATORDB + uri_format: http://identifiers.org/validatordb/$1 + example: 2h6o + fairsharing: + abbreviation: ValidatorDB + description: ValidatorDB is a collection of validation results for the entire Protein Data Bank. Annotation (3-letter code) of HET residues larger than 6 heavy atoms is inspected, i.e. if the residue has the same topology and stereochemistry as the model ligand or residue stored in the wwCCD. Validation reports for the entire database can be inspected as well as for the arbitrary set of PDB entries or PDB annotations (3-letter residue code). Results are available in graphical form via Web UI and can be downloaded in the form of CSV files for further inspection. + id: '2336' + name: ValidatorDB + prefix: FAIRsharing.c9psgb + subjects: + - Life Science + mappings: + biocontext: VALIDATORDB + fairsharing: FAIRsharing.c9psgb + miriam: validatordb + n2t: validatordb + miriam: + deprecated: false + description: Database of validation results for ligands and non-standard residues in the Protein Data Bank. + homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ + id: '00000633' + name: ValidatorDB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\/]+$ + prefix: validatordb + sampleId: ByStructure/2h6o + uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1 + n2t: + description: Database of validation results for ligands and non-standard residues in the Protein Data Bank. + example: ByStructure/2h6o + homepage: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ + name: ValidatorDB + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z0-9\/]+$ + prefix: validatordb + uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$1 + provides: pdb + uri_format: https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1 +vandf: + biolink: + is_identifiers: false + is_obo: false + prefix: VANDF + uri_format: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/$1 + bioportal: + name: Veterans Health Administration National Drug File + prefix: VANDF + description: 'The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ' + example: '4019477' + fairsharing: + abbreviation: VANDF + description: Veterans Health Administration National Drug File is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. + id: '339' + name: Veterans Health Administration National Drug File + prefix: FAIRsharing.xn3pb3 + subjects: + - Pharmacology + - Biomedical Science + homepage: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF + mappings: + biolink: VANDF + bioportal: VANDF + fairsharing: FAIRsharing.xn3pb3 + name: Veterans Administration National Drug File + pattern: ^\d+$ + references: + - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244318/ +vario: + banana: VariO + biocontext: + is_identifiers: false + is_obo: true + prefix: VARIO + uri_format: http://purl.obolibrary.org/obo/VARIO_$1 + bioportal: + name: Variation Ontology + prefix: VARIO + example: '0376' + fairsharing: + abbreviation: VariO + description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. VariO allows unambiguous description of variation effects as well as computerized analyses over databases utilizing the ontology for annotation. VariO is a position specific ontology that can be used to describe effects of variations on DNA, RNA and/or proteins. + id: '546' + name: Variation Ontology + prefix: FAIRsharing.65xkbs + subjects: + - Genetics + mappings: + biocontext: VARIO + bioportal: VARIO + fairsharing: FAIRsharing.65xkbs + miriam: vario + n2t: vario + obofoundry: vario + ols: vario + ontobee: VariO + miriam: + deprecated: false + description: The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. + homepage: http://bioportal.bioontology.org/ontologies/VARIO + id: '00000406' + name: VariO + namespaceEmbeddedInLui: true + pattern: ^VariO:\d+$ + prefix: vario + providers: + - code: CURATOR_REVIEW + description: VariO at Lund University + homepage: http://www.variationontology.org/ + name: VariO at Lund University + uri_format: http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms + sampleId: '0294' + uri_format: http://purl.bioontology.org/ontology/VARIO/VariO:$1 + n2t: + description: The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. + example: '0294' + homepage: http://bioportal.bioontology.org/ontologies/VARIO + name: VariO through BioPortal + namespaceEmbeddedInLui: true + pattern: ^VariO:\d+$ + prefix: vario + uri_format: http://purl.bioontology.org/ontology/VARIO/VariO:$1 + name: Variation Ontology + obofoundry: + contact: mauno.vihinen@med.lu.se + contact.label: Mauno Vihinen + deprecated: true + description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. + download.obo: http://purl.obolibrary.org/obo/vario.obo + download.owl: http://purl.obolibrary.org/obo/vario.owl + homepage: http://variationontology.org + name: Variation Ontology + preferredPrefix: VariO + prefix: vario + ols: + description: Variation Ontology, VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations. + download: http://purl.obolibrary.org/obo/vario.owl + homepage: http://variationontology.org + name: Variation Ontology + prefix: vario + version: 2018-11-09 + version.iri: http://purl.obolibrary.org/obo/vario/2018-11-09/vario.owl + ontobee: + library: Library + name: Variation Ontology + prefix: VariO + pattern: ^\d+$ + preferred_prefix: VariO +vbase2: + biocontext: + is_identifiers: true + is_obo: false + prefix: VBASE2 + uri_format: http://identifiers.org/vbase2/$1 + fairsharing: + abbreviation: VBASE2 + description: VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank. + id: '2093' + name: VBASE2 + prefix: FAIRsharing.qvxhb1 + subjects: + - Life Science + mappings: + biocontext: VBASE2 + fairsharing: FAIRsharing.qvxhb1 + miriam: vbase2 + n2t: vbase2 + ncbi: VBASE2 + prefixcommons: vbase2 + miriam: + deprecated: false + description: The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. + homepage: http://www.vbase2.org/vbase2.php + id: '00000320' + name: Vbase2 + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vbase2 + sampleId: humIGHV025 + uri_format: http://www.vbase2.org/vgene.php?id=$1 + n2t: + description: The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. + example: humIGHV025 + homepage: http://www.vbase2.org/vbase2.php + name: Vbase2 at German Research Centre for Biotechnology + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vbase2 + uri_format: http://www.vbase2.org/vgene.php?id=$1 + ncbi: + example: humIGKV165 + homepage: http://www.vbase2.org/ + name: Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse + prefix: VBASE2 + prefixcommons: + description: VBASE2 is an integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank. + example: humIGHV025 + homepage: http://www.vbase2.org + keywords: + - gene + name: VBASE2 + pattern: ^\w+$ + prefix: vbase2 + pubmed_ids: + - '15608286' + uri_format: http://www.vbase2.org/vgene.php?id=$1 +vbrc: + biocontext: + is_identifiers: true + is_obo: false + prefix: VBRC + uri_format: http://identifiers.org/vbrc/$1 + mappings: + biocontext: VBRC + miriam: vbrc + n2t: vbrc + prefixcommons: vbrc + miriam: + deprecated: false + description: The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. + homepage: http://vbrc.org/ + id: '00000448' + name: VBRC + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: vbrc + sampleId: '35742' + uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1 + n2t: + description: The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. + example: '35742' + homepage: http://vbrc.org/ + name: VBRC at University of Alabama + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: vbrc + uri_format: http://vbrc.org/gene_detail.asp?gene_id=$1 + name: Viral Bioinformatics Resource Center + prefixcommons: + description: The VBRC is one of eight NIH/NIAID-funded Bioinformatics Resource Centers nationwide providing a comprehensive web-based battery of informational and analytical tools and resources. + example: VP0033331 + homepage: http://vbrc.org + name: Viral Bioinformatics Resource Center + pattern: ^VP\d+$ + prefix: vbrc +vcell: + mappings: + miriam: vcell + miriam: + deprecated: false + description: Models developed with the Virtual Cell (VCell) software prorgam. + homepage: https://health.uconn.edu/ + id: '00000893' + name: VCell Published Models + namespaceEmbeddedInLui: false + pattern: ^\d{5,}$ + prefix: vcell + sampleId: '201022999' + uri_format: https://vcell.org/biomodel-$1 +vectorbase: + biocontext: + is_identifiers: true + is_obo: false + prefix: VECTORBASE + uri_format: http://identifiers.org/vectorbase/$1 + fairsharing: + abbreviation: VectorBase + description: VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrated resource for the research community. VectorBase contains genome information for organisms such as Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. + id: '2118' + name: VectorBase + prefix: FAIRsharing.3etvdn + subjects: + - Functional Genomics + - Population Dynamics + - Genomics + - Comparative Genomics + - Population Genetics + mappings: + biocontext: VECTORBASE + fairsharing: FAIRsharing.3etvdn + miriam: vectorbase + n2t: vectorbase + ncbi: VectorBase + prefixcommons: vectorbase + miriam: + deprecated: false + description: 'VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.' + homepage: https://www.vectorbase.org/ + id: '00000232' + name: VectorBase + namespaceEmbeddedInLui: false + pattern: ^\D{4}\d{6}(\-\D{2})?$ + prefix: vectorbase + sampleId: ISCW007415 + uri_format: https://www.vectorbase.org/search/site/$1?&site="Genome" + n2t: + description: 'VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.' + example: ISCW007415 + homepage: https://www.vectorbase.org/ + name: Vectorbase at EMBL-EBI + namespaceEmbeddedInLui: false + pattern: ^\D{4}\d{6}(\-\D{2})?$ + prefix: vectorbase + uri_format: https://www.vectorbase.org/search/site/$1?&site="Genome" + ncbi: + example: ENSANGG00000007825 + homepage: http://www.vectorbase.org/index.php + name: Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens + prefix: VectorBase + prefixcommons: + description: 'VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever.' + example: ISCW007415 + homepage: http://www.vectorbase.org/index.php + keywords: + - gene + - genome + - protein + name: Invertebrate Vectors of Human Pathogens + pattern: ^\D{4}\d{6}(\-\D{2})?$ + prefix: vectorbase + pubmed_ids: + - '19028744' + uri_format: http://www.vectorbase.org/[?species_name]/Gene/Summary?db=core;g=$1 + uri_format: https://vectorbase.org/vectorbase/app/record/gene/$1 +vega: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A repository for high-quality gene models produced by the manual annotation of vertebrate genomes. + example: OTTHUMG00000169812 + fairsharing: + abbreviation: VEGA + description: The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence. + id: '2049' + name: The Vertebrate Genome Annotation Database + prefix: FAIRsharing.mr293q + subjects: + - Life Science + homepage: https://vega.archive.ensembl.org/index.html + mappings: + fairsharing: FAIRsharing.mr293q + prefixcommons: vega + name: Vertebrate Genome Annotation Database + prefixcommons: + description: The Vertebrate Genome Annotation (VEGA) database is a central repository for high quality manual annotation of vertebrate finished genome sequence. + example: OTTHUMG00000017411 + homepage: http://vega.sanger.ac.uk/ + keywords: + - genome + name: The Vertebrate Genome Annotation Database + pattern: ^[A-Z]+\d+$ + prefix: vega + uri_format: http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1 + synonyms: + - VEGA +vegbank: + mappings: + miriam: vegbank + miriam: + deprecated: false + description: "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. " + homepage: http://vegbank.org/ + id: '00000723' + name: VegBank + namespaceEmbeddedInLui: false + pattern: ^VB\.[A-Za-z][A-Za-z]\..*$ + prefix: vegbank + sampleId: VB.Ob.3736.GRSM125 + uri_format: http://vegbank.org/cite/$1 +vfb: + fairsharing: + abbreviation: VFB + description: VFB is an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster. Our goal is to make it easier for researchers to find relevant anatomical information and reagents. We integrate the neuroanatomical and expression data from the published literature, as well as image datasets onto the same brain template, making it possible to run cross searches, find similar neurons and compare image data on our 3D Viewer. + id: '2374' + name: Virtual Fly Brain + prefix: FAIRsharing.nzaz6z + subjects: + - Neurobiology + - Life Science + mappings: + fairsharing: FAIRsharing.nzaz6z + miriam: vfb + n2t: vfb + miriam: + deprecated: false + description: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster. + homepage: https://VirtualFlyBrain.org + id: '00000680' + name: Virtual Fly Brain + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z]{8}$ + prefix: vfb + sampleId: '00000001' + uri_format: http://virtualflybrain.org/reports/$1 + n2t: + description: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster. + example: '00000001' + homepage: https://VirtualFlyBrain.org + name: Virtual Fly Brain + namespaceEmbeddedInLui: false + pattern: ^[0-9a-zA-Z]{8}$ + prefix: vfb + uri_format: http://virtualflybrain.org/reports/$1 +vfdb.gene: + biocontext: + is_identifiers: true + is_obo: false + prefix: VFDB.GENE + uri_format: http://identifiers.org/vfdb.gene/$1 + mappings: + biocontext: VFDB.GENE + miriam: vfdb.gene + n2t: vfdb.gene + miriam: + deprecated: false + description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. + homepage: http://www.mgc.ac.cn/VFs/ + id: '00000472' + name: VFDB Gene + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vfdb.gene + sampleId: VFG2154 + uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1 + n2t: + description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. + example: VFG2154 + homepage: http://www.mgc.ac.cn/VFs/ + name: VFDB Gene at Institute of Pathogen Biology + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vfdb.gene + uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1 +vfdb.genus: + biocontext: + is_identifiers: true + is_obo: false + prefix: VFDB.GENUS + uri_format: http://identifiers.org/vfdb.genus/$1 + mappings: + biocontext: VFDB.GENUS + miriam: vfdb.genus + n2t: vfdb.genus + miriam: + deprecated: false + description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. + homepage: http://www.mgc.ac.cn/VFs/ + id: '00000471' + name: VFDB Genus + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vfdb.genus + sampleId: Chlamydia + uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1 + n2t: + description: VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. + example: Chlamydia + homepage: http://www.mgc.ac.cn/VFs/ + name: VFDB Genus at Institute of Pathogen Biology + namespaceEmbeddedInLui: false + pattern: ^\w+$ + prefix: vfdb.genus + uri_format: http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1 +vgnc: + cellosaurus: + category: Organism-specific databases + homepage: https://vertebrate.genenames.org/ + name: Vertebrate Gene Nomenclature Committee Database + prefix: VGNC + uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/VGNC:$1 + fairsharing: + abbreviation: VGNC + description: The VGNC approves both a short-form abbreviation known as a gene symbol, and also a longer and more descriptive name. Each symbol is unique and the committee ensures that each gene is only given one approved gene symbol. This allows for clear and unambiguous reference to genes in scientific communications, and facilitates electronic data retrieval from databases and publications. + id: '722' + name: VGNC Gene Symbols, Gene Names and IDs + prefix: FAIRsharing.5NhJFK + subjects: + - Life Science + mappings: + cellosaurus: VGNC + fairsharing: FAIRsharing.5NhJFK + miriam: vgnc + ncbi: VGNC + uniprot: VGNC + miriam: + deprecated: false + description: The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. + homepage: https://vertebrate.genenames.org + id: '00000765' + name: VGNC + namespaceEmbeddedInLui: false + pattern: ^((VGNC|vgnc):)?\d{1,9}$ + prefix: vgnc + sampleId: VGNC:3792 + uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1 + ncbi: + example: VGNC:4927 + homepage: http://vertebrate.genenames.org/data/gene-symbol-report/#!/ + name: Vertebrate Gene Nomenclature Committee + prefix: VGNC + uniprot: + category: Organism-specific databases + identifier: '226' + link_is_explicit: 'true' + name: Vertebrate Gene Nomenclature Database + prefix: VGNC + uri_format: https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1 +vhog: + biocontext: + is_identifiers: false + is_obo: true + prefix: VHOG + uri_format: http://purl.obolibrary.org/obo/VHOG_$1 + bioportal: + name: Vertebrate Homologous Organ Group Ontology + prefix: VHOG + download_obo: ftp://ftp.bgee.org/general/ontologies/vHOG.obo + example: '0000411' + mappings: + biocontext: VHOG + bioportal: VHOG + obofoundry: vhog + prefixcommons: vhog + name: Vertebrate Homologous Organ Group Ontology + obofoundry: + deprecated: true + download.owl: http://purl.obolibrary.org/obo/vhog.owl + name: Vertebrate Homologous Ontology Group Ontology + prefix: vhog + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1574' + description: 'vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 "historical homology". Each mapping has been manually reviewed, and we provide confidence codes and references when available.' + example: VHOG_0000555 + homepage: http://bgee.unil.ch + keywords: + - obo + - anatomy + - development + name: vertebrate Homologous Organ Groups + pattern: ^VHOG_\d{7}$ + prefix: vhog + synonyms: + - VHOG_RETIRED +viaf: + mappings: + miriam: viaf + n2t: viaf + scholia: viaf + miriam: + deprecated: false + description: The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web. + homepage: http://viaf.org + id: '00000685' + name: Virtual International Authority File + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: viaf + sampleId: '75121530' + uri_format: http://viaf.org/viaf/$1 + n2t: + description: The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web. + example: '75121530' + homepage: http://viaf.org + name: Virtual International Authority File + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: viaf + uri_format: http://viaf.org/viaf/$1 +vido: + bioportal: + name: Virus Infectious Disease Ontology + prefix: VIDO + contact: + email: johnbeverley2021@u.northwestern.edu + github: johnbeve + name: John Beverly + orcid: 0000-0002-1118-1738 + example: '0001114' + homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus + mappings: + bioportal: VIDO + ols: vido + ontobee: VIDO + ols: + contact: johnbeverley2021@u.northwestern.edu + description: The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc. + download: https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl + homepage: https://github.com/infectious-disease-ontology-extensions/ido-virus + name: The Virus Infectious Disease Ontology + prefix: vido + version: 2020-08-25 + version.iri: http://purl.obolibrary.org/obo/2020-25-08/vido.owl + ontobee: + library: Not Specified/No + name: Virus Infectious Disease Ontology + prefix: VIDO + pattern: ^\d{7}$ + repository: https://github.com/infectious-disease-ontology-extensions/ido-virus +vipr: + biocontext: + is_identifiers: true + is_obo: false + prefix: VIPR + uri_format: http://identifiers.org/vipr/$1 + fairsharing: + abbreviation: ViPR + description: The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses. + id: '1697' + name: Virus Pathogen Database and Analysis Resource + prefix: FAIRsharing.2qx8n8 + subjects: + - Genomics + - Proteomics + - Virology + - Life Science + - Biomedical Science + - Epidemiology + mappings: + biocontext: VIPR + fairsharing: FAIRsharing.2qx8n8 + miriam: vipr + n2t: vipr + ncbi: ViPR + miriam: + deprecated: false + description: The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. + homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr + id: '00000407' + name: ViPR Strain + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z 0-9]+$ + prefix: vipr + sampleId: BeAn 70563 + uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena + n2t: + description: The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. + example: BeAn 70563 + homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr + name: ViPR Strain at J. Craig Venter Institute + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z 0-9]+$ + prefix: vipr + uri_format: http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena + ncbi: + example: HRV-A34_p1058_sR263_2008 + homepage: http://www.viprbrc.org/brc/home.do?decorator=vipr + name: Virus Pathogen Resource + prefix: ViPR +viralzone: + biocontext: + is_identifiers: true + is_obo: false + prefix: VIRALZONE + uri_format: http://identifiers.org/viralzone/$1 + fairsharing: + abbreviation: ViralZone + description: ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries. + id: '2399' + name: ViralZone + prefix: FAIRsharing.tppk10 + subjects: + - Molecular biology + - Virology + - Life Science + - Epidemiology + mappings: + biocontext: VIRALZONE + fairsharing: FAIRsharing.tppk10 + miriam: viralzone + n2t: viralzone + miriam: + deprecated: false + description: ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures. + homepage: http://www.expasy.org/viralzone/ + id: '00000449' + name: ViralZone + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: viralzone + sampleId: '992' + uri_format: http://viralzone.expasy.org/all_by_protein/$1.html + n2t: + description: ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures. + example: '992' + homepage: http://www.expasy.org/viralzone/ + name: ViralZone at SIB + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: viralzone + uri_format: http://viralzone.expasy.org/all_by_protein/$1.html +virsirna: + biocontext: + is_identifiers: true + is_obo: false + prefix: VIRSIRNA + uri_format: http://identifiers.org/virsirna/$1 + mappings: + biocontext: VIRSIRNA + miriam: virsirna + n2t: virsirna + miriam: + deprecated: false + description: The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region. + homepage: http://crdd.osdd.net/servers/virsirnadb + id: '00000249' + name: VIRsiRNA + namespaceEmbeddedInLui: false + pattern: ^virsi\d+$ + prefix: virsirna + sampleId: virsi1909 + uri_format: http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1 + n2t: + description: The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region. + example: virsi1909 + homepage: http://crdd.osdd.net/servers/virsirnadb + name: VIRsiRNA at Institute of Microbial Technology + namespaceEmbeddedInLui: false + pattern: ^virsi\d+$ + prefix: virsirna + uri_format: http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1 +vmc: + biolink: + is_identifiers: false + is_obo: false + prefix: VMC + uri_format: https://github.com/ga4gh/vr-spec/$1 + deprecated: true + mappings: + biolink: VMC + name: Variation Modelling Collaboration + references: + - https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z + - https://github.com/ga4gh/vr-spec +vmhgene: + mappings: + miriam: vmhgene + miriam: + deprecated: false + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + homepage: https://www.vmh.life/ + id: '00000774' + name: VMH Gene + namespaceEmbeddedInLui: false + pattern: ^[0-9]+\.[0-9]+ + prefix: vmhgene + sampleId: '8639.1' + uri_format: https://www.vmh.life/#gene/$1 +vmhmetabolite: + biocontext: + is_identifiers: true + is_obo: false + prefix: VMHMETABOLITE + uri_format: http://identifiers.org/vmhmetabolite/$1 + mappings: + biocontext: VMHMETABOLITE + miriam: vmhmetabolite + n2t: vmhmetabolite + miriam: + deprecated: false + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + homepage: https://www.vmh.life/ + id: '00000636' + name: VMH metabolite + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9_\(\_\)\[\]]+' + prefix: vmhmetabolite + sampleId: h2o + uri_format: https://www.vmh.life/#metabolite/$1 + n2t: + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + example: h2o + homepage: http://vmh.uni.lu + name: VMH metabolite + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9_\(\_\)\[\]]+' + prefix: vmhmetabolite + uri_format: http://vmh.uni.lu/#metabolite/$1 +vmhreaction: + biocontext: + is_identifiers: true + is_obo: false + prefix: VMHREACTION + uri_format: http://identifiers.org/vmhreaction/$1 + mappings: + biocontext: VMHREACTION + miriam: vmhreaction + n2t: vmhreaction + miriam: + deprecated: false + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + homepage: https://www.vmh.life/ + id: '00000640' + name: VMH reaction + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9_\(\_\)\[\]]+' + prefix: vmhreaction + sampleId: HEX1 + uri_format: https://www.vmh.life/#reaction/$1 + n2t: + description: The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. + example: HEX1 + homepage: https://vmh.uni.lu + name: VMH reaction + namespaceEmbeddedInLui: false + pattern: '[a-zA-Z0-9_\(\_\)\[\]]+' + prefix: vmhreaction + uri_format: https://vmh.uni.lu/#reaction/$1 +vo: + biocontext: + is_identifiers: false + is_obo: true + prefix: VO + uri_format: http://purl.obolibrary.org/obo/VO_$1 + bioportal: + name: Vaccine Ontology + prefix: VO + example: '0000093' + fairsharing: + abbreviation: VO + description: The Vaccine Ontology (VO) was created as part of an international community-based effort to represent vaccine knowledge and to support automated reasoning. VO describes the detailed classification and definitions of vaccine components and vaccine administration processes. The Vaccine Ontology is being used in a variety of applications by many user groups in academia and industry. + id: '62' + name: Vaccine Ontology + prefix: FAIRsharing.zwtww5 + subjects: + - Biomedical Science + mappings: + biocontext: VO + bioportal: VO + fairsharing: FAIRsharing.zwtww5 + obofoundry: vo + ols: vo + ontobee: VO + prefixcommons: vo + obofoundry: + appears_in: + - scdo + contact: yongqunh@med.umich.edu + contact.github: yongqunh + contact.label: Yongqunh He + contact.orcid: 0000-0001-9189-9661 + deprecated: false + description: VO is a biomedical ontology in the domain of vaccine and vaccination. + download.owl: http://purl.obolibrary.org/obo/vo.owl + homepage: http://www.violinet.org/vaccineontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Vaccine Ontology + preferredPrefix: VO + prefix: vo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/23256535 + title: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses + - id: https://www.ncbi.nlm.nih.gov/pubmed/21624163 + title: Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology + repository: https://github.com/vaccineontology/VO + ols: + description: The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. + download: http://purl.obolibrary.org/obo/vo.owl + homepage: http://www.violinet.org/vaccineontology + name: Vaccine Ontology + prefix: vo + version: 1.1.193 + ontobee: + library: Library + name: Vaccine Ontology + prefix: VO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1172' + description: A biomedical ontology in the vaccine domain + example: VO_0000811 + homepage: http://www.violinet.org/vaccineontology + keywords: + - obo + - ontology + - small molecule + - vaccine + name: Vaccine ontology + pattern: ^VO_\d{7}$ + prefix: vo +void: + biocontext: + is_identifiers: false + is_obo: false + prefix: void + uri_format: http://rdfs.org/ns/void#$1 + description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary. + example: feature + homepage: http://vocab.deri.ie/void + mappings: + biocontext: void + name: Vocabulary of Interlinked Datasets + uri_format: http://rdfs.org/ns/void#$1 +vsao: + biocontext: + is_identifiers: false + is_obo: true + prefix: VSAO + uri_format: http://purl.obolibrary.org/obo/VSAO_$1 + bioportal: + name: Vertebrate Skeletal Anatomy Ontology + prefix: VSAO + mappings: + biocontext: VSAO + bioportal: VSAO + obofoundry: vsao + name: Vertebrate Skeletal Anatomy Ontology + obofoundry: + contact: wasila.dahdul@usd.edu + contact.label: Wasila Dahdul + contact.orcid: 0000-0003-3162-7490 + deprecated: true + description: Vertebrate skeletal anatomy ontology. + download.owl: http://purl.obolibrary.org/obo/vsao.owl + homepage: https://www.nescent.org/phenoscape/Main_Page + name: Vertebrate Skeletal Anatomy Ontology- + prefix: vsao + synonyms: + - VSAO_RETIRED +vsdb: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source. + example: '1868' + homepage: https://sitem.herts.ac.uk/aeru/vsdb + name: Veterinary Substances DataBase + pattern: ^\d+$ + uri_format: https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm +vso: + bioportal: + name: Vital Sign Ontology + prefix: VSO + description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ' + example: '0000041' + fairsharing: + abbreviation: VSO + description: 'The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.' + id: '1167' + name: Vital Sign Ontology + prefix: FAIRsharing.jjb2p2 + subjects: + - Health Science + - Biomedical Science + homepage: https://bioportal.bioontology.org/ontologies/VSO + mappings: + bioportal: VSO + fairsharing: FAIRsharing.jjb2p2 + prefixcommons: vso + pattern: ^\d{7}$ + prefixcommons: + bioportal: '3124' + description: 'The Vital Sign Ontology (VSO) covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.' + example: VSO_0000015 + homepage: http://code.google.com/p/vital-sign-ontology/ + keywords: + - owl + - health + name: Vital Sign Ontology + pattern: ^VSO_\d{7}$ + prefix: vso + uri_format: https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1 +vt: + biocontext: + is_identifiers: false + is_obo: true + prefix: VT + uri_format: http://purl.obolibrary.org/obo/VT_$1 + bioportal: + name: Vertebrate Trait Ontology + prefix: VT + download_obo: https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo + example: '0000685' + fairsharing: + abbreviation: VT + description: The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. + id: '1081' + name: Vertebrate Trait Ontology + prefix: FAIRsharing.10gr18 + subjects: + - Animal Physiology + - Developmental Biology + - Physiology + - Biology + mappings: + biocontext: VT + bioportal: VT + fairsharing: FAIRsharing.10gr18 + obofoundry: vt + ols: vt + ontobee: VT + prefixcommons: vt + obofoundry: + appears_in: + - scdo + contact: caripark@iastate.edu + contact.github: caripark + contact.label: Carissa Park + contact.orcid: 0000-0002-2346-5201 + deprecated: false + description: An ontology of traits covering vertebrates + download.owl: http://purl.obolibrary.org/obo/vt.owl + homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: Vertebrate trait ontology + preferredPrefix: VT + prefix: vt + repository: https://github.com/AnimalGenome/vertebrate-trait-ontology + ols: + description: An ontology of traits covering vertebrates + download: http://purl.obolibrary.org/obo/vt.owl + homepage: https://github.com/AnimalGenome/vertebrate-trait-ontology + name: Vertebrate trait ontology + prefix: vt + ontobee: + library: Library + name: Vertebrate trait ontology + prefix: VT + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1659' + description: The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. + example: VT_0015074 + keywords: + - obo + - vertebrate + - trait + name: Vertebrate Trait Ontology + pattern: ^VT_\d{7}$ + prefix: vt +vto: + biocontext: + is_identifiers: false + is_obo: true + prefix: VTO + uri_format: http://purl.obolibrary.org/obo/VTO_$1 + bioportal: + name: Vertebrate Taxonomy Ontology + prefix: VTO + example: '9008500' + fairsharing: + abbreviation: VTO + description: The Vertebrate Taxonomy Ontology includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, we also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups. + id: '900' + name: Vertebrate Taxonomy Ontology + prefix: FAIRsharing.akmeb9 + subjects: [] + mappings: + biocontext: VTO + bioportal: VTO + fairsharing: FAIRsharing.akmeb9 + obofoundry: vto + ols: vto + ontobee: VTO + obofoundry: + contact: balhoff@renci.org + contact.github: balhoff + contact.label: Jim Balhoff + contact.orcid: 0000-0002-8688-6599 + deprecated: false + description: Comprehensive hierarchy of extinct and extant vertebrate taxa. + download.obo: http://purl.obolibrary.org/obo/vto.obo + download.owl: http://purl.obolibrary.org/obo/vto.owl + homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology + license: CC0 1.0 + license.url: http://creativecommons.org/publicdomain/zero/1.0/ + name: Vertebrate Taxonomy Ontology + preferredPrefix: VTO + prefix: vto + publications: + - id: https://doi.org/10.1186/2041-1480-4-34 + title: 'The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes' + repository: https://github.com/phenoscape/vertebrate-taxonomy-ontology + ols: + description: Comprehensive hierarchy of extinct and extant vertebrate taxa. + download: http://purl.obolibrary.org/obo/vto.owl + homepage: https://github.com/phenoscape/vertebrate-taxonomy-ontology + name: Vertebrate Taxonomy Ontology + prefix: vto + version: 2020-11-13 + version.iri: http://purl.obolibrary.org/obo/vto/2020-11-13/vto.owl + ontobee: + library: Library + name: Vertebrate Taxonomy Ontology + prefix: VTO + pattern: ^\d{7}$ +vuid: + comment: The example corresponds to acetaminophen + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year. + example: '4007166' + homepage: https://www.va.gov/health + name: Veterans Health Administration (VHA) unique identifier + pattern: ^\d+$ + references: + - https://academic.oup.com/jamia/article/17/4/432/866953 +vz: + description: ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. + example: '886' + go: + homepage: http://viralzone.expasy.org/ + name: ViralZone + prefix: VZ + uri_format: http://viralzone.expasy.org/all_by_protein/$1.html + mappings: + go: VZ + prefixcommons: vz + name: ViralZone + pattern: ^\d+$ + prefixcommons: + description: ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures + example: '886' + homepage: http://viralzone.expasy.org/ + keywords: + - virus + name: ViralZone + pattern: ^\d+$ + prefix: vz + uri_format: http://viralzone.expasy.org/all_by_protein/$1.html + uri_format: https://viralzone.expasy.org/$1 + wikidata: + database: Q15674507 +wb.rnai: + biocontext: + is_identifiers: true + is_obo: false + prefix: WB.RNAI + uri_format: http://identifiers.org/wb.rnai/$1 + mappings: + biocontext: WB.RNAI + miriam: wb.rnai + n2t: wb.rnai + miriam: + deprecated: false + description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. + homepage: https://www.wormbase.org/ + id: '00000466' + name: WormBase RNAi + namespaceEmbeddedInLui: false + pattern: ^WBRNAi\d{8}$ + prefix: wb.rnai + sampleId: WBRNAi00086878 + uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1 + n2t: + description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. + example: WBRNAi00086878 + homepage: https://www.wormbase.org/ + name: WormBase RNAi + namespaceEmbeddedInLui: false + pattern: ^WBRNAi\d{8}$ + prefix: wb.rnai + uri_format: https://www.wormbase.org/species/c_elegans/rnai/$1 +wbbt: + biocontext: + is_identifiers: false + is_obo: true + prefix: WBBT + uri_format: http://purl.obolibrary.org/obo/WBBT_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: WBbt + uri_format: http://purl.obolibrary.org/obo/WBBT_$1 + bioportal: + name: C. elegans Gross Anatomy Vocabulary + prefix: WB-BT + example: '0001290' + fairsharing: + abbreviation: WB-BT + description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. + id: '152' + name: C. elegans gross anatomy + prefix: FAIRsharing.phk7dd + subjects: + - Anatomy + - Life Science + go: + homepage: http://www.wormbase.org/ + name: C. elegans gross anatomy + prefix: WBbt + mappings: + biocontext: WBBT + biolink: WBbt + bioportal: WB-BT + fairsharing: FAIRsharing.phk7dd + go: WBbt + obofoundry: wbbt + ols: wbbt + ontobee: WBbt + prefixcommons: wbbt + obofoundry: + contact: raymond@caltech.edu + contact.github: raymond91125 + contact.label: Raymond Lee + contact.orcid: 0000-0002-8151-7479 + deprecated: false + description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. + download.obo: http://purl.obolibrary.org/obo/wbbt.obo + download.owl: http://purl.obolibrary.org/obo/wbbt.owl + homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: C. elegans Gross Anatomy Ontology + preferredPrefix: WBbt + prefix: wbbt + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/18629098 + title: Building a cell and anatomy ontology of Caenorhabditis elegans + repository: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology + ols: + description: Ontology about the gross anatomy of the C. elegans + download: http://purl.obolibrary.org/obo/wbbt.owl + homepage: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology + name: C. elegans Gross Anatomy Ontology + prefix: wbbt + version: 2022-03-22 + version.iri: http://purl.obolibrary.org/obo/wbbt/releases/2022-03-22/wbbt.owl + ontobee: + library: Library + name: C. elegans Gross Anatomy Ontology + prefix: WBbt + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1048' + description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. + example: WBbt_0005733 + homepage: http://www.wormbase.org/ + keywords: + - obo + - anatomy + - worm + name: C. elegans gross anatomy + pattern: ^WBbt_\d{7}$ + prefix: wbbt + uri_format: http://wormbase.org/db/ontology/anatomy?name=$1 + synonyms: + - WBbt +wbls: + biocontext: + is_identifiers: false + is_obo: true + prefix: WBLS + uri_format: http://purl.obolibrary.org/obo/WBLS_$1 + biolink: + is_identifiers: false + is_obo: true + prefix: WBls + uri_format: http://purl.obolibrary.org/obo/WBBL_$1 + bioportal: + name: C. elegans Development Vocabulary + prefix: WB-LS + example: '0000690' + fairsharing: + abbreviation: WB-LS + description: A structured controlled vocabulary of the development of Caenorhabditis elegans. This resource is also referred to as the Life Stage ontology on the wormbase database. + id: '35' + name: C. elegans development + prefix: FAIRsharing.sm90nh + subjects: + - Developmental Biology + - Life Science + go: + homepage: http://www.wormbase.org/ + name: C. elegans development + prefix: WBls + uri_format: http://www.wormbase.org/get?name=$1 + mappings: + biocontext: WBLS + biolink: WBls + bioportal: WB-LS + fairsharing: FAIRsharing.sm90nh + go: WBls + obofoundry: wbls + ols: wbls + ontobee: WBLS + prefixcommons: wbls + obofoundry: + contact: cgrove@caltech.edu + contact.github: chris-grove + contact.label: Chris Grove + contact.orcid: 0000-0001-9076-6015 + deprecated: false + description: A structured controlled vocabulary of the development of Caenorhabditis elegans. + download.obo: http://purl.obolibrary.org/obo/wbls.obo + download.owl: http://purl.obolibrary.org/obo/wbls.owl + homepage: https://github.com/obophenotype/c-elegans-development-ontology + license: CC BY 4.0 + license.url: https://creativecommons.org/licenses/by/4.0/ + name: C. elegans development ontology + preferredPrefix: WBls + prefix: wbls + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/31642470 + title: 'WormBase: a modern Model Organism Information Resource' + repository: https://github.com/obophenotype/c-elegans-development-ontology + ols: + description: Ontology about the development and life stages of the C. elegans + download: http://purl.obolibrary.org/obo/wbls.owl + homepage: https://github.com/obophenotype/c-elegans-development-ontology + name: C. elegans Development Ontology + prefix: wbls + version: 2022-03-22 + version.iri: http://purl.obolibrary.org/obo/wbls/releases/2022-03-22/wbls.owl + ontobee: + library: Library + name: C. elegans development ontology + prefix: WBLS + part_of: wormbase + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1049' + description: A structured controlled vocabulary of the development of Caenorhabditis elegans. + example: WBls_0000003 + homepage: http://www.wormbase.org/ + keywords: + - obo + - development + - worm + name: C. elegans development + pattern: ^WBIs_\d{7}$ + prefix: wbls + uri_format: http://purl.obolibrary.org/obo/$1 + synonyms: + - WBls +wbphenotype: + biocontext: + is_identifiers: false + is_obo: true + prefix: WBPhenotype + uri_format: http://purl.obolibrary.org/obo/WBPhenotype_$1 + bioportal: + name: C. elegans Phenotype Vocabulary + prefix: WB-PHENOTYPE + example: '0000983' + fairsharing: + abbreviation: WB-PHENOTYPE + description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes . + id: '61' + name: C. elegans phenotype + prefix: FAIRsharing.agvc7y + subjects: + - Anatomy + - Life Science + go: + homepage: http://www.wormbase.org/ + name: WormBase phenotype ontology + prefix: WBPhenotype + uri_format: http://www.wormbase.org/get?name=$1 + mappings: + biocontext: WBPhenotype + bioportal: WB-PHENOTYPE + fairsharing: FAIRsharing.agvc7y + go: WBPhenotype + obofoundry: wbphenotype + ols: wbphenotype + ontobee: WBPhenotype + prefixcommons: wbphenotype + obofoundry: + contact: cgrove@caltech.edu + contact.github: chris-grove + contact.label: Chris Grove + contact.orcid: 0000-0001-9076-6015 + deprecated: false + description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes + download.obo: http://purl.obolibrary.org/obo/wbphenotype.obo + download.owl: http://purl.obolibrary.org/obo/wbphenotype.owl + homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology + license: CC BY 4.0 + license.url: http://creativecommons.org/licenses/by/4.0/ + name: C. elegans phenotype + preferredPrefix: WBPhenotype + prefix: wbphenotype + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/21261995 + title: 'Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.' + repository: https://github.com/obophenotype/c-elegans-phenotype-ontology + ols: + description: Ontology about C. elegans and other nematode phenotypes + download: http://purl.obolibrary.org/obo/wbphenotype.owl + homepage: https://github.com/obophenotype/c-elegans-phenotype-ontology + name: C elegans Phenotype Ontology + prefix: wbphenotype + version: 2022-03-22 + version.iri: http://purl.obolibrary.org/obo/wbphenotype/releases/2022-03-22/wbphenotype.owl + ontobee: + library: Library + name: C. elegans phenotype + prefix: WBPhenotype + part_of: wormbase + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1067' + description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes + example: WBPhenotype_0000517 + homepage: http://www.wormbase.org/ + keywords: + - obo + - phenotype + - worm + name: C. elegans phenotype + pattern: ^WBPhenotype_\d{7}$ + prefix: wbphenotype + uri_format: http://purl.obolibrary.org/obo/$1 + synonyms: + - WBPhenotype +webelements: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Browser for the periodic table of the elements + example: chromium + homepage: https://www.webelements.com/ + name: Web Elements + pattern: ^\w+$ + uri_format: https://www.webelements.com/$1 +wgs84: + biolink: + is_identifiers: false + is_obo: false + prefix: wgs + uri_format: http://www.w3.org/2003/01/geo/wgs84_pos$1 + description: A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum + example: latitude + homepage: https://www.w3.org/2003/01/geo/wgs84_pos + mappings: + biolink: wgs + name: WGS84 Geo Positioning + uri_format: http://www.w3.org/2003/01/geo/wgs84_pos#$1 +wicell: + cellosaurus: + category: Cell line collections + homepage: https://www.wicell.org + name: WiCell Research Institute Cell Collection + prefix: WiCell + uri_format: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true + example: ai10e-kctd13b + mappings: + cellosaurus: WiCell +wikidata: + biocontext: + is_identifiers: false + is_obo: false + prefix: WD_Entity + uri_format: https://www.wikidata.org/wiki/$1 + biolink: + is_identifiers: false + is_obo: false + prefix: WIKIDATA + uri_format: https://www.wikidata.org/wiki/$1 + cellosaurus: + category: Encyclopedic resources + homepage: https://www.wikidata.org/wiki/Wikidata:Main_Page + name: Wikidata + prefix: Wikidata + uri_format: https://www.wikidata.org/wiki/$1 + fairsharing: + abbreviation: Wikidata + description: Free knowledge database project hosted by Wikimedia and edited by volunteers. + id: '2329' + name: Wikidata + prefix: FAIRsharing.6s749p + subjects: + - Genomics + - Proteomics + - Chemistry + - Metabolomics + - Subject Agnostic + mappings: + biocontext: WD_Entity + biolink: WIKIDATA + cellosaurus: Wikidata + cheminf: '000567' + fairsharing: FAIRsharing.6s749p + miriam: wikidata + n2t: wikidata + miriam: + deprecated: false + description: Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. + homepage: https://www.wikidata.org/ + id: '00000549' + name: Wikidata + namespaceEmbeddedInLui: false + pattern: ^(Q|P)\d+$ + prefix: wikidata + sampleId: Q2207226 + uri_format: http://www.wikidata.org/entity/$1 + n2t: + description: Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. + example: Q2207226 + homepage: https://www.wikidata.org/ + name: Wikidata at Wikimedia Foundation + namespaceEmbeddedInLui: false + pattern: ^Q\d+$ + prefix: wikidata + uri_format: https://www.wikidata.org/wiki/$1 + providers: + - code: scholia + description: Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains + homepage: https://scholia.toolforge.org + name: Scholia + uri_format: https://scholia.toolforge.org/$1 + synonyms: + - WD_Entity + - wd +wikidata.property: + biocontext: + is_identifiers: false + is_obo: false + prefix: WD_Prop + uri_format: https://www.wikidata.org/wiki/Property:$1 + biolink: + is_identifiers: false + is_obo: false + prefix: WIKIDATA_PROPERTY + uri_format: https://www.wikidata.org/wiki/Property:$1 + description: >- + Wikidata is a free and open knowledge base that can be read and edited by + both humans and machines. + + Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. + example: P4355 + homepage: https://www.wikidata.org + mappings: + biocontext: WD_Prop + biolink: WIKIDATA_PROPERTY + name: Wikidata Property + pattern: ^P\d+$ + providers: + - code: scholia + description: Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains + homepage: https://scholia.toolforge.org + name: Scholia + uri_format: https://scholia.toolforge.org/$1 +wikigenes: + biocontext: + is_identifiers: true + is_obo: false + prefix: WIKIGENES + uri_format: http://identifiers.org/wikigenes/$1 + mappings: + biocontext: WIKIGENES + miriam: wikigenes + n2t: wikigenes + miriam: + deprecated: false + description: WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process. + homepage: http://www.wikigenes.org/ + id: '00000437' + name: WikiGenes + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: wikigenes + sampleId: '3771877' + uri_format: http://www.wikigenes.org/e/gene/e/$1.html + n2t: + description: WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process. + example: '3771877' + homepage: http://www.wikigenes.org/ + name: WikiGenes at Massachusetts Institute of Technology + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: wikigenes + uri_format: http://www.wikigenes.org/e/gene/e/$1.html + provides: ncbigene +wikipathways: + biocontext: + is_identifiers: true + is_obo: false + prefix: WIKIPATHWAYS + uri_format: http://identifiers.org/wikipathways/$1 + bioportal: + name: WikiPathways + prefix: WIKIPATHWAYS + example: WP732 + fairsharing: + abbreviation: WIKIPATHWAYS + description: '"WikiPathways" is a standard, specialising in the fields described under "scope and data types", below. Until this entry is claimed, more information on this project can be found at http://www.wikipathways.org/. This text was generated automatically. If you work on the project responsible for "WikiPathways" then please consider helping us by claiming this record and updating it appropriately.' + id: '826' + name: WikiPathways + prefix: FAIRsharing.g7b4rj + subjects: [] + mappings: + biocontext: WIKIPATHWAYS + bioportal: WIKIPATHWAYS + fairsharing: FAIRsharing.g7b4rj + miriam: wikipathways + n2t: wikipathways + prefixcommons: wikipathways + scholia: wikipathways + wikidata: P2410 + miriam: + deprecated: false + description: "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.\r\nAll content is under the Creative Commons Attribution 3.0 Unported license." + homepage: http://www.wikipathways.org/ + id: '00000076' + name: WikiPathways + namespaceEmbeddedInLui: false + pattern: WP\d{1,5}(\_r\d+)?$ + prefix: wikipathways + providers: + - code: scholia + description: > + Scholia is a service that creates visual scholarly profiles for topic, + people, organizations, species, chemicals, etc using bibliographic and + other information in Wikidata. + homepage: https://scholia.toolforge.org/ + name: Scholia + uri_format: https://scholia.toolforge.org/wikipathways/$1 + sampleId: WP100 + uri_format: http://www.wikipathways.org/instance/$1 + n2t: + description: WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. All content is under the Creative Commons Attribution 3.0 Unported license. + example: WP100 + homepage: http://www.wikipathways.org/ + name: Wikipathways + namespaceEmbeddedInLui: false + pattern: WP\d{1,5}(\_r\d+)?$ + prefix: wikipathways + uri_format: http://www.wikipathways.org/instance/$1 + name: WikiPathways + prefixcommons: + description: WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. + example: WP100 + homepage: http://wikipathways.org/ + keywords: + - pathway + name: WikiPathways + pattern: ^P\d{1,5}(\_r\d+)?$ + prefix: wikipathways + pubmed_ids: + - '18651794' + uri_format: http://www.wikipathways.org/index.php/Pathway:$1 + wikidata: + database: Q7999828 + database.homepage: https://www.wikipathways.org/ + database.label: WikiPathways + format.rdf: http://identifiers.org/wikipathways/$1 + homepage: http://www.wikipathways.org + name: WikiPathways ID + pattern: WP\d{1,4} + prefix: P2410 + uri_format: https://www.wikipathways.org/index.php/Pathway:$1 +wikipedia.en: + biocontext: + is_identifiers: true + is_obo: false + prefix: WIKIPEDIA.EN + uri_format: http://identifiers.org/wikipedia.en/$1 + go: + homepage: http://en.wikipedia.org/ + name: Wikipedia + prefix: Wikipedia + uri_format: http://en.wikipedia.org/wiki/$1 + mappings: + biocontext: WIKIPEDIA.EN + go: Wikipedia + miriam: wikipedia.en + n2t: wikipedia.en + prefixcommons: wikipedia + miriam: + deprecated: false + description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. + homepage: http://en.wikipedia.org/wiki/Main_Page + id: '00000384' + name: Wikipedia (En) + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+$ + prefix: wikipedia.en + providers: + - code: CURATOR_REVIEW + description: Wikipedia structured content through DBpedia + homepage: http://wiki.dbpedia.org/ + name: Wikipedia structured content through DBpedia + uri_format: http://dbpedia.org/page/$1 + sampleId: SM_UB-81 + uri_format: http://en.wikipedia.org/wiki/$1 + n2t: + description: Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. + example: SM_UB-81 + homepage: http://wiki.dbpedia.org/ + name: Wikipedia structured content through DBpedia + namespaceEmbeddedInLui: false + pattern: ^[A-Za-z-0-9_]+$ + prefix: wikipedia.en + uri_format: http://dbpedia.org/page/$1 + name: Wikipedia + prefixcommons: + description: Encyclopedia of Everything. + example: SM_UB-81 + homepage: http://en.wikipedia.org/ + name: Wikipedia + pattern: ^[A-Za-z0-9_]+$ + prefix: wikipedia + uri_format: http://en.wikipedia.org/wiki/$1 + synonyms: + - wikipedia +worfdb: + biocontext: + is_identifiers: true + is_obo: false + prefix: WORFDB + uri_format: http://identifiers.org/worfdb/$1 + mappings: + biocontext: WORFDB + miriam: worfdb + n2t: worfdb + ncbi: WorfDB + prefixcommons: worfdb + miriam: + deprecated: false + description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). + homepage: http://worfdb.dfci.harvard.edu/ + id: '00000288' + name: Worfdb + namespaceEmbeddedInLui: false + pattern: ^\w+(\.\d+)? + prefix: worfdb + sampleId: T01B6.1 + uri_format: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1 + n2t: + description: WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). + example: T01B6.1 + homepage: http://worfdb.dfci.harvard.edu/ + name: Worm Orf DB at Harvard + namespaceEmbeddedInLui: false + pattern: ^\w+(\.\d+)? + prefix: worfdb + uri_format: http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1 + ncbi: + example: pos-1 + homepage: http://worfdb.dfci.harvard.edu/ + name: C. elegans ORFeome cloning project + prefix: WorfDB + prefixcommons: + description: In total, approximately 12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions. + example: R10E9.1 + homepage: http://worfdb.dfci.harvard.edu/ + keywords: + - DNA + name: The C.elegans ORFeome cloning project + pattern: ^[A-Z,0-9]+$ + prefix: worfdb + uri_format: http://worfdb.dfci.harvard.edu/searchallwormorfs.pl?sid=$1 +wormbase: + biocontext: + is_identifiers: false + is_obo: false + prefix: WormBase + uri_format: https://www.wormbase.org/get?name=$1 + biolink: + is_identifiers: false + is_obo: false + prefix: WBVocab + uri_format: http://bio2rdf.org/wormbase_vocabulary$1 + fairsharing: + abbreviation: WormBase + description: WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. + id: '1699' + name: WormBase + prefix: FAIRsharing.zx1td8 + subjects: + - Anatomy + - Life Science + go: + homepage: http://www.wormbase.org/ + name: WormBase database of nematode biology + prefix: WB_REF + uri_format: http://www.wormbase.org/get?name=$1 + mappings: + biocontext: WormBase + biolink: WBVocab + fairsharing: FAIRsharing.zx1td8 + go: WB_REF + miriam: wb + n2t: wb + ncbi: WormBase + prefixcommons: wormbase + uniprot: WormBase + miriam: + deprecated: false + description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities. + homepage: https://www.wormbase.org/ + id: '00000027' + name: WormBase + namespaceEmbeddedInLui: false + pattern: ^WB[A-Z][a-z]+\d+$ + prefix: wb + providers: + - code: bioentitylink + description: WormBase through BioEntity Link + homepage: https://bioentity.link/ + name: WormBase through BioEntity Link + uri_format: https://bioentity.link/#/lexicon/public/$1 + - code: agr + description: WormBase through the Alliance of Genome Resources + homepage: https://www.alliancegenome.org + name: WormBase through the Alliance of Genome Resources + uri_format: https://www.alliancegenome.org/gene/WB:$1 + sampleId: WBGene00000001 + uri_format: https://www.wormbase.org/get?name=$1 + n2t: + description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities. + example: WBGene00000001 + homepage: https://www.wormbase.org/ + name: WormBase + namespaceEmbeddedInLui: false + pattern: ^WB[A-Z][a-z]+\d+$ + prefix: wb + uri_format: https://www.wormbase.org/get?name=$1 + ncbi: + example: R13H7 + homepage: http://www.wormbase.org/ + name: Caenorhabditis elegans Genome Database + prefix: WormBase + preferred_prefix: WormBase + prefixcommons: + description: WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. + example: WBGene00000001 + homepage: http://www.wormbase.org/ + keywords: + - genome + - gene + - anatomy + name: WormBase + pattern: ^WBGene\d{8}$ + prefix: wormbase + pubmed_ids: + - '11125056' + synonyms: + - WB_REF + - wb + - wormbase + uniprot: + category: Organism-specific databases + identifier: '110' + link_is_explicit: 'true' + name: WormBase + prefix: WormBase + uri_format: https://wormbase.org/db/seq/protein?name=$1;class=CDS + wikidata: + database: Q3570042 + prefix: P3860 +wormpep: + biocontext: + is_identifiers: true + is_obo: false + prefix: WORMPEP + uri_format: http://identifiers.org/wormpep/$1 + mappings: + biocontext: WORMPEP + miriam: wormpep + n2t: wormpep + prefixcommons: wormpep + miriam: + deprecated: false + description: Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. + homepage: https://www.wormbase.org/db/seq/protein + id: '00000031' + name: Wormpep + namespaceEmbeddedInLui: false + pattern: ^CE\d{5}$ + prefix: wormpep + sampleId: CE28239 + uri_format: https://www.wormbase.org/db/seq/protein?name=$1 + n2t: + description: Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. + example: CE28239 + homepage: https://www.wormbase.org/db/seq/protein + name: Wormpep (Master) + namespaceEmbeddedInLui: false + pattern: ^CE\d{5}$ + prefix: wormpep + uri_format: https://www.wormbase.org/db/seq/protein?name=WP:$1 + prefixcommons: + description: Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. + example: CE28239 + homepage: http://www.wormbase.org/db/seq/protein + keywords: + - protein + - structure + name: Caenorhabditis elegans genome sequencing project protein database + pattern: ^CE\d{5}$ + prefix: wormpep + uri_format: http://www.wormbase.org/db/seq/protein?name=$1 +worms: + biocontext: + is_identifiers: true + is_obo: false + prefix: WORMS + uri_format: http://identifiers.org/worms/$1 + fairsharing: + abbreviation: WoRMS + description: The aim of a World Register of Marine Species (WoRMS) is to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. + id: '1120' + name: World Register of Marine Species + prefix: FAIRsharing.7g1bzj + subjects: + - Environmental Science + - Taxonomy + - Biodiversity + mappings: + biocontext: WORMS + fairsharing: FAIRsharing.7g1bzj + miriam: worms + n2t: worms + miriam: + deprecated: false + description: The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. + homepage: http://www.marinespecies.org/ + id: '00000581' + name: World Register of Marine Species + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: worms + sampleId: '146421' + uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1 + n2t: + description: The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. + example: '146421' + homepage: http://www.marinespecies.org/ + name: World Register of Marine Species + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: worms + uri_format: http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1 +wwf.ecoregion: + comment: ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658 + contributor: + email: cjmungall@lbl.gov + github: cmungall + name: Chris Mungall + orcid: 0000-0002-6601-2165 + description: WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. + example: AT1402 + homepage: https://www.worldwildlife.org/biomes + name: World Wildlife Fund Ecoregion + pattern: ^AT\d+$ + reviewer: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + synonyms: + - WWF + uri_format: https://www.worldwildlife.org/ecoregions/$1 + wikidata: + database: Q929975 + prefix: P1294 +xao: + biocontext: + is_identifiers: false + is_obo: true + prefix: XAO + uri_format: http://purl.obolibrary.org/obo/XAO_$1 + bioportal: + name: Xenopus Anatomy Ontology + prefix: XAO + example: '0004486' + fairsharing: + abbreviation: XAO + description: The Xenopus Anatomical Ontology (XAO) describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. XAO terms describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research. + id: '158' + name: Xenopus Anatomy Ontology + prefix: FAIRsharing.17zapb + subjects: + - Anatomy + - Developmental Biology + - Life Science + mappings: + biocontext: XAO + bioportal: XAO + fairsharing: FAIRsharing.17zapb + obofoundry: xao + ols: xao + ontobee: XAO + obofoundry: + appears_in: + - xpo + contact: Erik.Segerdell@cchmc.org + contact.github: seger + contact.label: Erik Segerdell + contact.orcid: 0000-0002-9611-1279 + deprecated: false + description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. + download.obo: http://purl.obolibrary.org/obo/xao.obo + download.owl: http://purl.obolibrary.org/obo/xao.owl + homepage: http://www.xenbase.org/anatomy/xao.do?method=display + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Xenopus Anatomy Ontology + preferredPrefix: XAO + prefix: xao + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/18817563 + title: An ontology for Xenopus anatomy and development. + - id: https://www.ncbi.nlm.nih.gov/pubmed/24139024 + title: 'Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.' + repository: https://github.com/xenopus-anatomy/xao + ols: + description: XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. + download: http://purl.obolibrary.org/obo/xao.owl + homepage: http://www.xenbase.org/anatomy/xao.do?method=display + name: Xenopus Anatomy Ontology + prefix: xao + version: 2021-03-04 + version.iri: http://purl.obolibrary.org/obo/xao/releases/2021-03-04/xao.owl + ontobee: + library: Foundry + name: Xenopus Anatomy Ontology + prefix: XAO + pattern: ^\d{7}$ + wikidata: + prefix: P4495 +xco: + biocontext: + is_identifiers: false + is_obo: true + prefix: XCO + uri_format: http://purl.obolibrary.org/obo/XCO_$1 + bioportal: + name: Experimental Conditions Ontology + prefix: XCO + example: '0000780' + fairsharing: + abbreviation: XCO + description: The Experimental Conditions Ontology is designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. + id: '1485' + name: Experimental Conditions Ontology + prefix: FAIRsharing.x39h5y + subjects: + - Life Science + - Biomedical Science + mappings: + biocontext: XCO + bioportal: XCO + fairsharing: FAIRsharing.x39h5y + obofoundry: xco + ols: xco + ontobee: XCO + prefixcommons: xco + obofoundry: + appears_in: + - agro + - ecto + contact: jrsmith@mcw.edu + contact.github: jrsjrs + contact.label: Jennifer Smith + contact.orcid: 0000-0002-6443-9376 + deprecated: false + description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. + download.obo: http://purl.obolibrary.org/obo/xco.obo + download.owl: http://purl.obolibrary.org/obo/xco.owl + homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 + license: CC0 1.0 + license.url: https://creativecommons.org/publicdomain/zero/1.0/ + name: Experimental condition ontology + preferredPrefix: XCO + prefix: xco + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/22654893 + title: Three ontologies to define phenotype measurement data. + - id: https://www.ncbi.nlm.nih.gov/pubmed/24103152 + title: 'The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.' + repository: https://github.com/rat-genome-database/XCO-experimental-condition-ontology + ols: + description: Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. + download: http://purl.obolibrary.org/obo/xco.owl + homepage: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 + name: Experimental condition ontology + prefix: xco + version: 2019-12-18 + version.iri: http://purl.obolibrary.org/obo/xco/4.46/xco.owl + ontobee: + library: Library + name: Experimental condition ontology + prefix: XCO + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1585' + description: The Experimental Conditions Ontology is designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. + example: XCO_0000001 + homepage: http://sourceforge.net/projects/phenoonto/ + keywords: + - obo + - measurement + name: Experimental Conditions Ontology + pattern: ^XCO_\d{7}$ + prefix: xco +xenbase: + biocontext: + is_identifiers: false + is_obo: false + prefix: Xenbase + uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 + biolink: + is_identifiers: false + is_obo: false + prefix: Xenbase + uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 + fairsharing: + abbreviation: Xenbase + description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically-significant interactions. + id: '2087' + name: Xenopus laevis and tropicalis biology and genomics resource + prefix: FAIRsharing.jrv6wj + subjects: + - Functional Genomics + - Anatomy + - Genomics + - Genetics + - Proteomics + - Developmental Biology + - Cell Biology + go: + homepage: http://www.xenbase.org/ + name: Xenbase + prefix: Xenbase + mappings: + biocontext: Xenbase + biolink: Xenbase + fairsharing: FAIRsharing.jrv6wj + go: Xenbase + miriam: xenbase + n2t: xenbase + ncbi: Xenbase + prefixcommons: xenbase + uniprot: Xenbase + miriam: + deprecated: false + description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. + homepage: https://www.xenbase.org/ + id: '00000186' + name: Xenbase + namespaceEmbeddedInLui: false + pattern: ^XB\-\w+\-\d+$ + prefix: xenbase + sampleId: XB-GENE-922462 + uri_format: https://www.xenbase.org/common/xsearch.do?exactSearch=true&searchIn=7&searchValue=$1 + n2t: + description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. + example: '922462' + homepage: http://www.xenbase.org/ + name: Xenbase at University of Calgary + namespaceEmbeddedInLui: false + pattern: ^(XB-GENE-)?\d+$ + prefix: xenbase + uri_format: http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$1 + ncbi: + example: XB-GENE-1019547 + homepage: http://www.xenbase.org/common/ + name: Xenopus laevis and tropicalis biology and genomics resource + prefix: Xenbase + prefixcommons: + description: Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. + example: '6453898' + homepage: http://www.xenbase.org + keywords: + - expression + - genome + name: Xenopus laevis and tropicalis biology and genomics resource + pattern: ^\d+$ + prefix: xenbase + pubmed_ids: + - '19884130' + uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 + uniprot: + category: Organism-specific databases + identifier: '129' + link_is_explicit: 'true' + name: Xenopus laevis and tropicalis biology and genomics resource + prefix: Xenbase + uri_format: https://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 +ximbio: + cellosaurus: + category: Cell line collections + homepage: https://ximbio.com + name: Ximbio reagents online portal + prefix: Ximbio + uri_format: https://ximbio.com/reagent/$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + example: '151022' + homepage: https://ximbio.com + mappings: + cellosaurus: Ximbio + name: Ximbio + pattern: ^\d+$ + uri_format: https://ximbio.com/reagent/$1 +xl: + biocontext: + is_identifiers: false + is_obo: true + prefix: XL + uri_format: http://purl.obolibrary.org/obo/XL_$1 + deprecated: true + mappings: + biocontext: XL + ols: xl + ontobee: XL + ols: + contact: psidev-ms-vocab@lists.sourceforge.net + description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. + download: http://purl.obolibrary.org/obo/xl.owl + homepage: http://www.psidev.info/groups/controlled-vocabularies + name: Cross-linker reagents ontology + prefix: xl + ontobee: + library: Library + name: Cross-linker reagents ontology + prefix: XL +xlmod: + bioportal: + name: mass spectrometry cross-linking and derivatization reagents + prefix: XLMOD + download_obo: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo + example: '00050' + mappings: + bioportal: XLMOD + obofoundry: xlmod + ols: xlmod + ontobee: XLMOD + obofoundry: + contact: lutz.fischer@tu-berlin.de + contact.github: lutzfischer + contact.label: Lutz Fischer + contact.orcid: 0000-0003-4978-0864 + deprecated: false + description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. + download.obo: http://purl.obolibrary.org/obo/xlmod.obo + download.owl: http://purl.obolibrary.org/obo/xlmod.owl + homepage: http://www.psidev.info/groups/controlled-vocabularies + license: CC BY 3.0 + license.url: https://creativecommons.org/licenses/by/3.0/ + name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary + preferredPrefix: XLMOD + prefix: xlmod + repository: https://github.com/HUPO-PSI/xlmod-CV + ols: + contact: psidev-ms-vocab@lists.sourceforge.net + description: A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. + download: http://purl.obolibrary.org/obo/xlmod.owl + homepage: http://www.psidev.info/groups/controlled-vocabularies + name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary + prefix: xlmod + version: 2019-10-28 + version.iri: http://purl.obolibrary.org/obo/xlmod/release/2019-10-28/xlmod.owl + ontobee: + library: Library + name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary + prefix: XLMOD + pattern: ^\d{5}$ +xmetdb: + banana: XMETDB + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + description: Metabolites in the Xenobiotics Metabolism Database. + example: '171' + homepage: https://xmetdb.org + name: Xenobiotics Metabolism Database + pattern: ^\d+$ + uri_format: http://www.xmetdb.org/xmetdb/protocol/$1 +xml: + biocontext: + is_identifiers: false + is_obo: false + prefix: xml + uri_format: http://www.w3.org/XML/1998/namespace$1 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML. + example: lang + homepage: https://www.w3.org/TR/xml/ + mappings: + biocontext: xml + name: Extensible Markup Language + uri_format: http://www.w3.org/XML/1998/namespace$1 +xpo: + biolink: + is_identifiers: false + is_obo: true + prefix: XPO + uri_format: http://purl.obolibrary.org/obo/XPO_$1 + bioportal: + name: Xenopus Phenotype Ontology + prefix: XPO + example: '0100002' + mappings: + biolink: XPO + bioportal: XPO + obofoundry: xpo + ols: xpo + ontobee: XPO + obofoundry: + contact: Erik.Segerdell@cchmc.org + contact.github: seger + contact.label: Erik Segerdell + contact.orcid: 0000-0002-9611-1279 + depends_on: + - bfo + - chebi + - cl + - go + - iao + - pato + - ro + - xao + deprecated: false + description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. + download.obo: http://purl.obolibrary.org/obo/xpo.obo + download.owl: http://purl.obolibrary.org/obo/xpo.owl + homepage: https://github.com/obophenotype/xenopus-phenotype-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Xenopus Phenotype Ontology + preferredPrefix: XPO + prefix: xpo + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/35317743 + title: 'The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.' + repository: https://github.com/obophenotype/xenopus-phenotype-ontology + ols: + description: XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. + download: http://purl.obolibrary.org/obo/xpo.owl + homepage: https://github.com/obophenotype/xenopus-phenotype-ontology + name: Xenopus Phenotype Ontology + prefix: xpo + version: 2021-03-05 + version.iri: http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/xpo.owl + ontobee: + library: Library + name: Xenopus Phenotype Ontology + prefix: XPO + pattern: ^\d+$ +xsd: + biocontext: + is_identifiers: false + is_obo: false + prefix: xsd + uri_format: http://www.w3.org/2001/XMLSchema#$1 + description: This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language. + example: decimal + homepage: http://www.w3.org/2001/XMLSchema + mappings: + biocontext: xsd + name: XML Schema Definition + uri_format: http://www.w3.org/2001/XMLSchema#$1 +xuo: + appears_in: + - hsapdv + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + deprecated: true + name: XUO +ydpm: + biocontext: + is_identifiers: true + is_obo: false + prefix: YDPM + uri_format: http://identifiers.org/ydpm/$1 + mappings: + biocontext: YDPM + miriam: ydpm + n2t: ydpm + prefixcommons: ydpm + miriam: + deprecated: false + description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. + homepage: http://www-deletion.stanford.edu/YDPM/ + id: '00000465' + name: YDPM + namespaceEmbeddedInLui: false + pattern: ^Y[A-Z]{2}\d+[CW]$ + prefix: ydpm + sampleId: YAL001C + uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 + n2t: + description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. + example: YAL001C + homepage: http://www-deletion.stanford.edu/YDPM/ + name: YDPM at Stanford University School of Medicine + namespaceEmbeddedInLui: false + pattern: ^Y[A-Z]{2}\d+[CW]$ + prefix: ydpm + uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 + name: Yeast Deletion and the Mitochondrial Proteomics Project + prefixcommons: + description: The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The database is hyperlinked with other public databases. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell + example: YBL031W + homepage: http://www-deletion.stanford.edu/YDPM/YDPM_index.html + keywords: + - protein + name: Yeast Deletion Project and Proteomics of Mitochondria Database + pattern: ^[A-Z,0-9]+$ + prefix: ydpm +yeastintron: + biocontext: + is_identifiers: true + is_obo: false + prefix: YEASTINTRON + uri_format: http://identifiers.org/yeastintron/$1 + mappings: + biocontext: YEASTINTRON + miriam: yeastintron + n2t: yeastintron + miriam: + deprecated: false + description: The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]. + homepage: http://intron.ucsc.edu/yeast4.3/ + id: '00000521' + name: Yeast Intron Database v4.3 + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: yeastintron + sampleId: SNR17A + uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1 + n2t: + description: The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]. + example: SNR17A + homepage: http://intron.ucsc.edu/yeast4.3/ + name: Yeast Intron Database version 4.3 at Baskin School of Engineering + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: yeastintron + uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1 +yetfasco: + biocontext: + is_identifiers: true + is_obo: false + prefix: YETFASCO + uri_format: http://identifiers.org/yetfasco/$1 + mappings: + biocontext: YETFASCO + miriam: yetfasco + n2t: yetfasco + miriam: + deprecated: false + description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. + homepage: http://yetfasco.ccbr.utoronto.ca/ + id: '00000339' + name: YeTFasCo + namespaceEmbeddedInLui: false + pattern: ^\w+\_\d+(\.\d+)?$ + prefix: yetfasco + sampleId: YOR172W_571.0 + uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 + n2t: + description: The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. + example: YOR172W_571.0 + homepage: http://yetfasco.ccbr.utoronto.ca/ + name: YeTFasCo at University of Toronto + namespaceEmbeddedInLui: false + pattern: ^\w+\_\d+(\.\d+)?$ + prefix: yetfasco + uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 +yid: + biocontext: + is_identifiers: true + is_obo: false + prefix: YID + uri_format: http://identifiers.org/yid/$1 + mappings: + biocontext: YID + miriam: yid + n2t: yid + miriam: + deprecated: false + description: The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. + homepage: http://compbio.soe.ucsc.edu/yeast_introns.html + id: '00000460' + name: Yeast Intron Database v3 + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: yid + sampleId: SNR17A + uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 + n2t: + description: The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. + example: SNR17A + homepage: http://compbio.soe.ucsc.edu/yeast_introns.html + name: Yeast Intron Database version 3 at Baskin School of Engineering + namespaceEmbeddedInLui: false + pattern: ^[A-Z0-9]+$ + prefix: yid + uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 +ymdb: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). + example: YMDB00001 + fairsharing: + abbreviation: YMDB + description: The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. + id: '1700' + name: The Yeast Metabolome Database + prefix: FAIRsharing.tawpg2 + subjects: + - Life Science + - Metabolomics + homepage: http://www.ymdb.ca + mappings: + fairsharing: FAIRsharing.tawpg2 + name: Yeast Metabolome Database + pattern: ^YMDB\d+$ + uri_format: http://www.ymdb.ca/compounds/$1 +ypo: + mappings: + obofoundry: ypo + ols: ypo + obofoundry: + contact: cherry@genome.stanford.edu + contact.label: Mike Cherry + contact.orcid: 0000-0001-9163-5180 + deprecated: true + homepage: http://www.yeastgenome.org/ + name: Yeast phenotypes + prefix: ypo +yrcpdr: + biocontext: + is_identifiers: true + is_obo: false + prefix: YRCPDR + uri_format: http://identifiers.org/yrcpdr/$1 + fairsharing: + abbreviation: YRC PDR + description: The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae. + id: '2121' + name: Yeast Resource Center Public Data Repository + prefix: FAIRsharing.karvzj + subjects: + - Computational Biology + - Life Science + mappings: + biocontext: YRCPDR + fairsharing: FAIRsharing.karvzj + miriam: yrcpdr + n2t: yrcpdr + miriam: + deprecated: false + description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. + homepage: http://www.yeastrc.org/pdr/ + id: '00000459' + name: YRC PDR + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: yrcpdr + sampleId: '2673500' + uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1 + n2t: + description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. + example: '2673500' + homepage: http://www.yeastrc.org/pdr/ + name: YRC PDR at University of Washington + namespaceEmbeddedInLui: false + pattern: ^\d+$ + prefix: yrcpdr + uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1 +zea: + biocontext: + is_identifiers: false + is_obo: true + prefix: ZEA + uri_format: http://purl.obolibrary.org/obo/ZEA_$1 + bioportal: + name: Maize Gross Anatomy Ontology + prefix: ZEA + mappings: + biocontext: ZEA + bioportal: ZEA + obofoundry: zea + prefixcommons: zea + obofoundry: + contact: Leszek@missouri.edu + contact.label: Leszek Vincent + contact.orcid: 0000-0002-9316-2919 + deprecated: true + homepage: http://www.maizemap.org/ + name: Maize gross anatomy + prefix: zea + prefixcommons: + bioportal: '1050' + description: Maize gross anatomy + example: ZEA_0015177 + homepage: http://www.maizemap.org/ + keywords: + - obo + - anatomy + - maize + name: Maize gross anatomy + pattern: ^ZEA_\d{7}$ + prefix: zea +zeco: + biocontext: + is_identifiers: false + is_obo: true + prefix: ZECO + uri_format: http://purl.obolibrary.org/obo/ZECO_$1 + bioportal: + name: Zebrafish Experimental Conditions Ontology + prefix: ZECO + example: '0000171' + fairsharing: + abbreviation: ZECO + description: This ontology is designed to represent the experimental conditions applied to zebrafish and has been developed to facilitate experiment condition annotation at ZFIN. + id: '483' + name: Zebrafish Experimental Conditions Ontology + prefix: FAIRsharing.np2wfz + subjects: [] + mappings: + biocontext: ZECO + bioportal: ZECO + fairsharing: FAIRsharing.np2wfz + obofoundry: zeco + ols: zeco + ontobee: ZECO + obofoundry: + appears_in: + - mco + contact: ybradford@zfin.org + contact.github: ybradford + contact.label: Yvonne Bradford + contact.orcid: 0000-0002-9900-7880 + deprecated: false + description: Experimental conditions applied to zebrafish, developed to facilitate experiment condition annotation at ZFIN + download.json: http://purl.obolibrary.org/obo/zeco.json + download.obo: http://purl.obolibrary.org/obo/zeco.obo + download.owl: http://purl.obolibrary.org/obo/zeco.owl + homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Zebrafish Experimental Conditions Ontology + preferredPrefix: ZECO + prefix: zeco + repository: https://github.com/ybradford/zebrafish-experimental-conditions-ontology + ols: + description: Ontology of Zebrafish Experimental Conditions + download: http://purl.obolibrary.org/obo/zeco.owl + homepage: https://github.com/ybradford/zebrafish-experimental-conditions-ontology + name: Zebrafish Experimental Conditions Ontology + prefix: zeco + version: 2022-02-14 + version.iri: http://purl.obolibrary.org/obo/zeco/releases/2022-02-14/zeco.owl + ontobee: + library: Library + name: Zebrafish Experimental Conditions Ontology + prefix: ZECO + pattern: ^\d{7}$ +zfa: + biocontext: + is_identifiers: false + is_obo: true + prefix: ZFA + uri_format: http://purl.obolibrary.org/obo/ZFA_$1 + bioportal: + name: Zebrafish Anatomy and Development Ontology + prefix: ZFA + example: '0005926' + fairsharing: + abbreviation: ZFA + description: A structured controlled vocabulary of the anatomy and development of the Zebrafish. If you work on the project responsible for "Zebrafish anatomy and development" then please consider helping us by claiming this record and updating it appropriately. + id: '564' + name: Zebrafish anatomy and development + prefix: FAIRsharing.s3r6sk + subjects: + - Anatomy + - Developmental Biology + - Life Science + mappings: + biocontext: ZFA + bioportal: ZFA + fairsharing: FAIRsharing.s3r6sk + obofoundry: zfa + ols: zfa + ontobee: ZFA + prefixcommons: zfa + obofoundry: + appears_in: + - zp + contact: van_slyke@zfin.org + contact.github: cerivs + contact.label: Ceri Van Slyke + contact.orcid: 0000-0002-2244-7917 + deprecated: false + description: A structured controlled vocabulary of the anatomy and development of the Zebrafish + download.obo: http://purl.obolibrary.org/obo/zfa.obo + download.owl: http://purl.obolibrary.org/obo/zfa.owl + homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Zebrafish anatomy and development ontology + preferredPrefix: ZFA + prefix: zfa + publications: + - id: https://www.ncbi.nlm.nih.gov/pubmed/24568621 + title: 'The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.' + repository: https://github.com/cerivs/zebrafish-anatomical-ontology + ols: + description: ZFA description. + download: http://purl.obolibrary.org/obo/zfa.owl + homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources + name: Zebrafish Anatomy Ontology (ZFA) + prefix: zfa + version: 2022-03-15 + version.iri: http://purl.obolibrary.org/obo/zfa/releases/2022-03-15/zfa.owl + ontobee: + library: Foundry + name: Zebrafish anatomy and development ontology + prefix: ZFA + pattern: ^\d{7}$ + prefixcommons: + bioportal: '1051' + description: A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). + example: ZFS_0000011 + homepage: http://zfin.org/zf_info/anatomy/dict/sum.html + keywords: + - obo + - anatomy + - zebrafish + name: Zebrafish anatomy and development Ontology + pattern: ^ZFS_\d{7}$ + prefix: zfa + uri_format: http://purl.obolibrary.org/obo/$1 + synonyms: + - ZFA_RETIRED +zfin: + biocontext: + is_identifiers: false + is_obo: false + prefix: ZFIN + uri_format: http://zfin.org/$1 + fairsharing: + abbreviation: ZFIN + description: The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases. + id: '2106' + name: The Zebrafish Information Network + prefix: FAIRsharing.ybxnhg + subjects: + - Genomics + - Animal Physiology + - Genetics + - Developmental Biology + go: + homepage: http://zfin.org/ + name: Zebrafish Information Network + prefix: ZFIN + mappings: + biocontext: ZFIN + fairsharing: FAIRsharing.ybxnhg + go: ZFIN + miriam: zfin + n2t: zfin + ncbi: ZFIN + prefixcommons: zfin + uniprot: ZFIN + wikidata: P3870 + miriam: + deprecated: false + description: ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN. + homepage: http://zfin.org + id: '00000079' + name: ZFIN Bioentity + namespaceEmbeddedInLui: false + pattern: ^ZDB\-\w+\-\d+\-\d+$ + prefix: zfin + providers: + - code: bioentitylink + description: ZFIN through BioEntity Link + homepage: https://bioentity.link/ + name: ZFIN through BioEntity Link + uri_format: https://bioentity.link/#/lexicon/public/$1 + - code: agr + description: ZFIN through the Alliance of Genome Resources + homepage: https://www.alliancegenome.org + name: ZFIN through the Alliance of Genome Resources + uri_format: https://test.alliancegenome.org/gene/ZFIN:$1 + sampleId: ZDB-GENE-041118-11 + uri_format: http://zfin.org/$1 + n2t: + description: ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN. + example: ZDB-GENE-041118-11 + homepage: http://zfin.org + name: ZFIN at University of Oregon + namespaceEmbeddedInLui: false + pattern: ^ZDB\-\w+\-\d+\-\d+$ + prefix: zfin + uri_format: http://zfin.org/$1 + name: Zebrafish Information Network Gene + ncbi: + example: ZDB-GENE-011205-17 + homepage: http://zfin.org + name: Zebrafish Information Network + prefix: ZFIN + prefixcommons: + description: ZFIN serves as the zebrafish model organism database. + example: ZDB-GENE-041118-11 + homepage: http://zfin.org/ + keywords: + - zebrafish + - gene + - genome + name: Zebrafish Information Network genome database + pattern: ^ZDB\-GENE\-\d+\-\d+$ + prefix: zfin + pubmed_ids: + - '17991680' + uri_format: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=$1 + synonyms: + - ZFIN + uniprot: + category: Organism-specific databases + identifier: '113' + link_is_explicit: 'true' + name: Zebrafish Information Network genome database + prefix: ZFIN + uri_format: https://zfin.org/$1 + wikidata: + database: Q29128476 + database.homepage: https://zfin.org/ + database.label: Zebrafish Model Organism Database + homepage: http://zfin.org + name: ZFIN Gene ID + prefix: P3870 + uri_format: https://zfin.org/$1 +zfs: + biocontext: + is_identifiers: false + is_obo: true + prefix: ZFS + uri_format: http://purl.obolibrary.org/obo/ZFS_$1 + bioportal: + name: Zebrafish Developmental Stages + prefix: ZFS + example: '0000050' + fairsharing: + abbreviation: ZFS + description: An ontology of developmental stages of the Zebrafish (Danio rerio). Note that ZFA includes the leaf nodes of this ontology. + id: '631' + name: Zebrafish Developmental Stages + prefix: FAIRsharing.bc8ayj + subjects: [] + mappings: + biocontext: ZFS + bioportal: ZFS + fairsharing: FAIRsharing.bc8ayj + obofoundry: zfs + ols: zfs + ontobee: ZFS + obofoundry: + contact: van_slyke@zfin.org + contact.github: cerivs + contact.label: Ceri Van Slyke + contact.orcid: 0000-0002-2244-7917 + deprecated: false + description: Developmental stages of the Zebrafish + download.obo: http://purl.obolibrary.org/obo/zfs.obo + download.owl: http://purl.obolibrary.org/obo/zfs.owl + homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Zebrafish developmental stages ontology + preferredPrefix: ZFS + prefix: zfs + repository: https://github.com/cerivs/zebrafish-anatomical-ontology + ols: + description: Developmental stages of the Zebrafish + download: http://purl.obolibrary.org/obo/zfs.owl + homepage: https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources + name: Zebrafish developmental stages ontology + prefix: zfs + version: 2020-03-10 + version.iri: http://purl.obolibrary.org/obo/zfs/releases/2020-03-10/zfs.owl + ontobee: + library: Library + name: Zebrafish developmental stages ontology + prefix: ZFS + pattern: ^\d{7}$ +zinc: + biocontext: + is_identifiers: true + is_obo: false + prefix: ZINC + uri_format: http://identifiers.org/zinc/$1 + mappings: + biocontext: ZINC + miriam: zinc + n2t: zinc + miriam: + deprecated: false + description: ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. + homepage: http://zinc15.docking.org/ + id: '00000529' + name: ZINC + namespaceEmbeddedInLui: false + pattern: ^(ZINC)?\d+$ + prefix: zinc + sampleId: ZINC1084 + uri_format: http://zinc15.docking.org/substances/$1 + n2t: + description: ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. + example: ZINC1084 + homepage: http://zinc15.docking.org/ + name: ZINC at University of California (San Francisco) + namespaceEmbeddedInLui: false + pattern: ^(ZINC)?\d+$ + prefix: zinc + uri_format: http://zinc15.docking.org/substances/$1 + name: ZINC is not Commercial + wikidata: + prefix: P2084 +zp: + biocontext: + is_identifiers: false + is_obo: true + prefix: ZP + uri_format: http://purl.obolibrary.org/obo/ZP_$1 + bioportal: + name: Zebrafish Phenotype Ontology + prefix: ZP + example: '0019030' + mappings: + biocontext: ZP + bioportal: ZP + obofoundry: zp + ols: zp + ontobee: ZP + obofoundry: + contact: ybradford@zfin.org + contact.github: ybradford + contact.label: Yvonne Bradford + contact.orcid: 0000-0002-9900-7880 + depends_on: + - bfo + - bspo + - go + - pato + - ro + - uberon + - zfa + deprecated: false + description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. + download.obo: http://purl.obolibrary.org/obo/zp.obo + download.owl: http://purl.obolibrary.org/obo/zp.owl + homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology + license: CC BY 3.0 + license.url: http://creativecommons.org/licenses/by/3.0/ + name: Zebrafish Phenotype Ontology + preferredPrefix: ZP + prefix: zp + repository: https://github.com/obophenotype/zebrafish-phenotype-ontology + ols: + description: The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. + download: http://purl.obolibrary.org/obo/zp.owl + homepage: https://github.com/obophenotype/zebrafish-phenotype-ontology + name: Zebrafish Phenotype Ontology (ZP) + prefix: zp + version: 2021-12-12 + version.iri: http://purl.obolibrary.org/obo/zp/releases/2021-12-12/zp.owl + ontobee: + library: Library + name: Zebrafish Phenotype Ontology + prefix: ZP + pattern: ^\d+$ diff --git a/fuji_server/data/linked_vocabs/bioregistry_ontologies.json b/fuji_server/data/linked_vocabs/bioregistry_ontologies.json deleted file mode 100644 index 0af1eeb6..00000000 --- a/fuji_server/data/linked_vocabs/bioregistry_ontologies.json +++ /dev/null @@ -1,46201 +0,0 @@ -{ - 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biological sciences + uri_format: http://bacmap.wishartlab.com/maps/$1/index.html +bioregistry.bactibase: + authority: bioregistry + homepage: http://bactibase.hammamilab.org + id: bioregistry.bactibase + name: 'Bactibase: database dedicated to bacteriocins' + prefix: bactibase + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://bactibase.pfba-lab-tun.org/$1 +bioregistry.bactibase.prefixcommons: + authority: prefixcommons + homepage: http://bactibase.pfba-lab-tun.org/main.php + id: bioregistry.bactibase.prefixcommons + name: 'Bactibase: database dedicated to bacteriocins' + prefix: bactibase + sameas: bioregistry.bactibase + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://bactibase.pfba-lab-tun.org/$1 +bioregistry.bao: + authority: bioregistry + homepage: + id: bioregistry.bao + name: BioAssay Ontology through BioPortal + prefix: bao + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1 +bioregistry.bao.miriam: + authority: miriam + homepage: http://bioportal.bioontology.org/ontologies/BAO/ + id: bioregistry.bao.miriam + name: BioAssay Ontology + prefix: bao + sameas: bioregistry.bao + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: https://bbp.epfl.ch/nexus/web/studios/public/$1 +bioregistry.bbkg.miriam: + authority: miriam + homepage: https://portal.bluebrain.epfl.ch + id: bioregistry.bbkg.miriam + name: Blue Brain Project Knowledge Graph + prefix: bbkg + sameas: bioregistry.bbkg + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://bbp.epfl.ch/nexus/web/studios/public/$1 +bioregistry.bbtp: + authority: bioregistry + homepage: + id: bioregistry.bbtp + name: Blue Brain Project Topological sampling Knowledge Graph + prefix: bbtp + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1 +bioregistry.bbtp.miriam: + authority: miriam + homepage: https://portal.bluebrain.epfl.ch + id: bioregistry.bbtp.miriam + name: Blue Brain Project Topological sampling Knowledge Graph + prefix: bbtp + sameas: bioregistry.bbtp + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1 +bioregistry.bcgo: + authority: bioregistry + homepage: + id: bioregistry.bcgo + name: Breast Cancer Grading Ontology + prefix: bcgo + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1 +bioregistry.bcgo.cellosaurus: + authority: cellosaurus + homepage: https://github.com/obi-bcgo/bcgo + id: bioregistry.bcgo.cellosaurus + name: Beta Cell Genomics Ontology + prefix: BCGO + sameas: bioregistry.bcgo + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1 +bioregistry.bcrc: + authority: bioregistry + homepage: https://catalog.bcrc.firdi.org.tw + id: bioregistry.bcrc + name: Taiwan Bioresource Collection and Research Center + prefix: bcrc + source: bioregistry.io + subjects: + - cell biology + uri_format: https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 +bioregistry.bcrc.cellosaurus: + authority: cellosaurus + homepage: https://catalog.bcrc.firdi.org.tw/ + id: bioregistry.bcrc.cellosaurus + name: Taiwan Bioresource Collection and Research Center + prefix: BCRC + sameas: bioregistry.bcrc + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 +bioregistry.bdgp.insertion.prefixcommons: + authority: prefixcommons + homepage: + id: bioregistry.bdgp.insertion.prefixcommons + name: Drosphila Gene Disruption Database + prefix: bdgp + sameas: bioregistry.bdgp.insertion + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1 +bioregistry.bdsc: + authority: bioregistry + homepage: + id: bioregistry.bdsc + name: Bloomington Drosophila Stock Center + prefix: bdsc + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://bdsc.indiana.edu/stocks/$1 +bioregistry.bdsc.miriam: + authority: miriam + homepage: https://bdsc.indiana.edu/about/mission.html + id: bioregistry.bdsc.miriam + name: Bloomington Drosophila Stock Center + prefix: bdsc + sameas: bioregistry.bdsc + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://bdsc.indiana.edu/stocks/$1 +bioregistry.bdsc.n2t: + authority: n2t + homepage: https://bdsc.indiana.edu/about/mission.html + id: bioregistry.bdsc.n2t + name: BDSC at Indiana University + prefix: bdsc + sameas: bioregistry.bdsc + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://bdsc.indiana.edu/stocks/$1 +bioregistry.beetlebase: + authority: bioregistry + homepage: + id: bioregistry.beetlebase + name: Tribolium Genome Database -- Insertion + prefix: beetlebase + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 +bioregistry.beetlebase.miriam: + authority: miriam + homepage: http://beetlebase.org/ + id: bioregistry.beetlebase.miriam + name: BeetleBase + prefix: beetlebase + sameas: bioregistry.beetlebase + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 +bioregistry.beetlebase.n2t: + authority: n2t + homepage: http://beetlebase.org/ + id: bioregistry.beetlebase.n2t + name: BeetleBase at Kansas State University + prefix: beetlebase + sameas: bioregistry.beetlebase + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 +bioregistry.beetlebase.prefixcommons: + authority: prefixcommons + homepage: http://www.beetlebase.org/ + id: bioregistry.beetlebase.prefixcommons + name: BeetleBase + prefix: beetlebase + sameas: bioregistry.beetlebase + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1 +bioregistry.begdb: + authority: bioregistry + homepage: + id: bioregistry.begdb + name: The Benchmark Energy & Geometry Database + prefix: begdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 +bioregistry.begdb.miriam: + authority: miriam + homepage: http://www.begdb.com + id: bioregistry.begdb.miriam + name: Benchmark Energy & Geometry Database + prefix: begdb + sameas: bioregistry.begdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 +bioregistry.begdb.n2t: + authority: n2t + homepage: http://www.begdb.com + id: bioregistry.begdb.n2t + name: Benchmark Energy & Geometry Database + prefix: begdb + sameas: bioregistry.begdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 +bioregistry.beiresources: + authority: bioregistry + homepage: https://www.beiresources.org + id: bioregistry.beiresources + name: BEI Resources + prefix: beiresources + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 +bioregistry.bgee.family.n2t: + authority: n2t + homepage: http://bgee.unil.ch/bgee/bgee + id: bioregistry.bgee.family.n2t + name: Bgee at Lausanne + prefix: bgee.family + sameas: bioregistry.bgee.family + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 +bioregistry.bgee.gene: + authority: bioregistry + homepage: https://www.bgee.org + id: bioregistry.bgee.gene + name: Bgee DataBase for Gene Expression Evolution + prefix: bgee.gene + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: https://www.bgee.org/gene/$1 +bioregistry.bgee.gene.miriam: + authority: miriam + homepage: https://www.bgee.org/ + id: bioregistry.bgee.gene.miriam + name: Bgee gene + prefix: bgee.gene + sameas: bioregistry.bgee.gene + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://www.bgee.org/gene/$1 +bioregistry.bgee.gene.n2t: + authority: n2t + homepage: https://bgee.org/ + id: bioregistry.bgee.gene.n2t + name: Bgee gene + prefix: bgee.gene + sameas: bioregistry.bgee.gene + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://bgee.org/?page=gene&gene_id=$1 +bioregistry.bgee.gene.prefixcommons: + authority: prefixcommons + homepage: http://bgee.unil.ch + id: bioregistry.bgee.gene.prefixcommons + name: Bgee DataBase for Gene Expression Evolution + prefix: bgee + sameas: bioregistry.bgee.gene + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=$1 +bioregistry.bgee.organ: + authority: bioregistry + homepage: + id: bioregistry.bgee.organ + name: Bgee at Lausanne + prefix: bgee.organ + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$1&organ_children=on +bioregistry.bgee.organ.miriam: + authority: miriam + homepage: http://bgee.unil.ch/bgee/bgee + id: bioregistry.bgee.organ.miriam + name: Bgee organ + prefix: bgee.organ + sameas: bioregistry.bgee.organ + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: http://foodb.ca/compounds/$1 +bioregistry.foodb.compound.n2t: + authority: n2t + homepage: http://foodb.ca/foods + id: bioregistry.foodb.compound.n2t + name: FooDB database of food additives at University of Alberta + prefix: foodb.compound + sameas: bioregistry.foodb.compound + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://foodb.ca/compounds/$1 +bioregistry.foodb.compound.wikidata: + authority: wikidata + homepage: + id: bioregistry.foodb.compound.wikidata + name: FooDB compound ID + prefix: P8117 + sameas: bioregistry.foodb.compound + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://foodb.ca/compounds/$1 +bioregistry.foodb.food: + authority: bioregistry + homepage: https://foodb.ca/foods + id: bioregistry.foodb.food + name: FooDB Food + prefix: foodb.food + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://foodb.ca/compounds/$1 +bioregistry.foodb.food.biolink: + authority: biolink + homepage: + id: bioregistry.foodb.food.biolink + name: + prefix: foodb.food + sameas: bioregistry.foodb.food + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://foodb.ca/compounds/$1 +bioregistry.foodon: + authority: bioregistry + homepage: + id: bioregistry.foodon + name: FoodOn Food Ontology through OLS + prefix: foodon + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://www.ebi.ac.uk/ols4/ontologies/foodon/terms?obo_id=FOODON:$1 +bioregistry.foodon.miriam: + authority: miriam + homepage: https://foodon.org + id: bioregistry.foodon.miriam + name: FoodOn Food Ontology + prefix: foodon + sameas: bioregistry.foodon + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://www.ebi.ac.uk/ols4/ontologies/foodon/terms?obo_id=FOODON:$1 +bioregistry.foodon.n2t: + authority: n2t + homepage: https://foodon.org + id: bioregistry.foodon.n2t + name: FoodOn Food Ontology through OLS + prefix: foodon + sameas: bioregistry.foodon + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 +bioregistry.fossilworks.journal: + authority: bioregistry + homepage: http://fossilworks.org + id: bioregistry.fossilworks.journal + name: Fossilworks ID for this journal article + prefix: fossilworks.journal + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 +bioregistry.funcbase.mouse.miriam: + authority: miriam + homepage: http://func.mshri.on.ca/mouse/ + id: bioregistry.funcbase.mouse.miriam + name: FuncBase Mouse + prefix: funcbase.mouse + sameas: bioregistry.funcbase.mouse + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 +bioregistry.funcbase.mouse.n2t: + authority: n2t + homepage: http://func.mshri.on.ca/mouse/ + id: bioregistry.funcbase.mouse.n2t + name: FuncBase Mouse at Harvard Medical School + prefix: funcbase.mouse + sameas: bioregistry.funcbase.mouse + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1 +bioregistry.funcbase.yeast: + authority: bioregistry + homepage: + id: bioregistry.funcbase.yeast + name: FuncBase Yeast at Harvard Medical School + prefix: funcbase.yeast + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 +bioregistry.funcbase.yeast.miriam: + authority: miriam + homepage: http://func.mshri.on.ca/yeast + id: bioregistry.funcbase.yeast.miriam + name: FuncBase Yeast + prefix: funcbase.yeast + sameas: bioregistry.funcbase.yeast + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 +bioregistry.funcbase.yeast.n2t: + authority: n2t + homepage: http://func.mshri.on.ca/yeast + id: bioregistry.funcbase.yeast.n2t + name: FuncBase Yeast at Harvard Medical School + prefix: funcbase.yeast + sameas: bioregistry.funcbase.yeast + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1 +bioregistry.funderregistry: + authority: bioregistry + homepage: + id: bioregistry.funderregistry + name: FunderRegistry + prefix: funderregistry + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 +bioregistry.oryzabase.strain.n2t: + authority: n2t + homepage: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ + id: bioregistry.oryzabase.strain.n2t + name: Oryzabase v4 Strain at National Institute of Genetics (Japan) + prefix: oryzabase.strain + sameas: bioregistry.oryzabase.strain + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 +bioregistry.otl: + authority: bioregistry + homepage: + id: bioregistry.otl + name: 'Oryza Tag Line: An integrated database for the functional analysis of the rice genome' + prefix: otl + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://urgi.versailles.inra.fr/OryzaTagLine/cgi-bin/general_mutant.pl?line=$1 +bioregistry.otl.miriam: + authority: miriam + homepage: http://oryzatagline.cirad.fr/ + id: bioregistry.otl.miriam + name: Oryza Tag Line + prefix: otl + sameas: bioregistry.otl + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: https://github.com/cmungall/owlstar/blob/master/owlstar.ttl$1 +bioregistry.owlstar.biolink: + authority: biolink + homepage: + id: bioregistry.owlstar.biolink + name: + prefix: os + sameas: bioregistry.owlstar + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://github.com/cmungall/owlstar/blob/master/owlstar.ttl$1 +bioregistry.p3db.protein: + authority: bioregistry + homepage: + id: bioregistry.p3db.protein + name: P3DB Protein at University of Missouri + prefix: p3db.protein + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://www.p3db.org/protein.php?id=$1&ref=0 +bioregistry.p3db.protein.miriam: + authority: miriam + homepage: http://www.p3db.org/ + id: bioregistry.p3db.protein.miriam + name: P3DB Protein + prefix: p3db.protein + sameas: bioregistry.p3db.protein + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.p3db.org/protein.php?id=$1&ref=0 +bioregistry.p3db.protein.n2t: + authority: n2t + homepage: http://www.p3db.org/ + id: bioregistry.p3db.protein.n2t + name: P3DB Protein at University of Missouri + prefix: p3db.protein + sameas: bioregistry.p3db.protein + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: http://www.pharmgkb.org/disease/$1 +bioregistry.pharmgkb.disease.prefixcommons: + authority: prefixcommons + homepage: + id: bioregistry.pharmgkb.disease.prefixcommons + name: PharmGKB Disease + prefix: pharmgkb.disease + sameas: bioregistry.pharmgkb.disease + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.pharmgkb.org/disease/$1 +bioregistry.pharmgkb.drug: + authority: bioregistry + homepage: + id: bioregistry.pharmgkb.drug + name: PharmGKB Drug at Stanford + prefix: pharmgkb.drug + source: bioregistry.io + subjects: + - biological sciences + - genetics + - pharmacology and pharmacy + uri_format: http://www.pharmgkb.org/drug/$1 +bioregistry.pharmgkb.drug.miriam: + authority: miriam + homepage: http://www.pharmgkb.org/ + id: bioregistry.pharmgkb.drug.miriam + name: PharmGKB Drug + prefix: pharmgkb.drug + sameas: bioregistry.pharmgkb.drug + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.pharmgkb.org/drug/$1 +bioregistry.pharmgkb.drug.n2t: + authority: n2t + homepage: http://www.pharmgkb.org/ + id: bioregistry.pharmgkb.drug.n2t + name: PharmGKB Drug at Stanford + prefix: pharmgkb.drug + sameas: bioregistry.pharmgkb.drug + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.pharmgkb.org/drug/$1 +bioregistry.pharmgkb.drug.prefixcommons: + authority: prefixcommons + homepage: + id: bioregistry.pharmgkb.drug.prefixcommons + name: PharmGKB Drug + prefix: pharmgkb.drug + sameas: bioregistry.pharmgkb.drug + source: bioregistry.io + subjects: + - biological sciences + - genetics + - pharmacology and pharmacy + uri_format: http://www.pharmgkb.org/drug/$1 +bioregistry.pharmgkb.gene: + authority: bioregistry + homepage: + id: bioregistry.pharmgkb.gene + name: The Pharmacogenetics and Pharmacogenomics Knowledge Base + prefix: pharmgkb.gene + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: https://www.pharmgkb.org/gene/$1 +bioregistry.pharmgkb.gene.biolink: + authority: biolink + homepage: + id: bioregistry.pharmgkb.gene.biolink + name: + prefix: PHARMGKB.GENE + sameas: bioregistry.pharmgkb.gene + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: https://www.pharmgkb.org/gene/$1 +bioregistry.pharmgkb.gene.go: + authority: go + homepage: https://www.pharmgkb.org + id: bioregistry.pharmgkb.gene.go + name: Pharmacogenetics and Pharmacogenomics Knowledge Base + prefix: PharmGKB + sameas: bioregistry.pharmgkb.gene + source: bioregistry.io + subjects: + - 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biological sciences + uri_format: http://phenol-explorer.eu/foods/$1 +bioregistry.phenolexplorer.n2t: + authority: n2t + homepage: http://www.phenol-explorer.eu/foods/ + id: bioregistry.phenolexplorer.n2t + name: Phenol-Explorer Database on Phenol content of foods + prefix: phenolexplorer + sameas: bioregistry.phenolexplorer + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://phenol-explorer.eu/foods/$1 +bioregistry.phosphopoint.kinase: + authority: bioregistry + homepage: + id: bioregistry.phosphopoint.kinase + name: PhosphoPoint Kinase at National Taiwan University + prefix: phosphopoint.kinase + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 +bioregistry.phosphopoint.kinase.miriam: + authority: miriam + homepage: http://kinase.bioinformatics.tw/ + id: bioregistry.phosphopoint.kinase.miriam + name: PhosphoPoint Kinase + prefix: phosphopoint.kinase + sameas: bioregistry.phosphopoint.kinase + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 +bioregistry.phosphopoint.kinase.n2t: + authority: n2t + homepage: http://kinase.bioinformatics.tw/ + id: bioregistry.phosphopoint.kinase.n2t + name: PhosphoPoint Kinase at National Taiwan University + prefix: phosphopoint.kinase + sameas: bioregistry.phosphopoint.kinase + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 +bioregistry.phosphopoint.protein: + authority: bioregistry + homepage: + id: bioregistry.phosphopoint.protein + name: PhosphoPoint Phosphoprotein at National Taiwan University + prefix: phosphopoint.protein + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 +bioregistry.phosphopoint.protein.miriam: + authority: miriam + homepage: http://kinase.bioinformatics.tw/ + id: bioregistry.phosphopoint.protein.miriam + name: PhosphoPoint Phosphoprotein + prefix: phosphopoint.protein + sameas: bioregistry.phosphopoint.protein + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 +bioregistry.phosphopoint.protein.n2t: + authority: n2t + homepage: http://kinase.bioinformatics.tw/ + id: bioregistry.phosphopoint.protein.n2t + name: PhosphoPoint Phosphoprotein at National Taiwan University + prefix: phosphopoint.protein + sameas: bioregistry.phosphopoint.protein + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 +bioregistry.phosphosite.protein: + authority: bioregistry + homepage: + id: bioregistry.phosphosite.protein + name: PhosphoSite Protein + prefix: phosphosite.protein + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phosphosite.org/proteinAction.do?id=$1 +bioregistry.phosphosite.protein.miriam: + authority: miriam + homepage: http://www.phosphosite.org/homeAction.do + id: bioregistry.phosphosite.protein.miriam + name: PhosphoSite Protein + prefix: phosphosite.protein + sameas: bioregistry.phosphosite.protein + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phosphosite.org/proteinAction.do?id=$1 +bioregistry.phosphosite.protein.n2t: + authority: n2t + homepage: http://www.phosphosite.org/homeAction.do + id: bioregistry.phosphosite.protein.n2t + name: PhosphoSite + prefix: phosphosite.protein + sameas: bioregistry.phosphosite.protein + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phosphosite.org/proteinAction.do?id=$1 +bioregistry.phosphosite.residue: + authority: bioregistry + homepage: + id: bioregistry.phosphosite.residue + name: PhosphoSite Residue + prefix: phosphosite.residue + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phosphosite.org/siteAction.do?id=$1 +bioregistry.phosphosite.residue.miriam: + authority: miriam + homepage: http://www.phosphosite.org/homeAction.do + id: bioregistry.phosphosite.residue.miriam + name: PhosphoSite Residue + prefix: phosphosite.residue + sameas: bioregistry.phosphosite.residue + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phosphosite.org/siteAction.do?id=$1 +bioregistry.phosphosite.residue.n2t: + authority: n2t + homepage: http://www.phosphosite.org/homeAction.do + id: bioregistry.phosphosite.residue.n2t + name: PhosphoSite Residue + prefix: phosphosite.residue + sameas: bioregistry.phosphosite.residue + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phosphosite.org/siteAction.do?id=$1 +bioregistry.phylomedb: + authority: bioregistry + homepage: + id: bioregistry.phylomedb + name: PhylomeDB at Centro de Investigación Príncipe Felipe + prefix: phylomedb + source: bioregistry.io + subjects: + - biological sciences + - genetics + - biochemistry + uri_format: http://phylomedb.org/search_phylome/?seqid=$1 +bioregistry.phylomedb.miriam: + authority: miriam + homepage: http://phylomedb.org/ + id: bioregistry.phylomedb.miriam + name: PhylomeDB + prefix: phylomedb + sameas: bioregistry.phylomedb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://phylomedb.org/?seqid=$1 +bioregistry.phylomedb.n2t: + authority: n2t + homepage: http://phylomedb.org/ + id: bioregistry.phylomedb.n2t + name: PhylomeDB at Centro de Investigación Príncipe Felipe + prefix: phylomedb + sameas: bioregistry.phylomedb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://phylomedb.org/?seqid=$1 +bioregistry.phylomedb.prefixcommons: + authority: prefixcommons + homepage: http://phylomedb.bioinfo.cipf.es + id: bioregistry.phylomedb.prefixcommons + name: Database for complete collections of gene phylogenies + prefix: phylomedb + sameas: bioregistry.phylomedb + source: bioregistry.io + subjects: + - biological sciences + - genetics + - biochemistry + uri_format: http://phylomedb.org/?seqid=$1 +bioregistry.phylomedb.uniprot: + authority: uniprot + homepage: http://phylomedb.org/ + id: bioregistry.phylomedb.uniprot + name: Database for complete collections of gene phylogenies + prefix: DB-0144 + sameas: bioregistry.phylomedb + source: bioregistry.io + subjects: + - biological sciences + - genetics + - biochemistry + uri_format: http://phylomedb.org/search_phylome/?seqid=$1 +bioregistry.phytozome.locus: + authority: bioregistry + homepage: + id: bioregistry.phytozome.locus + name: Phytozome Locus at Joint Genome Institute + prefix: phytozome.locus + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 +bioregistry.phytozome.locus.miriam: + authority: miriam + homepage: http://www.phytozome.net/ + id: bioregistry.phytozome.locus.miriam + name: Phytozome Locus + prefix: phytozome.locus + sameas: bioregistry.phytozome.locus + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 +bioregistry.phytozome.locus.n2t: + authority: n2t + homepage: http://www.phytozome.net/ + id: bioregistry.phytozome.locus.n2t + name: Phytozome Locus at Joint Genome Institute + prefix: phytozome.locus + sameas: bioregistry.phytozome.locus + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1 +bioregistry.pibase: + authority: bioregistry + homepage: + id: bioregistry.pibase + name: 'PIBASE: a database of structurally defined protein interfaces' + prefix: pibase + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1 +bioregistry.pibase.prefixcommons: + authority: prefixcommons + homepage: http://salilab.org/pibase + id: bioregistry.pibase.prefixcommons + name: 'PIBASE: a database of structurally defined protein interfaces' + prefix: pibase + sameas: bioregistry.pibase + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1 +bioregistry.pid.pathway: + authority: bioregistry + homepage: + id: bioregistry.pid.pathway + name: NCI Pathway Interaction Database (Pathway) + prefix: pid.pathway + source: bioregistry.io + subjects: + - 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biological sciences + - genetics + - biochemistry + uri_format: http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1 +bioregistry.pigqtldb: + authority: bioregistry + homepage: + id: bioregistry.pigqtldb + name: Animal QTL Pig at Iowa State University + prefix: pigqtldb + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 +bioregistry.pigqtldb.miriam: + authority: miriam + homepage: https://www.animalgenome.org/QTLdb + id: bioregistry.pigqtldb.miriam + name: Animal Genome Pig QTL + prefix: pigqtldb + sameas: bioregistry.pigqtldb + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 +bioregistry.pigqtldb.n2t: + authority: n2t + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/SS/index + id: bioregistry.pigqtldb.n2t + name: Animal QTL Pig at Iowa State University + prefix: pigqtldb + sameas: bioregistry.pigqtldb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1 +bioregistry.pigqtldb.prefixcommons: + authority: prefixcommons + homepage: http://www.animalgenome.org/cgi-bin/QTLdb/SS/index + id: bioregistry.pigqtldb.prefixcommons + name: Pig Quantitative Trait Locus database + prefix: pigqtldb + sameas: bioregistry.pigqtldb + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$1 +bioregistry.pina: + authority: bioregistry + homepage: + id: bioregistry.pina + name: Protein Interaction Network Analysis (PINA) at Garvan Institute + prefix: pina + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null +bioregistry.pina.miriam: + authority: miriam + homepage: http://cbg.garvan.unsw.edu.au/pina/ + id: bioregistry.pina.miriam + name: PINA + prefix: pina + sameas: bioregistry.pina + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null +bioregistry.pina.n2t: + authority: n2t + homepage: http://cbg.garvan.unsw.edu.au/pina/ + id: bioregistry.pina.n2t + name: Protein Interaction Network Analysis (PINA) at Garvan Institute + prefix: pina + sameas: bioregistry.pina + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$1&showExtend=null +bioregistry.piroplasma: + authority: bioregistry + homepage: + id: bioregistry.piroplasma + name: PiroplasmaBD at EuPathDB + prefix: piroplasma + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +bioregistry.piroplasma.miriam: + authority: miriam + homepage: http://piroplasmadb.org/ + id: bioregistry.piroplasma.miriam + name: PiroplasmaDB + prefix: piroplasma + sameas: bioregistry.piroplasma + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +bioregistry.piroplasma.n2t: + authority: n2t + homepage: http://piroplasmadb.org/ + id: bioregistry.piroplasma.n2t + name: PiroplasmaBD at EuPathDB + prefix: piroplasma + sameas: bioregistry.piroplasma + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 +bioregistry.pirsf: + authority: bioregistry + homepage: + id: bioregistry.pirsf + name: PIRSF; a whole-protein classification database + prefix: pirsf + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: https://proteininformationresource.org/cgi-bin/ipcSF?id=$1 +bioregistry.pirsf.go: + authority: go + homepage: http://pir.georgetown.edu/pirsf/ + id: bioregistry.pirsf.go + name: PIR Superfamily Classification System + prefix: PIRSF + sameas: bioregistry.pirsf + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 +bioregistry.pirsf.miriam: + authority: miriam + homepage: https://pir.georgetown.edu/ + id: bioregistry.pirsf.miriam + name: PIRSF + prefix: pirsf + sameas: bioregistry.pirsf + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 +bioregistry.pirsf.n2t: + authority: n2t + homepage: https://pir.georgetown.edu/ + id: bioregistry.pirsf.n2t + name: PIRSF + prefix: pirsf + sameas: bioregistry.pirsf + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 +bioregistry.pirsf.prefixcommons: + authority: prefixcommons + homepage: http://pir.georgetown.edu/pirsf/ + id: bioregistry.pirsf.prefixcommons + name: PIRSF; a whole-protein classification database + prefix: pirsf + sameas: bioregistry.pirsf + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 +bioregistry.pirsf.uniprot: + authority: uniprot + homepage: https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml + id: bioregistry.pirsf.uniprot + name: PIRSF; a whole-protein classification database + prefix: DB-0079 + sameas: bioregistry.pirsf + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: https://proteininformationresource.org/cgi-bin/ipcSF?id=$1 +bioregistry.pkdb: + authority: bioregistry + homepage: + id: bioregistry.pkdb + name: Pharmacokinetics Database + prefix: pkdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://pk-db.com/data/$1 +bioregistry.pkdb.miriam: + authority: miriam + homepage: https://www.hu-berlin.de/?set_language=en&cl=en + id: bioregistry.pkdb.miriam + name: PK-DB + prefix: pkdb + sameas: bioregistry.pkdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://pk-db.com/data/$1 +bioregistry.planttfdb: + authority: bioregistry + homepage: + id: bioregistry.planttfdb + name: Plant Transcription Factor Database + prefix: planttfdb + source: bioregistry.io + subjects: + - biological sciences + - genetics + - biochemistry + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 +bioregistry.planttfdb.miriam: + authority: miriam + homepage: http://planttfdb.cbi.pku.edu.cn + id: bioregistry.planttfdb.miriam + name: Plant Transcription Factor Database + prefix: planttfdb + sameas: bioregistry.planttfdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 +bioregistry.planttfdb.n2t: + authority: n2t + homepage: http://planttfdb.cbi.pku.edu.cn + id: bioregistry.planttfdb.n2t + name: PlantTFDB at Peking University + prefix: planttfdb + sameas: bioregistry.planttfdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 +bioregistry.planttfdb.prefixcommons: + authority: prefixcommons + homepage: http://planttfdb.cbi.pku.edu.cn + id: bioregistry.planttfdb.prefixcommons + name: Plant Transcription Factor Database + prefix: planttfdb + sameas: bioregistry.planttfdb + source: bioregistry.io + subjects: + - biological sciences + - genetics + - biochemistry + uri_format: http://planttfdb.cbi.pku.edu.cn/tf.php?sp=[?species_name]&did=$1 +bioregistry.plasmodb: + authority: bioregistry + homepage: + id: bioregistry.plasmodb + name: Plasmodium Genome Resources + prefix: plasmodb + source: bioregistry.io + subjects: + - 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biological sciences + - genetics + uri_format: http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1&project_id=PlasmoDB +bioregistry.pmap.cutdb: + authority: bioregistry + homepage: + id: bioregistry.pmap.cutdb + name: CutDB at The Burnham Institute for Medical Research + prefix: pmap.cutdb + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://www.proteolysis.org/proteases/m_summarypg/$1 +bioregistry.pmap.cutdb.miriam: + authority: miriam + homepage: http://cutdb.burnham.org + id: bioregistry.pmap.cutdb.miriam + name: CutDB + prefix: pmap.cutdb + sameas: bioregistry.pmap.cutdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://cutdb.burnham.org/relation/show/$1 +bioregistry.pmap.cutdb.n2t: + authority: n2t + homepage: http://cutdb.burnham.org + id: bioregistry.pmap.cutdb.n2t + name: CutDB at The Burnham Institute for Medical Research + prefix: pmap.cutdb + sameas: bioregistry.pmap.cutdb + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://cutdb.burnham.org/relation/show/$1 +bioregistry.pmap.cutdb.prefixcommons: + authority: prefixcommons + homepage: http://www.proteolysis.org/ + id: bioregistry.pmap.cutdb.prefixcommons + name: CutDB - Proteolytic event database + prefix: pmap.cutdb + sameas: bioregistry.pmap.cutdb + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://www.proteolysis.org/proteases/m_summarypg/$1 +bioregistry.pmap.substratedb: + authority: bioregistry + homepage: + id: bioregistry.pmap.substratedb + name: SubstrateDB at The Burnham Institute for Medical Research + prefix: pmap.substratedb + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://substrate.burnham.org/protein/annotation/$1/html +bioregistry.pmap.substratedb.miriam: + authority: miriam + homepage: http://substrate.burnham.org/ + id: bioregistry.pmap.substratedb.miriam + name: SubstrateDB + prefix: pmap.substratedb + sameas: bioregistry.pmap.substratedb + source: bioregistry.io + subjects: + - 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biological sciences + - genetics + uri_format: https://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 +bioregistry.xenbase.biocontext: + authority: biocontext + homepage: + id: bioregistry.xenbase.biocontext + name: + prefix: Xenbase + sameas: bioregistry.xenbase + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 +bioregistry.xenbase.biolink: + authority: biolink + homepage: + id: bioregistry.xenbase.biolink + name: + prefix: Xenbase + sameas: bioregistry.xenbase + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 +bioregistry.xenbase.miriam: + authority: miriam + homepage: https://www.xenbase.org/ + id: bioregistry.xenbase.miriam + name: Xenbase + prefix: xenbase + sameas: bioregistry.xenbase + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://www.xenbase.org/entry/$1 +bioregistry.xenbase.n2t: + authority: n2t + homepage: http://www.xenbase.org/ + id: bioregistry.xenbase.n2t + name: Xenbase at University of Calgary + prefix: xenbase + sameas: bioregistry.xenbase + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$1 +bioregistry.xenbase.prefixcommons: + authority: prefixcommons + homepage: http://www.xenbase.org + id: bioregistry.xenbase.prefixcommons + name: Xenopus laevis and tropicalis biology and genomics resource + prefix: xenbase + sameas: bioregistry.xenbase + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 +bioregistry.xenbase.uniprot: + authority: uniprot + homepage: https://www.xenbase.org/ + id: bioregistry.xenbase.uniprot + name: Xenopus laevis and tropicalis biology and genomics resource + prefix: DB-0129 + sameas: bioregistry.xenbase + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: https://www.xenbase.org/gene/showgene.do?method=display&geneId=$1 +bioregistry.ximbio: + authority: bioregistry + homepage: https://ximbio.com + id: bioregistry.ximbio + name: Ximbio reagents online portal + prefix: ximbio + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://ximbio.com/reagent/$1 +bioregistry.ximbio.cellosaurus: + authority: cellosaurus + homepage: https://ximbio.com + id: bioregistry.ximbio.cellosaurus + name: Ximbio reagents online portal + prefix: Ximbio + sameas: bioregistry.ximbio + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://ximbio.com/reagent/$1 +bioregistry.xml: + authority: bioregistry + homepage: https://www.w3.org/TR/xml/ + id: bioregistry.xml + name: Extensible Markup Language + prefix: xml + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.w3.org/XML/1998/namespace$1 +bioregistry.xml.biocontext: + authority: biocontext + homepage: + id: bioregistry.xml.biocontext + name: + prefix: xml + sameas: bioregistry.xml + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.w3.org/XML/1998/namespace$1 +bioregistry.xpo: + authority: bioregistry + homepage: + id: bioregistry.xpo + name: Xenopus Phenotype Ontology + prefix: xpo + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://purl.obolibrary.org/obo/XPO_$1 +bioregistry.xpo.biolink: + authority: biolink + homepage: + id: bioregistry.xpo.biolink + name: + prefix: XPO + sameas: bioregistry.xpo + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://purl.obolibrary.org/obo/XPO_$1 +bioregistry.xsd: + authority: bioregistry + homepage: http://www.w3.org/2001/XMLSchema + id: bioregistry.xsd + name: XML Schema Definition + prefix: xsd + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.w3.org/2001/XMLSchema#$1 +bioregistry.xsd.biocontext: + authority: biocontext + homepage: + id: bioregistry.xsd.biocontext + name: + prefix: xsd + sameas: bioregistry.xsd + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www.w3.org/2001/XMLSchema#$1 +bioregistry.ydpm: + authority: bioregistry + homepage: + id: bioregistry.ydpm + name: Yeast Deletion Project and Proteomics of Mitochondria Database + prefix: ydpm + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 +bioregistry.ydpm.miriam: + authority: miriam + homepage: http://www-deletion.stanford.edu/YDPM/ + id: bioregistry.ydpm.miriam + name: YDPM + prefix: ydpm + sameas: bioregistry.ydpm + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 +bioregistry.ydpm.n2t: + authority: n2t + homepage: http://www-deletion.stanford.edu/YDPM/ + id: bioregistry.ydpm.n2t + name: YDPM at Stanford University School of Medicine + prefix: ydpm + sameas: bioregistry.ydpm + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 +bioregistry.yeastintron: + authority: bioregistry + homepage: + id: bioregistry.yeastintron + name: Yeast Intron Database version 4.3 at Baskin School of Engineering + prefix: yeastintron + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1 +bioregistry.yeastintron.miriam: + authority: miriam + homepage: http://intron.ucsc.edu/yeast4.3/ + id: bioregistry.yeastintron.miriam + name: Yeast Intron Database v4.3 + prefix: yeastintron + sameas: bioregistry.yeastintron + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1 +bioregistry.yeastintron.n2t: + authority: n2t + homepage: http://intron.ucsc.edu/yeast4.3/ + id: bioregistry.yeastintron.n2t + name: Yeast Intron Database version 4.3 at Baskin School of Engineering + prefix: yeastintron + sameas: bioregistry.yeastintron + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1 +bioregistry.yeastract: + authority: bioregistry + homepage: + id: bioregistry.yeastract + name: Yeast Searching for Transcriptional Regulators and Consensus Tracking + prefix: yeastract + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.yeastract.com/view.php?existing=locus&orfname=$1 +bioregistry.yeastract.prefixcommons: + authority: prefixcommons + homepage: http://www.yeastract.com + id: bioregistry.yeastract.prefixcommons + name: Yeast Searching for Transcriptional Regulators and Consensus Tracking + prefix: yeastract + sameas: bioregistry.yeastract + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://www.yeastract.com/view.php?existing=locus&orfname=$1 +bioregistry.yetfasco: + authority: bioregistry + homepage: + id: bioregistry.yetfasco + name: YeTFasCo at University of Toronto + prefix: yetfasco + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 +bioregistry.yetfasco.miriam: + authority: miriam + homepage: http://yetfasco.ccbr.utoronto.ca/ + id: bioregistry.yetfasco.miriam + name: YeTFasCo + prefix: yetfasco + sameas: bioregistry.yetfasco + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 +bioregistry.yetfasco.n2t: + authority: n2t + homepage: http://yetfasco.ccbr.utoronto.ca/ + id: bioregistry.yetfasco.n2t + name: YeTFasCo at University of Toronto + prefix: yetfasco + sameas: bioregistry.yetfasco + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 +bioregistry.ygob: + authority: bioregistry + homepage: + id: bioregistry.ygob + name: Yeast Genome Order Browser + prefix: ygob + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1 +bioregistry.ygob.prefixcommons: + authority: prefixcommons + homepage: http://wolfe.gen.tcd.ie/ygob + id: bioregistry.ygob.prefixcommons + name: Yeast Genome Order Browser + prefix: ygob + sameas: bioregistry.ygob + source: bioregistry.io + subjects: + - biological sciences + - genetics + uri_format: http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1 +bioregistry.yid: + authority: bioregistry + homepage: + id: bioregistry.yid + name: Yeast Intron Database version 3 at Baskin School of Engineering + prefix: yid + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 +bioregistry.yid.miriam: + authority: miriam + homepage: http://compbio.soe.ucsc.edu/yeast_introns.html + id: bioregistry.yid.miriam + name: Yeast Intron Database v3 + prefix: yid + sameas: bioregistry.yid + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 +bioregistry.yid.n2t: + authority: n2t + homepage: http://compbio.soe.ucsc.edu/yeast_introns.html + id: bioregistry.yid.n2t + name: Yeast Intron Database version 3 at Baskin School of Engineering + prefix: yid + sameas: bioregistry.yid + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 +bioregistry.yrcpdr: + authority: bioregistry + homepage: + id: bioregistry.yrcpdr + name: Yeast Resource Center Public Data Repository + prefix: yrcpdr + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1 +bioregistry.yrcpdr.miriam: + authority: miriam + homepage: http://www.yeastrc.org/pdr/ + id: bioregistry.yrcpdr.miriam + name: YRC PDR + prefix: yrcpdr + sameas: bioregistry.yrcpdr + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1 +bioregistry.yrcpdr.n2t: + authority: n2t + homepage: http://www.yeastrc.org/pdr/ + id: bioregistry.yrcpdr.n2t + name: YRC PDR at University of Washington + prefix: yrcpdr + sameas: bioregistry.yrcpdr + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://yeastrc.org/pdr/viewProtein.do?id=$1 +bioregistry.yrcpdr.prefixcommons: + authority: prefixcommons + homepage: http://www.yeastrc.org/pdr/ + id: bioregistry.yrcpdr.prefixcommons + name: Yeast Resource Center Public Data Repository + prefix: yrc + sameas: bioregistry.yrcpdr + source: bioregistry.io + subjects: + - biological sciences + - biochemistry + uri_format: http://www.yeastrc.org/pdr/viewProtein.do?id=$1 +bioregistry.zenodo.record: + authority: bioregistry + homepage: https://zenodo.org + id: bioregistry.zenodo.record + name: Zenodo ID + prefix: zenodo.record + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://zenodo.org/record/$1 +bioregistry.zenodo.record.wikidata: + authority: wikidata + homepage: + id: bioregistry.zenodo.record.wikidata + name: Zenodo ID + prefix: P4901 + sameas: bioregistry.zenodo.record + source: bioregistry.io + subjects: + - biological sciences + uri_format: https://zenodo.org/record/$1 +bioregistry.zfin: + authority: bioregistry + homepage: + id: bioregistry.zfin + name: Zebrafish Information Network genome database + prefix: zfin + source: bioregistry.io + subjects: + - biological sciences + - zoology + - genetics + uri_format: https://zfin.org/$1 +bioregistry.zfin.biocontext: + authority: biocontext + homepage: + id: bioregistry.zfin.biocontext + name: + prefix: ZFIN + sameas: bioregistry.zfin + source: bioregistry.io + subjects: + - biological sciences + - zoology + - genetics + uri_format: http://zfin.org/$1 +bioregistry.zfin.miriam: + authority: miriam + homepage: http://zfin.org + id: bioregistry.zfin.miriam + name: ZFIN Bioentity + prefix: zfin + sameas: bioregistry.zfin + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://zfin.org/$1 +bioregistry.zfin.n2t: + authority: n2t + homepage: http://zfin.org + id: bioregistry.zfin.n2t + name: ZFIN at University of Oregon + prefix: zfin + sameas: bioregistry.zfin + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://zfin.org/$1 +bioregistry.zfin.prefixcommons: + authority: prefixcommons + homepage: http://zfin.org/ + id: bioregistry.zfin.prefixcommons + name: Zebrafish Information Network genome database + prefix: zfin + sameas: bioregistry.zfin + source: bioregistry.io + subjects: + - biological sciences + - zoology + - genetics + uri_format: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=$1 +bioregistry.zfin.uniprot: + authority: uniprot + homepage: https://zfin.org/ + id: bioregistry.zfin.uniprot + name: Zebrafish Information Network genome database + prefix: DB-0113 + sameas: bioregistry.zfin + source: bioregistry.io + subjects: + - biological sciences + - zoology + - genetics + uri_format: https://zfin.org/$1 +bioregistry.zfin.wikidata: + authority: wikidata + homepage: http://zfin.org + id: bioregistry.zfin.wikidata + name: ZFIN Gene ID + prefix: P3870 + sameas: bioregistry.zfin + source: bioregistry.io + subjects: + - biological sciences + - zoology + - genetics + uri_format: https://zfin.org/$1 +bioregistry.zinc: + authority: bioregistry + homepage: + id: bioregistry.zinc + name: ZINC at University of California (San Francisco) + prefix: zinc + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://zinc15.docking.org/substances/$1 +bioregistry.zinc.miriam: + authority: miriam + homepage: http://zinc15.docking.org/ + id: bioregistry.zinc.miriam + name: ZINC + prefix: zinc + sameas: bioregistry.zinc + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://zinc15.docking.org/substances/$1 +bioregistry.zinc.n2t: + authority: n2t + homepage: http://zinc15.docking.org/ + id: bioregistry.zinc.n2t + name: ZINC at University of California (San Francisco) + prefix: zinc + sameas: bioregistry.zinc + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://zinc15.docking.org/substances/$1 +bioregistry.zinc.wikidata: + authority: wikidata + homepage: http://zinc.docking.org/ + id: bioregistry.zinc.wikidata + name: ZINC ID + prefix: P2084 + sameas: bioregistry.zinc + source: bioregistry.io + subjects: + - biological sciences + uri_format: http://zinc.docking.org/substances/ZINC$1 diff --git a/fuji_server/data/linked_vocabs/cessda_ontologies.json b/fuji_server/data/linked_vocabs/cessda_ontologies.json deleted file mode 100644 index 444db141..00000000 --- a/fuji_server/data/linked_vocabs/cessda_ontologies.json +++ /dev/null @@ -1,538 +0,0 @@ -{ - "cessda.AggregationMethod": { - "authority": "cessda", - "description": "Identifies the type of aggregation used to combine related categories, usually within a common branch of a hierarchy, to provide information at a broader level than the level at which detailed observations are taken. (From: The OECD Glossary of Statistical Terms)", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/AggregationMethod", - "id": "cessda.AggregationMethod", - "name": "Aggregation Method", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "AggregationMethod", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/AggregationMethod$1" - }, - "cessda.AnalysisUnit": { - "authority": "cessda", - "description": "Describes the entity being analyzed in the study or variable. This vocabulary can also be used to describe the unit of observation, which is the unit being observed, or from which data are collected. The unit of observation can be the same as, or different from the unit of analysis. ", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/AnalysisUnit", - "id": "cessda.AnalysisUnit", - "name": "Analysis Unit", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "AnalysisUnit", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/AnalysisUnit$1" - }, - "cessda.CdcPublisherNames": { - "authority": "cessda", - "description": "Names of organisations providing metadata for CESSDA Data Catalogue.", - "homepage": "https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames/6.0.0", - "id": "cessda.CdcPublisherNames", - "name": "CDC Publisher Names", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CdcPublisherNames", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames/6.0.0$1" - }, - "cessda.CessdaPersistentIdentifierTypes": { - "authority": "cessda", - "description": "Lists the types of persistent identifiers that CESSDA accepts as study level PIDs in its data catalogue.", - "homepage": "https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes", - "id": "cessda.CessdaPersistentIdentifierTypes", - "name": "CESSDA Persistent Identifier Types", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CessdaPersistentIdentifierTypes", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes$1" - }, - "cessda.CharacterSet": { - "authority": "cessda", - "description": "Standard set of characters upon which many character encodings are based (Wikipedia).", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/CharacterSet", - "id": "cessda.CharacterSet", - "name": "Character Set", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CharacterSet", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/CharacterSet$1" - }, - "cessda.CommonalityType": { - "authority": "cessda", - "description": "Describes the degree of similarity between two items or schemes (collections of items).", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/CommonalityType", - "id": "cessda.CommonalityType", - "name": "Commonality Type", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CommonalityType", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/CommonalityType$1" - }, - "cessda.ContributorRole": { - "authority": "cessda", - "description": "A classification of contributor roles.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/ContributorRole", - "id": "cessda.ContributorRole", - "name": "Contributor Role", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "ContributorRole", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/ContributorRole$1" - }, - "cessda.CountryNamesAndCodes": { - "authority": "cessda", - "description": "ISO 3166-1 alpha-2 country codes and names.", - "homepage": "https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes", - "id": "cessda.CountryNamesAndCodes", - "name": "Country Names and Codes", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CountryNamesAndCodes", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes$1" - }, - "cessda.DataSourceType": { - "authority": "cessda", - "description": "Includes a typology of data sources.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/DataSourceType", - "id": "cessda.DataSourceType", - "name": "Data Source Type", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "DataSourceType", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/DataSourceType$1" - }, - "cessda.DataType": { - "authority": "cessda", - "description": "Identifies the type of data, which has a bearing on the acceptable data values, the operations that can be performed with the data, and the ways in which the data are stored.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/DataType", - "id": "cessda.DataType", - "name": "Data Type", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "DataType", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/DataType$1" - }, - "cessda.DateType": { - "authority": "cessda", - "description": "Specifies the type of date.\n", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/DateType", - "id": "cessda.DateType", - "name": "Date Type", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "DateType", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/DateType$1" - }, - "cessda.GeneralDataFormat": { - "authority": "cessda", - "description": "Describes the physical format(s) of the data documented in the logical product(s) of a study unit.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/GeneralDataFormat", - "id": "cessda.GeneralDataFormat", - "name": "General Data Format", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "GeneralDataFormat", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/GeneralDataFormat$1" - }, - "cessda.KategorienschemaWahlstudien": { - "authority": "cessda", - "description": "The Category Scheme Election Studies provides the ability to categorize election studies at the question and/or variable level.", - "homepage": "https://www.gesis.org/vocabulary/KategorienschemaWahlstudien/1.0", - "id": "cessda.KategorienschemaWahlstudien", - "name": "Category Scheme Election Studies ", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "KategorienschemaWahlstudien", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://www.gesis.org/vocabulary/KategorienschemaWahlstudien/1.0$1" - }, - "cessda.LanguageProficiency": { - "authority": "cessda", - "description": "Describes the level of proficiency of an individual in a natural language.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/LanguageProficiency", - "id": "cessda.LanguageProficiency", - "name": "Language Proficiency", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "LanguageProficiency", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/LanguageProficiency$1" - }, - "cessda.LifecycleEventType": { - "authority": "cessda", - "description": "Specifies the event happening over the data life cycle that is considered significant enough to document.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/LifecycleEventType", - "id": "cessda.LifecycleEventType", - "name": "Lifecycle Event Type", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "LifecycleEventType", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/LifecycleEventType$1" - }, - "cessda.ModeOfCollection": { - "authority": "cessda", - "description": "The procedure, technique, or mode of inquiry used to attain the data.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/ModeOfCollection", - "id": "cessda.ModeOfCollection", - "name": "Mode Of Collection", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "ModeOfCollection", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/ModeOfCollection$1" - }, - "cessda.NumericType": { - "authority": "cessda", - "description": "Specifies the type of numeric data.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/NumericType", - "id": "cessda.NumericType", - "name": "Numeric Type", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "NumericType", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/NumericType$1" - }, - "cessda.ResponseUnit": { - "authority": "cessda", - "description": "Indicates the entity that provided the information carried by the variable.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/ResponseUnit", - "id": "cessda.ResponseUnit", - "name": "Response Unit", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "ResponseUnit", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/ResponseUnit$1" - }, - "cessda.SamplingProcedure": { - "authority": "cessda", - "description": "A typology of sampling methods.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/SamplingProcedure", - "id": "cessda.SamplingProcedure", - "name": "Sampling Procedure", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "SamplingProcedure", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/SamplingProcedure$1" - }, - "cessda.SoftwarePackage": { - "authority": "cessda", - "description": "Indicates the statistical software package used in the production/processing/dissemination of the data. Data collection software is not covered in this list.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/SoftwarePackage", - "id": "cessda.SoftwarePackage", - "name": "Software Package", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "SoftwarePackage", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/SoftwarePackage$1" - }, - "cessda.SummaryStatisticType": { - "authority": "cessda", - "description": "Specifies the type of summary statistic. Summary statistics are a single number representation of the characteristics of a set of values.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/SummaryStatisticType", - "id": "cessda.SummaryStatisticType", - "name": "Summary Statistic Type", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "SummaryStatisticType", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/SummaryStatisticType$1" - }, - "cessda.TimeMethod": { - "authority": "cessda", - "description": "Describes the time dimension of the data collection.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TimeMethod", - "id": "cessda.TimeMethod", - "name": "Time Method", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TimeMethod", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TimeMethod$1" - }, - "cessda.TimeZone": { - "authority": "cessda", - "description": "Time zone specification as an offset from UTC (Coordinated Universal Time) in terms of hours and minutes.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TimeZone", - "id": "cessda.TimeZone", - "name": "Time Zone", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TimeZone", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TimeZone$1" - }, - "cessda.TopicClassification": { - "authority": "cessda", - "description": "A typology of main themes or subjects of data.", - "homepage": "https://vocabularies.cessda.eu/vocabulary/TopicClassification", - "id": "cessda.TopicClassification", - "name": "CESSDA Topic Classification", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TopicClassification", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/vocabulary/TopicClassification$1" - }, - "cessda.TypeOfAddress": { - "authority": "cessda", - "description": "Identifies the type of address entered as contact information for an individual or an organization.\n\n", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfAddress", - "id": "cessda.TypeOfAddress", - "name": "Type of Address", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TypeOfAddress", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfAddress$1" - }, - "cessda.TypeOfConceptGroup": { - "authority": "cessda", - "description": "Specifies the rationale for creating a concept group.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfConceptGroup", - "id": "cessda.TypeOfConceptGroup", - "name": "Type of Concept Group", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TypeOfConceptGroup", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfConceptGroup$1" - }, - "cessda.TypeOfFrequency": { - "authority": "cessda", - "description": "Indicates the frequency of data collection events. \n", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfFrequency", - "id": "cessda.TypeOfFrequency", - "name": "Type of Frequency", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TypeOfFrequency", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfFrequency$1" - }, - "cessda.TypeOfInstrument": { - "authority": "cessda", - "description": "Includes a typology of data collection instruments.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfInstrument", - "id": "cessda.TypeOfInstrument", - "name": "Type of Instrument", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TypeOfInstrument", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfInstrument$1" - }, - "cessda.TypeOfNote": { - "authority": "cessda", - "description": "Includes a typology of notes.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfNote", - "id": "cessda.TypeOfNote", - "name": "Type of Note", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TypeOfNote", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfNote$1" - }, - "cessda.TypeOfTelephone": { - "authority": "cessda", - "description": "Identifies the type of telephone entered as contact information for an individual or an organization.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfTelephone", - "id": "cessda.TypeOfTelephone", - "name": "Type of Telephone", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TypeOfTelephone", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfTelephone$1" - }, - "cessda.TypeOfTranslationMethod": { - "authority": "cessda", - "description": "A typology of methods used to translate data collection instruments, including questionnaires, individual questions, measurements, data capture flows, etc.", - "homepage": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfTranslationMethod", - "id": "cessda.TypeOfTranslationMethod", - "name": "Type of Translation Method", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TypeOfTranslationMethod", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "http://rdf-vocabulary.ddialliance.org/cv/TypeOfTranslationMethod$1" - }, - "cessda.Variables-Relations": { - "authority": "cessda", - "description": "As the variable is one of the most relevant entities to enhance data reuse in the Social Sciences, we provide a framework design to better semantics the variables' relations descriptions. These explicit relations between variables enable comparability and facilitate harmonization across waves. We provide a brief textual identification of the relation type, supported by a controlled vocabulary (CV) and an extended description of the relationship. These relations within variables include but are not limited to different versions, derived formats in new waves, new labels and name wording, and alternative response schema through questionnaires and surveys. For instance, a given variable label is changed from one wave to another, even though its concept remains the same. Their values also are subject to change, such as new cardinalities settings, their categorization, or response scheme and scale measurement. They change based on different conditions, e.g., values are updated by any constraints or modified to comply with the study evolution requirements or a new sociological approach. In the Social Sciences, Economics, and Behaviour Sciences, which investigate, for instance, the social structure of the population, political attitudes of voters and candidates, opinions on family, work, religion, politics and society or competencies of adults, those topics are highly subject to change to fit the empirical reality in a constantly changing world. Thus, we propose widening relations descriptions for Social Sciences variables within datasets beginning from the BasedOnObjectType DDI as a first approach. ", - "homepage": "null/1.0.0", - "id": "cessda.Variables-Relations", - "name": "Variables relations for Social Sciences research data", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "Variables-Relations", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "null/1.0.0$1" - }, - "cessda.rexconcepts": { - "authority": "cessda", - "description": "This CV, developed within the framework of the DP-R|EX joint project, maps the central concepts and theoretical approaches in research on racism and right-wing extremism. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. The CV equally takes into account the different thematic (racism, right-wing extremism, discrimination) as well as methodological (qualitative research, standardised surveys, data from social media and messaging services) research strands. ", - "homepage": "null/1.0.0/1.1.0/1.2.0", - "id": "cessda.rexconcepts", - "name": " Central concepts of R|EX research ", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "rexconcepts", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "null/1.0.0/1.1.0/1.2.0$1" - }, - "cessda.rexgroups": { - "authority": "cessda", - "description": null, - "homepage": "null/1.0.0", - "id": "cessda.rexgroups", - "name": "rexgroups", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "rexgroups", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "null/1.0.0$1" - }, - "cessda:CdcPublisherNames.v2": { - "authority": "cessda", - "description": "Names of organisations providing metadata for CESSDA Data Catalogue.", - "homepage": "https://vocabularies.cessda.eu/v2/vocabularies/CdcPublisherNames/6.0.0", - "id": "cessda:CdcPublisherNames.v2", - "name": "CDC Publisher Names", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CdcPublisherNames", - "sameas": "cessda:CdcPublisherNames", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/v2/vocabularies/CdcPublisherNames/6.0.0$1" - }, - "cessda:CessdaPersistentIdentifierTypes.v2": { - "authority": "cessda", - "description": "Lists the types of persistent identifiers that CESSDA accepts as study level PIDs in its data catalogue.", - "homepage": "https://vocabularies.cessda.eu/v2/vocabularies/CessdaPersistentIdentifierTypes", - "id": "cessda:CessdaPersistentIdentifierTypes.v2", - "name": "CESSDA Persistent Identifier Types", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CessdaPersistentIdentifierTypes", - "sameas": "cessda:CessdaPersistentIdentifierTypes", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/v2/vocabularies/CessdaPersistentIdentifierTypes$1" - }, - "cessda:CountryNamesAndCodes.v2": { - "authority": "cessda", - "description": "ISO 3166-1 alpha-2 country codes and names.", - "homepage": "https://vocabularies.cessda.eu/v2/vocabularies/CountryNamesAndCodes", - "id": "cessda:CountryNamesAndCodes.v2", - "name": "Country Names and Codes", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "CountryNamesAndCodes", - "sameas": "cessda:CountryNamesAndCodes", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/v2/vocabularies/CountryNamesAndCodes$1" - }, - "cessda:TopicClassification.v2": { - "authority": "cessda", - "description": "A typology of main themes or subjects of data.", - "homepage": "https://vocabularies.cessda.eu/v2/vocabularies/TopicClassification", - "id": "cessda:TopicClassification.v2", - "name": "CESSDA Topic Classification", - "pattern": "\\/?(v\\=)?([0-9]\\.?)+", - "prefix": "TopicClassification", - "sameas": "cessda:TopicClassification", - "source": "https://vocabularies.cessda.eu/", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/v2/vocabularies/TopicClassification$1" - } -} diff --git a/fuji_server/data/linked_vocabs/cessda_ontologies.yaml b/fuji_server/data/linked_vocabs/cessda_ontologies.yaml new file mode 100644 index 00000000..df750298 --- /dev/null +++ b/fuji_server/data/linked_vocabs/cessda_ontologies.yaml @@ -0,0 +1,465 @@ +cessda.AggregationMethod: + authority: cessda + description: 'Identifies the type of aggregation used to combine related categories, usually within a common branch of a hierarchy, to provide information at a broader level than the level at which detailed observations are taken. (From: The OECD Glossary of Statistical Terms)' + homepage: http://rdf-vocabulary.ddialliance.org/cv/AggregationMethod + id: cessda.AggregationMethod + name: Aggregation Method + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: AggregationMethod + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/AggregationMethod$1 +cessda.AnalysisUnit: + authority: cessda + description: 'Describes the entity being analyzed in the study or variable. This vocabulary can also be used to describe the unit of observation, which is the unit being observed, or from which data are collected. The unit of observation can be the same as, or different from the unit of analysis. ' + homepage: http://rdf-vocabulary.ddialliance.org/cv/AnalysisUnit + id: cessda.AnalysisUnit + name: Analysis Unit + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: AnalysisUnit + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/AnalysisUnit$1 +cessda.CdcPublisherNames: + authority: cessda + description: Names of organisations providing metadata for CESSDA Data Catalogue. + homepage: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames/6.0.0 + id: cessda.CdcPublisherNames + name: CDC Publisher Names + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CdcPublisherNames + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/vocabulary/CdcPublisherNames/6.0.0$1 +cessda.CessdaPersistentIdentifierTypes: + authority: cessda + description: Lists the types of persistent identifiers that CESSDA accepts as study level PIDs in its data catalogue. + homepage: https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes + id: cessda.CessdaPersistentIdentifierTypes + name: CESSDA Persistent Identifier Types + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CessdaPersistentIdentifierTypes + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/vocabulary/CessdaPersistentIdentifierTypes$1 +cessda.CharacterSet: + authority: cessda + description: Standard set of characters upon which many character encodings are based (Wikipedia). + homepage: http://rdf-vocabulary.ddialliance.org/cv/CharacterSet + id: cessda.CharacterSet + name: Character Set + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CharacterSet + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/CharacterSet$1 +cessda.CommonalityType: + authority: cessda + description: Describes the degree of similarity between two items or schemes (collections of items). + homepage: http://rdf-vocabulary.ddialliance.org/cv/CommonalityType + id: cessda.CommonalityType + name: Commonality Type + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CommonalityType + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/CommonalityType$1 +cessda.ContributorRole: + authority: cessda + description: A classification of contributor roles. + homepage: http://rdf-vocabulary.ddialliance.org/cv/ContributorRole + id: cessda.ContributorRole + name: Contributor Role + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: ContributorRole + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/ContributorRole$1 +cessda.CountryNamesAndCodes: + authority: cessda + description: ISO 3166-1 alpha-2 country codes and names. + homepage: https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes + id: cessda.CountryNamesAndCodes + name: Country Names and Codes + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CountryNamesAndCodes + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/vocabulary/CountryNamesAndCodes$1 +cessda.DataSourceType: + authority: cessda + description: Includes a typology of data sources. + homepage: http://rdf-vocabulary.ddialliance.org/cv/DataSourceType + id: cessda.DataSourceType + name: Data Source Type + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: DataSourceType + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/DataSourceType$1 +cessda.DataType: + authority: cessda + description: Identifies the type of data, which has a bearing on the acceptable data values, the operations that can be performed with the data, and the ways in which the data are stored. + homepage: http://rdf-vocabulary.ddialliance.org/cv/DataType + id: cessda.DataType + name: Data Type + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: DataType + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/DataType$1 +cessda.DateType: + authority: cessda + description: | + Specifies the type of date. + homepage: http://rdf-vocabulary.ddialliance.org/cv/DateType + id: cessda.DateType + name: Date Type + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: DateType + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/DateType$1 +cessda.GeneralDataFormat: + authority: cessda + description: Describes the physical format(s) of the data documented in the logical product(s) of a study unit. + homepage: http://rdf-vocabulary.ddialliance.org/cv/GeneralDataFormat + id: cessda.GeneralDataFormat + name: General Data Format + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: GeneralDataFormat + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/GeneralDataFormat$1 +cessda.KategorienschemaWahlstudien: + authority: cessda + description: The Category Scheme Election Studies provides the ability to categorize election studies at the question and/or variable level. + homepage: https://www.gesis.org/vocabulary/KategorienschemaWahlstudien/1.0 + id: cessda.KategorienschemaWahlstudien + name: 'Category Scheme Election Studies ' + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: KategorienschemaWahlstudien + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://www.gesis.org/vocabulary/KategorienschemaWahlstudien/1.0$1 +cessda.LanguageProficiency: + authority: cessda + description: Describes the level of proficiency of an individual in a natural language. + homepage: http://rdf-vocabulary.ddialliance.org/cv/LanguageProficiency + id: cessda.LanguageProficiency + name: Language Proficiency + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: LanguageProficiency + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/LanguageProficiency$1 +cessda.LifecycleEventType: + authority: cessda + description: Specifies the event happening over the data life cycle that is considered significant enough to document. + homepage: http://rdf-vocabulary.ddialliance.org/cv/LifecycleEventType + id: cessda.LifecycleEventType + name: Lifecycle Event Type + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: LifecycleEventType + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/LifecycleEventType$1 +cessda.ModeOfCollection: + authority: cessda + description: The procedure, technique, or mode of inquiry used to attain the data. + homepage: http://rdf-vocabulary.ddialliance.org/cv/ModeOfCollection + id: cessda.ModeOfCollection + name: Mode Of Collection + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: ModeOfCollection + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/ModeOfCollection$1 +cessda.NumericType: + authority: cessda + description: Specifies the type of numeric data. + homepage: http://rdf-vocabulary.ddialliance.org/cv/NumericType + id: cessda.NumericType + name: Numeric Type + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: NumericType + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/NumericType$1 +cessda.ResponseUnit: + authority: cessda + description: Indicates the entity that provided the information carried by the variable. + homepage: http://rdf-vocabulary.ddialliance.org/cv/ResponseUnit + id: cessda.ResponseUnit + name: Response Unit + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: ResponseUnit + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/ResponseUnit$1 +cessda.SamplingProcedure: + authority: cessda + description: A typology of sampling methods. + homepage: http://rdf-vocabulary.ddialliance.org/cv/SamplingProcedure + id: cessda.SamplingProcedure + name: Sampling Procedure + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: SamplingProcedure + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/SamplingProcedure$1 +cessda.SoftwarePackage: + authority: cessda + description: Indicates the statistical software package used in the production/processing/dissemination of the data. Data collection software is not covered in this list. + homepage: http://rdf-vocabulary.ddialliance.org/cv/SoftwarePackage + id: cessda.SoftwarePackage + name: Software Package + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: SoftwarePackage + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/SoftwarePackage$1 +cessda.SummaryStatisticType: + authority: cessda + description: Specifies the type of summary statistic. Summary statistics are a single number representation of the characteristics of a set of values. + homepage: http://rdf-vocabulary.ddialliance.org/cv/SummaryStatisticType + id: cessda.SummaryStatisticType + name: Summary Statistic Type + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: SummaryStatisticType + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/SummaryStatisticType$1 +cessda.TimeMethod: + authority: cessda + description: Describes the time dimension of the data collection. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TimeMethod + id: cessda.TimeMethod + name: Time Method + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TimeMethod + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TimeMethod$1 +cessda.TimeZone: + authority: cessda + description: Time zone specification as an offset from UTC (Coordinated Universal Time) in terms of hours and minutes. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TimeZone + id: cessda.TimeZone + name: Time Zone + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TimeZone + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TimeZone$1 +cessda.TopicClassification: + authority: cessda + description: A typology of main themes or subjects of data. + homepage: https://vocabularies.cessda.eu/vocabulary/TopicClassification + id: cessda.TopicClassification + name: CESSDA Topic Classification + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TopicClassification + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/vocabulary/TopicClassification$1 +cessda.TypeOfAddress: + authority: cessda + description: >+ + Identifies the type of address entered as contact information for an + individual or an organization. + + homepage: http://rdf-vocabulary.ddialliance.org/cv/TypeOfAddress + id: cessda.TypeOfAddress + name: Type of Address + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TypeOfAddress + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TypeOfAddress$1 +cessda.TypeOfConceptGroup: + authority: cessda + description: Specifies the rationale for creating a concept group. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TypeOfConceptGroup + id: cessda.TypeOfConceptGroup + name: Type of Concept Group + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TypeOfConceptGroup + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TypeOfConceptGroup$1 +cessda.TypeOfFrequency: + authority: cessda + description: | + Indicates the frequency of data collection events. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TypeOfFrequency + id: cessda.TypeOfFrequency + name: Type of Frequency + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TypeOfFrequency + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TypeOfFrequency$1 +cessda.TypeOfInstrument: + authority: cessda + description: Includes a typology of data collection instruments. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TypeOfInstrument + id: cessda.TypeOfInstrument + name: Type of Instrument + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TypeOfInstrument + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TypeOfInstrument$1 +cessda.TypeOfNote: + authority: cessda + description: Includes a typology of notes. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TypeOfNote + id: cessda.TypeOfNote + name: Type of Note + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TypeOfNote + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TypeOfNote$1 +cessda.TypeOfTelephone: + authority: cessda + description: Identifies the type of telephone entered as contact information for an individual or an organization. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TypeOfTelephone + id: cessda.TypeOfTelephone + name: Type of Telephone + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TypeOfTelephone + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TypeOfTelephone$1 +cessda.TypeOfTranslationMethod: + authority: cessda + description: A typology of methods used to translate data collection instruments, including questionnaires, individual questions, measurements, data capture flows, etc. + homepage: http://rdf-vocabulary.ddialliance.org/cv/TypeOfTranslationMethod + id: cessda.TypeOfTranslationMethod + name: Type of Translation Method + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TypeOfTranslationMethod + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: http://rdf-vocabulary.ddialliance.org/cv/TypeOfTranslationMethod$1 +cessda.Variables-Relations: + authority: cessda + description: "As the variable is one of the most relevant entities to enhance data reuse in the Social Sciences, we provide a framework design to better semantics the variables' relations descriptions. These explicit relations between variables enable comparability and facilitate harmonization across waves. We provide a brief textual identification of the relation type, supported by a controlled vocabulary (CV) and an extended description of the relationship. These relations within variables include but are not limited to different versions, derived formats in new waves, new labels and name wording, and alternative response schema through questionnaires and surveys. For instance, a given variable label is changed from one wave to another, even though its concept remains the same. Their values also are subject to change, such as new cardinalities settings, their categorization, or response scheme and scale measurement. They change based on different conditions, e.g., values are updated by any constraints or modified to comply with the study evolution requirements or a new sociological approach. In the Social Sciences, Economics, and Behaviour Sciences, which investigate, for instance, the social structure of the population, political attitudes of voters and candidates, opinions on family, work, religion, politics and society or competencies of adults, those topics are highly subject to change to fit the empirical reality in a constantly changing world. Thus, we propose widening relations descriptions for Social Sciences variables within datasets beginning from the BasedOnObjectType DDI as a first approach. " + homepage: null/1.0.0 + id: cessda.Variables-Relations + name: Variables relations for Social Sciences research data + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: Variables-Relations + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: null/1.0.0$1 +cessda.rexconcepts: + authority: cessda + description: 'This CV, developed within the framework of the DP-R|EX joint project, maps the central concepts and theoretical approaches in research on racism and right-wing extremism. The compilation is based on a systematic evaluation of the relevant national and international empirical research literature. The CV equally takes into account the different thematic (racism, right-wing extremism, discrimination) as well as methodological (qualitative research, standardised surveys, data from social media and messaging services) research strands. ' + homepage: null/1.0.0/1.1.0/1.2.0 + id: cessda.rexconcepts + name: ' Central concepts of R|EX research ' + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: rexconcepts + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: null/1.0.0/1.1.0/1.2.0$1 +cessda.rexgroups: + authority: cessda + description: + homepage: null/1.0.0 + id: cessda.rexgroups + name: rexgroups + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: rexgroups + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: null/1.0.0$1 +cessda:CdcPublisherNames.v2: + authority: cessda + description: Names of organisations providing metadata for CESSDA Data Catalogue. + homepage: https://vocabularies.cessda.eu/v2/vocabularies/CdcPublisherNames/6.0.0 + id: cessda:CdcPublisherNames.v2 + name: CDC Publisher Names + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CdcPublisherNames + sameas: cessda:CdcPublisherNames + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/v2/vocabularies/CdcPublisherNames/6.0.0$1 +cessda:CessdaPersistentIdentifierTypes.v2: + authority: cessda + description: Lists the types of persistent identifiers that CESSDA accepts as study level PIDs in its data catalogue. + homepage: https://vocabularies.cessda.eu/v2/vocabularies/CessdaPersistentIdentifierTypes + id: cessda:CessdaPersistentIdentifierTypes.v2 + name: CESSDA Persistent Identifier Types + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CessdaPersistentIdentifierTypes + sameas: cessda:CessdaPersistentIdentifierTypes + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/v2/vocabularies/CessdaPersistentIdentifierTypes$1 +cessda:CountryNamesAndCodes.v2: + authority: cessda + description: ISO 3166-1 alpha-2 country codes and names. + homepage: https://vocabularies.cessda.eu/v2/vocabularies/CountryNamesAndCodes + id: cessda:CountryNamesAndCodes.v2 + name: Country Names and Codes + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: CountryNamesAndCodes + sameas: cessda:CountryNamesAndCodes + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/v2/vocabularies/CountryNamesAndCodes$1 +cessda:TopicClassification.v2: + authority: cessda + description: A typology of main themes or subjects of data. + homepage: https://vocabularies.cessda.eu/v2/vocabularies/TopicClassification + id: cessda:TopicClassification.v2 + name: CESSDA Topic Classification + pattern: \/?(v\=)?([0-9]\.?)+ + prefix: TopicClassification + sameas: cessda:TopicClassification + source: https://vocabularies.cessda.eu/ + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/v2/vocabularies/TopicClassification$1 diff --git a/fuji_server/data/linked_vocabs/fhir_ontologies.json b/fuji_server/data/linked_vocabs/fhir_ontologies.json deleted file mode 100644 index fb6f7e22..00000000 --- a/fuji_server/data/linked_vocabs/fhir_ontologies.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "fhir.codesystem": { - "id": "fuji.euroscivoc", - "name": "FHIR Code System", - "prefix": "fhir_cs", - "subjects": [ - "medical and health sciences" - ], - "uri_format": "http://hl7.org/fhir/CodeSystem/$1" - }, - "fhir.codesystem2": { - "id": "fuji.euroscivoc", - "name": "FHIR Code System", - "prefix": "fhir_cs", - "subjects": [ - "medical and health sciences" - ], - "uri_format": "http://terminology.hl7.org/CodeSystem/$1" - }, - "fhir.valueset": { - "id": "fuji.euroscivoc", - "name": "FHIR Value Set", - "prefix": "fhir_vs", - "subjects": [ - "medical and health sciences" - ], - "uri_format": "http://hl7.org/fhir/ValueSet/$1" - }, - "fhir.valueset2": { - "id": "fuji.euroscivoc", - "name": "FHIR Value Set", - "prefix": "fhir_vs", - "subjects": [ - "medical and health sciences" - ], - "uri_format": "http://terminology.hl7.org/ValueSet/$1" - } -} diff --git a/fuji_server/data/linked_vocabs/fhir_ontologies.yaml b/fuji_server/data/linked_vocabs/fhir_ontologies.yaml new file mode 100644 index 00000000..c1bb9ee5 --- /dev/null +++ b/fuji_server/data/linked_vocabs/fhir_ontologies.yaml @@ -0,0 +1,28 @@ +fhir.codesystem: + id: fuji.euroscivoc + name: FHIR Code System + prefix: fhir_cs + subjects: + - medical and health sciences + uri_format: http://hl7.org/fhir/CodeSystem/$1 +fhir.codesystem2: + id: fuji.euroscivoc + name: FHIR Code System + prefix: fhir_cs + subjects: + - medical and health sciences + uri_format: http://terminology.hl7.org/CodeSystem/$1 +fhir.valueset: + id: fuji.euroscivoc + name: FHIR Value Set + prefix: fhir_vs + subjects: + - medical and health sciences + uri_format: http://hl7.org/fhir/ValueSet/$1 +fhir.valueset2: + id: fuji.euroscivoc + name: FHIR Value Set + prefix: fhir_vs + subjects: + - medical and health sciences + uri_format: http://terminology.hl7.org/ValueSet/$1 diff --git a/fuji_server/data/linked_vocabs/fuji_ontologies.json b/fuji_server/data/linked_vocabs/fuji_ontologies.json deleted file mode 100644 index 25c06999..00000000 --- a/fuji_server/data/linked_vocabs/fuji_ontologies.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "fuji.euroscivoc": { - "id": "fuji.euroscivoc", - "name": "European Science Vocabulary (EuroSciVoc)", - "prefix": "euroscivoc", - "subjects": [ - "science and technology studies" - ], - "uri_format": "http://data.europa.eu/8mn/euroscivoc/$1" - }, - "fuji.hasset": { - "id": "fuji.hasset", - "name": "HASSET Thesaurus", - "prefix": "hasset", - "uri_format": "https://hasset.ukdataservice.ac.uk/$1" - }, - "fuji.i-adopt": { - "id": "fuji.i-adopt", - "name": "I-ADOPT Framework ontology", - "prefix": "i-adopt", - "uri_format": "https://w3id.org/iadopt/ont/$1" - }, - "fuji.icos": { - "id": "fuji.icos", - "name": "The Integrated Carbon Observation System (ICOS) ontology", - "prefix": "icos", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://meta.icos-cp.eu/ontologies/$1" - }, - "fuji.igsn": { - "id": "fuji.igsn", - "name": "The IGSN Ontology", - "prefix": "igsn", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://pid.geoscience.gov.au/def/ont/ga/igsn#$1" - }, - "fuji.meta-share": { - "id": "fuji.meta-share", - "name": "META-SHARE ontology", - "prefix": "meta-share", - "subjects": [ - "humanities", - "languages and literature" - ], - "uri_format": "http://w3id.org/meta-share/meta-share/$1" - }, - "fuji.mtlo": { - "description": "MarineTLO is a top-level ontology for the marine domain (also applicable to the terrestrial domain)", - "download.owl": "http://www.ics.forth.gr/isl/ontology/content-MTLO/marinetlo.owl", - "homepage": "http://www.ics.forth.gr/isl/ontology/MarineTLO/", - "id": "fuji.mtlo", - "name": "MarineTLO Ontology", - "prefix": "mtlo", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://www.ics.forth.gr/isl/ontology/MarineTLO/$1" - }, - "fuji.qudt": { - "homepage": "http://qudt.org", - "id": "fuji.qudt", - "pattern": "([\\d\\.]+\\/vocab\\/quantity#)", - "prefix": "qudt", - "uri_format": "http://qudt.org/$1" - }, - "fuji.wikidata": { - "id": "fuji.wikidata", - "name": "Wikidata", - "prefix": "wikidata", - "uri_format": "https://www.wikidata.org/wiki/$1" - } -} diff --git a/fuji_server/data/linked_vocabs/fuji_ontologies.yaml b/fuji_server/data/linked_vocabs/fuji_ontologies.yaml new file mode 100644 index 00000000..9583716f --- /dev/null +++ b/fuji_server/data/linked_vocabs/fuji_ontologies.yaml @@ -0,0 +1,60 @@ +fuji.euroscivoc: + id: fuji.euroscivoc + name: European Science Vocabulary (EuroSciVoc) + prefix: euroscivoc + subjects: + - science and technology studies + uri_format: http://data.europa.eu/8mn/euroscivoc/$1 +fuji.hasset: + id: fuji.hasset + name: HASSET Thesaurus + prefix: hasset + uri_format: https://hasset.ukdataservice.ac.uk/$1 +fuji.i-adopt: + id: fuji.i-adopt + name: I-ADOPT Framework ontology + prefix: i-adopt + uri_format: https://w3id.org/iadopt/ont/$1 +fuji.icos: + id: fuji.icos + name: The Integrated Carbon Observation System (ICOS) ontology + prefix: icos + subjects: + - earth and related environmental sciences + uri_format: http://meta.icos-cp.eu/ontologies/$1 +fuji.igsn: + id: fuji.igsn + name: The IGSN Ontology + prefix: igsn + subjects: + - earth and related environmental sciences + uri_format: http://pid.geoscience.gov.au/def/ont/ga/igsn#$1 +fuji.meta-share: + id: fuji.meta-share + name: META-SHARE ontology + prefix: meta-share + subjects: + - humanities + - languages and literature + uri_format: http://w3id.org/meta-share/meta-share/$1 +fuji.mtlo: + description: MarineTLO is a top-level ontology for the marine domain (also applicable to the terrestrial domain) + download.owl: http://www.ics.forth.gr/isl/ontology/content-MTLO/marinetlo.owl + homepage: http://www.ics.forth.gr/isl/ontology/MarineTLO/ + id: fuji.mtlo + name: MarineTLO Ontology + prefix: mtlo + subjects: + - earth and related environmental sciences + uri_format: http://www.ics.forth.gr/isl/ontology/MarineTLO/$1 +fuji.qudt: + homepage: http://qudt.org + id: fuji.qudt + pattern: ([\d\.]+\/vocab\/quantity#) + prefix: qudt + uri_format: http://qudt.org/$1 +fuji.wikidata: + id: fuji.wikidata + name: Wikidata + prefix: wikidata + uri_format: https://www.wikidata.org/wiki/$1 diff --git a/fuji_server/data/linked_vocabs/gesis_ontologies.json b/fuji_server/data/linked_vocabs/gesis_ontologies.json deleted file mode 100644 index 9536ed8b..00000000 --- a/fuji_server/data/linked_vocabs/gesis_ontologies.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "gesis.cessda-topic": { - "authority": "gesis", - "homepage": "https://lod.gesis.org/cessda-topic", - "id": "gesis.cessda-topic", - "name": "CESSDA Topic Classification", - "prefix": "gesis.cessda-topic", - "source": "lod.gesis.org", - "subjects": [ - "social sciences" - ], - "uri_format": "https://vocabularies.cessda.eu/vocabulary/TopicClassification?v=4.1$1" - }, - "gesis.iso-3166-1": { - "authority": "gesis", - "homepage": "https://lod.gesis.org/iso-3166-1", - "id": "gesis.iso-3166-1", - "name": "ISO 3166-1 Country Codes", - "prefix": "gesis.iso-3166-1", - "source": "lod.gesis.org", - "subjects": [ - "social sciences" - ], - "uri_format": "http://publications.europa.eu/resource/authority/country$1" - }, - "gesis.unesco": { - "authority": "gesis", - "homepage": "https://lod.gesis.org/unesco", - "id": "gesis.unesco", - "name": "UNESCO Thesaurus", - "prefix": "gesis.unesco", - "source": "lod.gesis.org", - "subjects": [ - "social sciences" - ], - "uri_format": "http://skos.um.es/unescothes/CS000$1" - } -} diff --git a/fuji_server/data/linked_vocabs/gesis_ontologies.yaml b/fuji_server/data/linked_vocabs/gesis_ontologies.yaml new file mode 100644 index 00000000..789389fc --- /dev/null +++ b/fuji_server/data/linked_vocabs/gesis_ontologies.yaml @@ -0,0 +1,30 @@ +gesis.cessda-topic: + authority: gesis + homepage: https://lod.gesis.org/cessda-topic + id: gesis.cessda-topic + name: CESSDA Topic Classification + prefix: gesis.cessda-topic + source: lod.gesis.org + subjects: + - social sciences + uri_format: https://vocabularies.cessda.eu/vocabulary/TopicClassification?v=4.1$1 +gesis.iso-3166-1: + authority: gesis + homepage: https://lod.gesis.org/iso-3166-1 + id: gesis.iso-3166-1 + name: ISO 3166-1 Country Codes + prefix: gesis.iso-3166-1 + source: lod.gesis.org + subjects: + - social sciences + uri_format: http://publications.europa.eu/resource/authority/country$1 +gesis.unesco: + authority: gesis + homepage: https://lod.gesis.org/unesco + id: gesis.unesco + name: UNESCO Thesaurus + prefix: gesis.unesco + source: lod.gesis.org + subjects: + - social sciences + uri_format: http://skos.um.es/unescothes/CS000$1 diff --git a/fuji_server/data/linked_vocabs/iso_ontologies.json b/fuji_server/data/linked_vocabs/iso_ontologies.json deleted file mode 100644 index 8330735e..00000000 --- a/fuji_server/data/linked_vocabs/iso_ontologies.json +++ /dev/null @@ -1,1065 +0,0 @@ -{ - "iso.gco": { - "uri_format": "http://www.isotc211.org/2005/gco$1" - }, - "iso.gfc": { - "uri_format": "http://www.isotc211.org/2005/gfc$1" - }, - "iso.gmd": { - "uri_format": "http://www.isotc211.org/2005/gmd$1" - }, - "iso.gmi": { - "uri_format": "http://www.isotc211.org/2005/gmi$1" - }, - "iso.gmicode": { - "name": "gmiCodelists", - "prefix": "iso.gmicode", - "subjects": [ - "earth and related environmental sciences", - "physical geography" - ], - "uri_format": "https://www.isotc211.org/2005/resources/Codelist/gmiCodelists.xml#$1" - }, - "iso.gml": { - "uri_format": "http://www.isotc211.org/2005/gml$1" - }, - "iso.gmx": { - "uri_format": "http://www.isotc211.org/2005/gmx$1" - }, - "iso.gmxcode": { - "name": "gmxCodelists", - "prefix": "iso.gmxcode", - "subjects": [ - "earth and related environmental sciences", - "physical geography" - ], - "uri_format": "https://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#$1" - }, - "iso.gplr": { - "uri_format": "http://www.isotc211.org/2005/gplr$1" - }, - "iso.gsr": { - "uri_format": "http://www.isotc211.org/2005/gsr$1" - }, - "iso.gss": { - "uri_format": "http://www.isotc211.org/2005/gss$1" - }, - "iso.gts": { - "uri_format": "http://www.isotc211.org/2005/gts$1" - }, - "isotc.iso:00639.iso": { - "authority": "isotc", - "homepage": "https://def.isotc211.org/ontologies/00639", - "id": "isotc.iso:00639.iso", - "name": "Codes for the representation of names of languages", - "pattern": "(?:\\/[0-9]{5})(?:\\/[-0-9]+)?(?:\\/[0-9]+)?(?:.*?)#(.*?)$", - "prefix": "iso:00639", - "source": "isotc211.org", - "subjects": [ - "earth and related environmental sciences", - "physical geography" - ], - "uri_format": "http://def.isotc211.org/00639$1" - 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], - "uri_format": "http://def.isotc211.org/iso19160$1" - }, - "isotc.orphans.iso": { - "authority": "isotc", - "homepage": "https://def.isotc211.org/ontologies/orphans", - "id": "isotc.orphans.iso", - "name": "Orphans", - "pattern": "(?:\\/[0-9]{5})(?:\\/[-0-9]+)?(?:\\/[0-9]+)?(?:.*?)#(.*?)$", - "prefix": "orphans", - "source": "isotc211.org", - "subjects": [ - "earth and related environmental sciences", - "physical geography" - ], - "uri_format": "http://def.isotc211.org/orphans$1" - }, - "isotc.orphans.iso2": { - "authority": "isotc", - "homepage": "https://def.isotc211.org/ontologies/orphans", - "id": "isotc.orphans.iso2", - "name": "Orphans", - "pattern": "(?:\\/[0-9]{5})(?:\\/[-0-9]+)?(?:\\/[0-9]+)?(?:.*?)#(.*?)$", - "prefix": "orphans", - "sameas": "isotc.orphans.iso", - "source": "isotc211.org", - "subjects": [ - "earth and related environmental sciences", - "physical geography" - ], - "uri_format": "http://def.isotc211.org/iso19160$1" - } -} diff --git a/fuji_server/data/linked_vocabs/iso_ontologies.yaml b/fuji_server/data/linked_vocabs/iso_ontologies.yaml new file mode 100644 index 00000000..1b7a3d65 --- /dev/null +++ b/fuji_server/data/linked_vocabs/iso_ontologies.yaml @@ -0,0 +1,909 @@ +iso.gco: + uri_format: http://www.isotc211.org/2005/gco$1 +iso.gfc: + uri_format: http://www.isotc211.org/2005/gfc$1 +iso.gmd: + uri_format: http://www.isotc211.org/2005/gmd$1 +iso.gmi: + uri_format: http://www.isotc211.org/2005/gmi$1 +iso.gmicode: + name: gmiCodelists + prefix: iso.gmicode + subjects: + - earth and related environmental sciences + - physical geography + uri_format: https://www.isotc211.org/2005/resources/Codelist/gmiCodelists.xml#$1 +iso.gml: + uri_format: http://www.isotc211.org/2005/gml$1 +iso.gmx: + uri_format: http://www.isotc211.org/2005/gmx$1 +iso.gmxcode: + name: gmxCodelists + prefix: iso.gmxcode + subjects: + - earth and related environmental sciences + - physical geography + uri_format: https://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml#$1 +iso.gplr: + uri_format: http://www.isotc211.org/2005/gplr$1 +iso.gsr: + uri_format: http://www.isotc211.org/2005/gsr$1 +iso.gss: + uri_format: http://www.isotc211.org/2005/gss$1 +iso.gts: + uri_format: http://www.isotc211.org/2005/gts$1 +isotc.iso:00639.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/00639 + id: isotc.iso:00639.iso + name: Codes for the representation of names of languages + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:00639 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/00639$1 +isotc.iso:00639.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/00639 + id: isotc.iso:00639.iso2 + name: Codes for the representation of names of languages + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:00639 + sameas: isotc.iso:00639.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso00639$1 +isotc.iso:19101.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19101 + id: isotc.iso:19101.iso + name: Geographic information -- Reference model + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19101 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19101$1 +isotc.iso:19101.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19101 + id: isotc.iso:19101.iso2 + name: Geographic information -- Reference model + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19101 + sameas: isotc.iso:19101.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19101$1 +isotc.iso:19103.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19103 + id: isotc.iso:19103.iso + name: Geographic information -- Conceptual schema language + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19103 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19103$1 +isotc.iso:19103.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19103 + id: isotc.iso:19103.iso2 + name: Geographic information -- Conceptual schema language + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19103 + sameas: isotc.iso:19103.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19103$1 +isotc.iso:19104.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19104 + id: isotc.iso:19104.iso + name: Geographic information -- Terminology + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19104 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19104$1 +isotc.iso:19104.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19104 + id: isotc.iso:19104.iso2 + name: Geographic information -- Terminology + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19104 + sameas: isotc.iso:19104.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19104$1 +isotc.iso:19107.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19107 + id: isotc.iso:19107.iso + name: Geographic information -- Spatial schema + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19107 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19107$1 +isotc.iso:19107.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19107 + id: isotc.iso:19107.iso2 + name: Geographic information -- Spatial schema + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19107 + sameas: isotc.iso:19107.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19107$1 +isotc.iso:19108.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19108 + id: isotc.iso:19108.iso + name: Geographic information -- Temporal schema + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19108 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19108$1 +isotc.iso:19108.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19108 + id: isotc.iso:19108.iso2 + name: Geographic information -- Temporal schema + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19108 + sameas: isotc.iso:19108.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19108$1 +isotc.iso:19109.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19109 + id: isotc.iso:19109.iso + name: Geographic information -- Rules for application schema + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19109 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19109$1 +isotc.iso:19109.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19109 + id: isotc.iso:19109.iso2 + name: Geographic information -- Rules for application schema + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19109 + sameas: isotc.iso:19109.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19109$1 +isotc.iso:19110.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19110 + id: isotc.iso:19110.iso + name: Geographic information -- Methodology for feature cataloguing + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19110 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19110$1 +isotc.iso:19110.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19110 + id: isotc.iso:19110.iso2 + name: Geographic information -- Methodology for feature cataloguing + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19110 + sameas: isotc.iso:19110.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19110$1 +isotc.iso:19111.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19111 + id: isotc.iso:19111.iso + name: Geographic information -- Spatial referencing by coordinates + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19111 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19111$1 +isotc.iso:19111.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19111 + id: isotc.iso:19111.iso2 + name: Geographic information -- Spatial referencing by coordinates + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19111 + sameas: isotc.iso:19111.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19111$1 +isotc.iso:19112.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19112 + id: isotc.iso:19112.iso + name: Geographic information -- Spatial referencing by geographic identifiers + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19112 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19112$1 +isotc.iso:19112.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19112 + id: isotc.iso:19112.iso2 + name: Geographic information -- Spatial referencing by geographic identifiers + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19112 + sameas: isotc.iso:19112.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19112$1 +isotc.iso:19115.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19115 + id: isotc.iso:19115.iso + name: Geographic information -- Metadata + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19115 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19115$1 +isotc.iso:19115.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19115 + id: isotc.iso:19115.iso2 + name: Geographic information -- Metadata + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19115 + sameas: isotc.iso:19115.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19115$1 +isotc.iso:19116.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19116 + id: isotc.iso:19116.iso + name: Geographic information -- Positioning services + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19116 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19116$1 +isotc.iso:19116.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19116 + id: isotc.iso:19116.iso2 + name: Geographic information -- Positioning services + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19116 + sameas: isotc.iso:19116.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19116$1 +isotc.iso:19117.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19117 + id: isotc.iso:19117.iso + name: Geographic information -- Portrayal + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19117 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19117$1 +isotc.iso:19117.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19117 + id: isotc.iso:19117.iso2 + name: Geographic information -- Portrayal + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19117 + sameas: isotc.iso:19117.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19117$1 +isotc.iso:19118.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19118 + id: isotc.iso:19118.iso + name: Geographic information -- Encoding + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19118 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19118$1 +isotc.iso:19118.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19118 + id: isotc.iso:19118.iso2 + name: Geographic information -- Encoding + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19118 + sameas: isotc.iso:19118.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19118$1 +isotc.iso:19123.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19123 + id: isotc.iso:19123.iso + name: Geographic information -- Schema for coverage geometry and functions + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19123 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19123$1 +isotc.iso:19123.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19123 + id: isotc.iso:19123.iso2 + name: Geographic information -- Schema for coverage geometry and functions + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19123 + sameas: isotc.iso:19123.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19123$1 +isotc.iso:19126.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19126 + id: isotc.iso:19126.iso + name: Geographic information -- Feature concept dictionaries and registers + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19126 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19126$1 +isotc.iso:19126.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19126 + id: isotc.iso:19126.iso2 + name: Geographic information -- Feature concept dictionaries and registers + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19126 + sameas: isotc.iso:19126.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19126$1 +isotc.iso:19128.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19128 + id: isotc.iso:19128.iso + name: Geographic information -- Web map server interface + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19128 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19128$1 +isotc.iso:19128.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19128 + id: isotc.iso:19128.iso2 + name: Geographic information -- Web map server interface + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19128 + sameas: isotc.iso:19128.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19128$1 +isotc.iso:19129.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19129 + id: isotc.iso:19129.iso + name: Geographic information -- Imagery, gridded and coverage data framework + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19129 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19129$1 +isotc.iso:19129.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19129 + id: isotc.iso:19129.iso2 + name: Geographic information -- Imagery, gridded and coverage data framework + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19129 + sameas: isotc.iso:19129.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19129$1 +isotc.iso:19130.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19130 + id: isotc.iso:19130.iso + name: Geographic information - Imagery sensor models for geopositioning + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19130 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19130$1 +isotc.iso:19130.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19130 + id: isotc.iso:19130.iso2 + name: Geographic information - Imagery sensor models for geopositioning + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19130 + sameas: isotc.iso:19130.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19130$1 +isotc.iso:19131.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19131 + id: isotc.iso:19131.iso + name: Geographic information -- Data product specifications + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19131 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19131$1 +isotc.iso:19131.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19131 + id: isotc.iso:19131.iso2 + name: Geographic information -- Data product specifications + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19131 + sameas: isotc.iso:19131.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19131$1 +isotc.iso:19132.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19132 + id: isotc.iso:19132.iso + name: Geographic information -- Location-based services -- Reference model + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19132 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19132$1 +isotc.iso:19132.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19132 + id: isotc.iso:19132.iso2 + name: Geographic information -- Location-based services -- Reference model + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19132 + sameas: isotc.iso:19132.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19132$1 +isotc.iso:19134.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19134 + id: isotc.iso:19134.iso + name: Geographic information -- Location-based services -- Multimodal routing and navigation + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19134 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19134$1 +isotc.iso:19134.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19134 + id: isotc.iso:19134.iso2 + name: Geographic information -- Location-based services -- Multimodal routing and navigation + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19134 + sameas: isotc.iso:19134.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19134$1 +isotc.iso:19135.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19135 + id: isotc.iso:19135.iso + name: Geographic information -- Procedures for item registration + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19135 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19135$1 +isotc.iso:19135.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19135 + id: isotc.iso:19135.iso2 + name: Geographic information -- Procedures for item registration + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19135 + sameas: isotc.iso:19135.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19135$1 +isotc.iso:19136.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19136 + id: isotc.iso:19136.iso + name: Geographic information -- Geography Markup Language (GML) + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19136 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19136$1 +isotc.iso:19136.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19136 + id: isotc.iso:19136.iso2 + name: Geographic information -- Geography Markup Language (GML) + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19136 + sameas: isotc.iso:19136.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19136$1 +isotc.iso:19139.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19139 + id: isotc.iso:19139.iso + name: Geographic information -- Metadata -- XML schema implementation + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19139 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19139$1 +isotc.iso:19139.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19139 + id: isotc.iso:19139.iso2 + name: Geographic information -- Metadata -- XML schema implementation + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19139 + sameas: isotc.iso:19139.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19139$1 +isotc.iso:19141.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19141 + id: isotc.iso:19141.iso + name: Geographic information -- Schema for moving features + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19141 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19141$1 +isotc.iso:19141.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19141 + id: isotc.iso:19141.iso2 + name: Geographic information -- Schema for moving features + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19141 + sameas: isotc.iso:19141.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19141$1 +isotc.iso:19144.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19144 + id: isotc.iso:19144.iso + name: Geographic information -- Classification systems + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19144 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19144$1 +isotc.iso:19144.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19144 + id: isotc.iso:19144.iso2 + name: Geographic information -- Classification systems + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19144 + sameas: isotc.iso:19144.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19144$1 +isotc.iso:19145.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19145 + id: isotc.iso:19145.iso + name: Geographic information -- Registry of representations of geographic point location + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19145 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19145$1 +isotc.iso:19145.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19145 + id: isotc.iso:19145.iso2 + name: Geographic information -- Registry of representations of geographic point location + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19145 + sameas: isotc.iso:19145.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19145$1 +isotc.iso:19146.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19146 + id: isotc.iso:19146.iso + name: Geographic information -- Cross-domain vocabularies + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19146 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19146$1 +isotc.iso:19146.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19146 + id: isotc.iso:19146.iso2 + name: Geographic information -- Cross-domain vocabularies + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19146 + sameas: isotc.iso:19146.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19146$1 +isotc.iso:19150.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19150 + id: isotc.iso:19150.iso + name: Geographic information -- Ontology + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19150 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19150$1 +isotc.iso:19150.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19150 + id: isotc.iso:19150.iso2 + name: Geographic information -- Ontology + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19150 + sameas: isotc.iso:19150.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19150$1 +isotc.iso:19155.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19155 + id: isotc.iso:19155.iso + name: Geographic information -- Place Identifier (PI) architecture + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19155 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19155$1 +isotc.iso:19155.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19155 + id: isotc.iso:19155.iso2 + name: Geographic information -- Place Identifier (PI) architecture + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19155 + sameas: isotc.iso:19155.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19155$1 +isotc.iso:19156.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19156 + id: isotc.iso:19156.iso + name: Geographic information -- Observations and measurements + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19156 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19156$1 +isotc.iso:19156.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19156 + id: isotc.iso:19156.iso2 + name: Geographic information -- Observations and measurements + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19156 + sameas: isotc.iso:19156.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19156$1 +isotc.iso:19157.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19157 + id: isotc.iso:19157.iso + name: Geographic information -- Data quality + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19157 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19157$1 +isotc.iso:19157.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19157 + id: isotc.iso:19157.iso2 + name: Geographic information -- Data quality + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19157 + sameas: isotc.iso:19157.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19157$1 +isotc.iso:19160.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19160 + id: isotc.iso:19160.iso + name: Addressing + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19160 + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/19160$1 +isotc.iso:19160.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/iso19160 + id: isotc.iso:19160.iso2 + name: Addressing + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: iso:19160 + sameas: isotc.iso:19160.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19160$1 +isotc.orphans.iso: + authority: isotc + homepage: https://def.isotc211.org/ontologies/orphans + id: isotc.orphans.iso + name: Orphans + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: orphans + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/orphans$1 +isotc.orphans.iso2: + authority: isotc + homepage: https://def.isotc211.org/ontologies/orphans + id: isotc.orphans.iso2 + name: Orphans + pattern: (?:\/[0-9]{5})(?:\/[-0-9]+)?(?:\/[0-9]+)?(?:.*?)#(.*?)$ + prefix: orphans + sameas: isotc.orphans.iso + source: isotc211.org + subjects: + - earth and related environmental sciences + - physical geography + uri_format: http://def.isotc211.org/iso19160$1 diff --git a/fuji_server/data/linked_vocabs/lov_ontologies.json b/fuji_server/data/linked_vocabs/lov_ontologies.json deleted file mode 100644 index 81abdbb0..00000000 --- a/fuji_server/data/linked_vocabs/lov_ontologies.json +++ /dev/null @@ -1,9672 +0,0 @@ -{ - "lov.a-loc": { - "authority": "lov", - "description": "The module Location models information related to the localization and georeferencing of a cultural property.\nIn this module are used as template the following Ontology Design Patterns:\n- http://www.ontologydesignpatterns.org/cp/owl/collectionentity.owl\n- http://www.ontologydesignpatterns.org/cp/owl/classification.owl\n- http://www.ontologydesignpatterns.org/cp/owl/place.owl\n- http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl\n- http://www.ontologydesignpatterns.org/cp/owl/situation.owl", - "homepage": "https://w3id.org/arco/ontology/location", - "id": "lov.a-loc", - "name": "Location Ontology (ArCo network)", - "prefix": "a-loc", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/arco/ontology/location/$1" - }, - "lov.ac": { - "authority": "lov", - "description": "This term list includes all currently valid terms that have been defined in the core Audubon Core namespace ac:.", - "homepage": "http://rs.tdwg.org/ac/terms/", - "id": "lov.ac", - "name": "Core terms defined by Audubon Core", - "prefix": "ac", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://rs.tdwg.org/ac/terms/$1" - }, - "lov.acco": { - "authority": "lov", - "description": "A vocabulary for the description of hotels, vacation homes, camping sites, and other accommodation offers for e-commerce", - "homepage": "http://purl.org/acco/ns", - "id": "lov.acco", - "name": "Accomodation Ontology", - "prefix": "acco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/acco/ns#$1" - }, - "lov.acl": { - "authority": "lov", - "description": "Defines the element of Authorization and its essential properties, and also some classes of access such as read and write.", - "homepage": "http://www.w3.org/ns/auth/acl", - "id": "lov.acl", - "name": "Basic Access Control ontology", - "prefix": "acl", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/ns/auth/acl#$1" - }, - "lov.acm": { - "authority": "lov", - "description": "This ontology is a representation of The ACM Computing Classification System [1998]", - "homepage": "http://www.rkbexplorer.com/ontologies/acm", - "id": "lov.acm", - "name": "ACM Classification Ontology", - "prefix": "acm", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://acm.rkbexplorer.com/ontologies/acm#$1" - }, - "lov.acrt": { - "authority": "lov", - "description": "This document specifies a vocabulary for asserting the existence of official endorsements or certifications of agents, such as people and organizations.", - "homepage": "http://privatealpha.com/ontology/certification/1#", - "id": "lov.acrt", - "name": "Agent Certification Ontology", - "prefix": "acrt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://privatealpha.com/ontology/certification/1#$1" - }, - "lov.adms": { - "authority": "lov", - "description": "ADMS is a profile of DCAT, used to describe semantic assets (or just 'Assets'), defined as highly reusable metadata (e.g. xml schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies) that are used for eGovernment system development.", - "homepage": "http://www.w3.org/ns/adms", - "id": "lov.adms", - "name": "Asset Description Metadata Schema", - "prefix": "adms", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/adms#$1" - }, - "lov.af": { - "authority": "lov", - "description": "This vocabulary expresses some common concepts to represent some features of audio signals.", - "homepage": "http://purl.org/ontology/af/", - "id": "lov.af", - "name": "Audio Features Ontology", - "prefix": "af", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/af/$1" - }, - "lov.agls": { - "authority": "lov", - "description": "The AGLS Metadata Terms Namespace provides URIs for the AGLS Metadata Terms Vocabulary in the context of AGLS Metadata Standard, a set of metadata properties and associated usage guidelines to improve the visibility, manageability and interoperability of online information and services. Vocabulary terms are declared using RDF Schema language to support RDF applications. It will be updated according to AGLS Working Group decisions.", - "homepage": "http://www.agls.gov.au/agls/terms", - "id": "lov.agls", - "name": "AGLS Metadata Terms", - "prefix": "agls", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.agls.gov.au/agls/terms/$1" - }, - "lov.agr": { - "authority": "lov", - "description": "This Agreements Ontology is designed to model 'agreements' which are social contracts that include licenses, laws, contracts, Memoranda of Understanding, standards and definitional metadata. Its purpose is to support data sharing by making explicit the relationships between agreements and data and agreements and Agents (people and organisations). Eventually it will also help with the interplay between different classes of agreements.", - "homepage": "http://promsns.org/def/agr", - "id": "lov.agr", - "name": "Agreements ontology", - "prefix": "agr", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences", - "law" - ], - "uri_format": "http://promsns.org/def/agr#$1" - }, - "lov.agrelon": { - "authority": "lov", - "description": "The ontology of agent relationships, AgRelOn, defines relations of persons to other persons and to organisations", - "homepage": "http://d-nb.info/standards/elementset/agrelon", - "id": "lov.agrelon", - "name": "Agent Relationship Ontology", - "prefix": "agrelon", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://d-nb.info/standards/elementset/agrelon#$1" - }, - "lov.aiiso": { - "authority": "lov", - "description": "The Academic Institution Internal Structure Ontology (AIISO) provides classes and properties to describe the internal organizational structure of an academic institution. AIISO is designed to work in partnership with Participation (http://purl.org/vocab/participation/schema), FOAF (http://xmlns.com/foaf/0.1/) and aiiso-roles (http://purl.org/vocab/aiiso-roles/schema) to describe the roles that people play within an institution.", - "homepage": "http://purl.org/vocab/aiiso/schema", - "id": "lov.aiiso", - "name": "Academic Institution Internal Structure Ontology", - "prefix": "aiiso", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://purl.org/vocab/aiiso/schema#$1" - }, - "lov.airo": { - "authority": "lov", - "description": "AIRO represents AI risk concepts and relations based on the AI Act draft and ISO 31000 standard series.", - "homepage": "https://w3id.org/AIRO", - "id": "lov.airo", - "name": "AI Risk Ontology", - "prefix": "airo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/AIRO#$1" - }, - "lov.airs": { - "authority": "lov", - "description": "The AIRS Linked Open Vocabulary is a way to describe human services information and referral (I&R) concepts. AIRS is the Alliance of Information and Referral Services (airs.org), which possesses over 1,000 member agencies primarily in the United States and Canada. The AIRS LOV is based on the AIRS XML Schema, available at: https://airs-xml.googlecode.com/hg/tags/3.1/airs.xsd", - "homepage": "https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl#", - "id": "lov.airs", - "name": "Alliance of Information and Referral Services (AIRS) Vocabulary", - "prefix": "airs", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl#$1" - }, - "lov.akt": { - "authority": "lov", - "description": "The AKT Reference Ontology has been designed to support the AKT-2 demonstrator (\"AKTive Portal\"), and subsequent activities. The ontology, designed by the AKT-2 group and codified by Enrico Motta, extends Version 1.", - "homepage": "http://www.aktors.org/ontology/portal", - "id": "lov.akt", - "name": "AKT Reference Ontology", - "prefix": "akt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.aktors.org/ontology/portal#$1" - }, - "lov.akts": { - "authority": "lov", - "description": "The AKT Reference Ontology has been designed to support the AKT-2 demonstrator (\"AKTive Portal\"), and subsequent activities", - "homepage": "http://www.aktors.org/ontology/support", - "id": "lov.akts", - "name": "AKT Support Ontology", - "prefix": "akts", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.aktors.org/ontology/support#$1" - }, - "lov.algo": { - "authority": "lov", - "description": "An ontology describing cryptographic algorithms", - "homepage": "http://securitytoolbox.appspot.com/securityAlgorithms#", - "id": "lov.algo", - "name": "Algorithms Ontology", - "prefix": "algo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://securitytoolbox.appspot.com/securityAlgorithms#$1" - }, - "lov.am": { - "authority": "lov", - "description": "This specification builds on the Open Services for Lifecycle Collaboration (OSLC) Core v2.0 Specification to define the resources, properties and operations supported by an OSLC Asset Management (OSLC-Asset) provider. Asset Management resources include Assets, Artifacts and supporting resources defined in the OSLC Core specification.", - "homepage": "http://open-services.net/ns/asset#", - "id": "lov.am", - "name": "OSLC Asset Management Vocabulary", - "prefix": "am", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://open-services.net/ns/asset#$1" - }, - "lov.aml": { - "authority": "lov", - "description": "A vocabulary to represent the AutomationML Standard - IEC 62714", - "homepage": "https://w3id.org/i40/aml", - "id": "lov.aml", - "name": "AutomationML Ontology", - "prefix": "aml", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/i40/aml#$1" - }, - "lov.amlo-core": { - "authority": "lov", - "description": "The AMLO-core is the main module of the AMLO projects that extends the Financial Industry Business Ontology (FIBO) with some concepts to describe the Anti Money Laundering (AML) knowledge and facts.", - "homepage": "http://w3id.org/amlo/core", - "id": "lov.amlo-core", - "name": "AMLO-core vocabulary", - "prefix": "amlo-core", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://w3id.org/amlo/core#$1" - }, - "lov.amv": { - "authority": "lov", - "description": "Metadata vocabularies are used in various domains of study. It provides an in-depth description of the resources. In this work, we develop Algorithm Metadata Vocabulary (AMV), a vocabulary for capturing and storing the metadata about the algorithms (a procedure or a set of rules that is followed step-by-step to solve a problem, especially by a computer). The snag faced by the researchers in the current time is the failure of getting relevant results when searching for algorithms in any search engine. AMV is represented as a semantic model and produced OWL file, which can be directly used by anyone interested to create and publish algorithm metadata as a knowledge graph, or to provide metadata service through SPARQL endpoint. To design the vocabulary, we propose a well-defined methodology, which considers real issues faced by the algorithm users and the practitioners. The evaluation shows a promising result.", - "homepage": "https://w3id.org/amv", - "id": "lov.amv", - "name": "AMV:Algorithm Metadata Vocabulary", - "prefix": "amv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/amv#$1" - }, - "lov.ao": { - "authority": "lov", - "description": "Provides basic concepts and properties for describing specific association statements to something, e.g. an occasion, a genre or a mood ...", - "homepage": "http://purl.org/ontology/ao/core#", - "id": "lov.ao", - "name": "Association Ontology", - "prefix": "ao", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/ao/core#$1" - }, - "lov.aos": { - "authority": "lov", - "description": "Appearances is an ontology that grew out of the need to record personal appearance details about individuals while taking into account errors of perception and translation between various diffferent standards. Originally it was meant to record physical caracteristics of Great War soldiers from their medical files, but it became evident that the resource was also useful for other purposes.", - "homepage": "http://rdf.muninn-project.org/ontologies/appearances", - "id": "lov.aos", - "name": "Appearances Ontology Specification", - "prefix": "aos", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdf.muninn-project.org/ontologies/appearances#$1" - }, - "lov.apco": { - "authority": "lov", - "description": "APCO est une ontologie ayant pour but la description des termes des march\u00e9s publics", - "homepage": "https://purl.org/cm/onto/apco", - "id": "lov.apco", - "name": "African Public Contract Ontology", - "prefix": "apco", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "https://purl.org/cm/onto/apco#$1" - }, - "lov.api": { - "authority": "lov", - "description": "Configuration vocabulary for the Linked Data API", - "homepage": "http://purl.org/linked-data/api/vocab#", - "id": "lov.api", - "name": "Linked Data API Vocabulary", - "prefix": "api", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/linked-data/api/vocab#$1" - }, - "lov.apps4x": { - "authority": "lov", - "description": "apps4X is an RDF vocabulary defined to facilitate the description of Open-Data-based Co-creation events", - "homepage": "http://semweb.mmlab.be/ns/apps4X", - "id": "lov.apps4x", - "name": "The vocabulary for Co-creation Events based on Open Data", - "prefix": "apps4X", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semweb.mmlab.be/ns/apps4X#$1" - }, - "lov.arch": { - "authority": "lov", - "description": "An RDF vocabulary for describing archival collections and the names associated with them", - "homepage": "http://purl.org/archival/vocab/arch", - "id": "lov.arch", - "name": "Archival collections ontology", - "prefix": "arch", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/archival/vocab/arch#$1" - }, - "lov.arco": { - "authority": "lov", - "description": "The Core module represents general-purpose concepts orthogonal to the whole network, which are imported by all other ontology modules (e.g. part-whole relation, classification).", - "homepage": "https://w3id.org/arco/ontology/core", - "id": "lov.arco", - "name": "Core Ontology (ArCo network)", - "prefix": "arco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/arco/ontology/core/$1" - }, - "lov.arp": { - "authority": "lov", - "description": "Arpenteur ontology is dedicated to photogrammetry, archeology and oceanology communities \n\t in order to perform tasks such as image processing, photogrammetry and modelling.", - "homepage": "http://www.arpenteur.org/ontology/Arpenteur.owl", - "id": "lov.arp", - "name": "Arpenteur Ontology", - "prefix": "arp", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://www.arpenteur.org/ontology/Arpenteur.owl#$1" - }, - "lov.atd": { - "authority": "lov", - "description": "Defines concepts related to airport status, including weather, forecasts, and airport operations", - "homepage": "https://data.nasa.gov/ontologies/atmonto/data#", - "id": "lov.atd", - "name": "Air Traffic Data", - "prefix": "atd", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://data.nasa.gov/ontologies/atmonto/data#$1" - }, - "lov.atm": { - "authority": "lov", - "description": "Defines specific air traffic management concepts used in aircraft navigation through the US National Airspace System", - "homepage": "https://data.nasa.gov/ontologies/atmonto/ATM#", - "id": "lov.atm", - "name": "Air Traffic Management (ATM) Vocabulary", - "prefix": "atm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://data.nasa.gov/ontologies/atmonto/ATM#$1" - }, - "lov.atts": { - "authority": "lov", - "description": "Defines temporal / spatial concepts and general-purpose datastructures", - "homepage": "https://data.nasa.gov/ontologies/atmonto/general#", - "id": "lov.atts", - "name": "Air Traffic Temporal and Spacial Vocabulary", - "prefix": "atts", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "mathematics", - "computer and information sciences" - ], - "uri_format": "https://data.nasa.gov/ontologies/atmonto/general#$1" - }, - "lov.awol": { - "authority": "lov", - "description": "The AtomOWL ontology is inspired from the work done by the atom working group. This ontology is working off the rfc 4287 published among othe places at http://www.atompub.org/rfc4287.html . The AtomOWL ontology uses as much as possible the same terms as the format there to make the relation easy to understand. The AtomOWL name space is slightly different from the atom namespace [see post http://www.imc.org/atom-syntax/mail-archive/msg16476.html]. But this is a good thing as it helps distinguish the ontology from the rfc 4287 serialisation.", - "homepage": "http://bblfish.net/work/atom-owl/2006-06-06/", - "id": "lov.awol", - "name": "Atom Syndication Ontology", - "prefix": "awol", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://bblfish.net/work/atom-owl/2006-06-06/#$1" - }, - "lov.aws": { - "authority": "lov", - "description": "This ontology is part of the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG). It is published here in order to generalize the potential usage and the alignment with other standardization efforts of the SSN ontology.", - "homepage": "http://purl.oclc.org/NET/ssnx/meteo/aws", - "id": "lov.aws", - "name": "Ontology for Meteorological sensors", - "prefix": "aws", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "http://purl.oclc.org/NET/ssnx/meteo/aws#$1" - }, - "lov.bag": { - "authority": "lov", - "description": "Basisregistraties Adressen en Gebouwen (BAG) vocabulaire", - "homepage": "http://bag.basisregistraties.overheid.nl/def/bag", - "id": "lov.bag", - "name": "Vocabulary for the Dutch base registration of buildings and addresses (BAG)", - "prefix": "bag", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://bag.basisregistraties.overheid.nl/def/bag#$1" - }, - "lov.basic": { - "authority": "lov", - "description": "An OWL representation of (some of) the basic types described in ISO 19103:2005, required as primitives in other ontologies based on ISO 19100 series standards", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic", - "id": "lov.basic", - "name": "OWL representation of ISO 19103 (Basic types package)", - "prefix": "basic", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic#$1" - }, - "lov.bbc": { - "authority": "lov", - "description": "The BBC ontology is used to describe BBC concepts in the store. For example, the BBC divisions (products) publishing linked data and interfacing with the triplestore, the platforms for which we produce content and the web documents that publish or are relevant to the BBC's content.", - "homepage": "http://www.bbc.co.uk/ontologies/bbc", - "id": "lov.bbc", - "name": "BBC Ontology", - "prefix": "bbc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.bbc.co.uk/ontologies/bbc/$1" - }, - "lov.bbccms": { - "authority": "lov", - "description": "An ontology to represent the content management systems and their interaction with the triplestore.", - "homepage": "http://www.bbc.co.uk/ontologies/cms", - "id": "lov.bbccms", - "name": "BBC CMS Ontology", - "prefix": "bbccms", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.bbc.co.uk/ontologies/cms/$1" - }, - "lov.bbccore": { - "authority": "lov", - "description": "The generic BBC ontology for people, places,events, organisations, themes which represent things that make sense across the BBC. This model is meant to be generic enough, and allow clients (domain experts) link their own concepts", - "homepage": "http://www.bbc.co.uk/ontologies/coreconcepts", - "id": "lov.bbccore", - "name": "BBC Core Concepts", - "prefix": "bbccore", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.bbc.co.uk/ontologies/coreconcepts/$1" - }, - "lov.bbcprov": { - "authority": "lov", - "description": "The provenance ontology supports data management and auditing tasks. It is used to define the different types of named graphs we used in the store (quad store) and enables their association with metadata that allow us to manage, validate and expose data to BBC services", - "homepage": "http://www.bbc.co.uk/ontologies/provenance", - "id": "lov.bbcprov", - "name": "BBC Provenance Ontology", - "prefix": "bbcprov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.bbc.co.uk/ontologies/provenance/$1" - }, - "lov.bci": { - "authority": "lov", - "description": "The BCI ontology specifies a foundational metadata model set for real-world multimodal Brain Computing Interface (BCI) data capture activities. The ontology defines a minimalist and simple abstract metadata foundational model for real-world BCI applications that monitors human activity in any scenario. BCI multimodal domain applications are encouraged to extend and use this ontology in their implementations.", - "homepage": "https://w3id.org/BCI-ontology", - "id": "lov.bci", - "name": "Brain Computing Interface (BCI) Ontology", - "prefix": "bci", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/BCI-ontology#$1" - }, - "lov.bcom": { - "authority": "lov", - "description": "The Building Concrete Monitoring Ontology (BCOM) is defined for capturing information of concrete work, concrete curing and testing of concrete properties. Further Information on the development and usage of the Ontology can be found in the following publication: Liu et al. (2021): An ontology integrating as-built information for infrastructure asset management using BIM and semantic web. In: Proceedings of 2021 European Conference on Computing in Construction, Online eConference, URL: https://ec-3.org/publications/conferences/2021/paper/?id=167", - "homepage": "https://w3id.org/bcom", - "id": "lov.bcom", - "name": "Building Concrete Monitoring Ontology (BCOM)", - "prefix": "bcom", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/bcom#$1" - }, - "lov.being": { - "authority": "lov", - "description": "A vocabulary to describe the interactions between persons and groups occurring in multimedia.", - "homepage": "http://contextus.net/ontology/ontomedia/ext/common/being#", - "id": "lov.being", - "name": "OntoMedia Being Representation", - "prefix": "being", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://contextus.net/ontology/ontomedia/ext/common/being#$1" - }, - "lov.bevon": { - "authority": "lov", - "description": "Beverage Ontology is a Web vocabulary for describing beverages, mainly alcoholic.", - "homepage": "http://rdfs.co/bevon/", - "id": "lov.bevon", - "name": "BEVON: Beverage Ontology", - "prefix": "bevon", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://rdfs.co/bevon/$1" - }, - "lov.bibo": { - "authority": "lov", - "description": "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.", - "homepage": "http://purl.org/ontology/bibo/", - "id": "lov.bibo", - "name": "The Bibliographic Ontology", - "prefix": "bibo", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/ontology/bibo/$1" - }, - "lov.bibtex": { - "authority": "lov", - "description": "Transformation of bibTeX into an OWL ontology", - "homepage": "http://purl.org/net/nknouf/ns/bibtex", - "id": "lov.bibtex", - "name": "BibTeX ontology", - "prefix": "bibtex", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/net/nknouf/ns/bibtex#$1" - }, - "lov.bimerr-op": { - "authority": "lov", - "description": "The Occupancy Profile ontology has been developed to represent people\u2019s behavior inside building spaces.", - "homepage": "http://bimerr.iot.linkeddata.es/def/occupancy-profile#", - "id": "lov.bimerr-op", - "name": "Occupancy Profile ontology", - "prefix": "bimerr-op", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://bimerr.iot.linkeddata.es/def/occupancy-profile#$1" - }, - "lov.bio": { - "authority": "lov", - "description": "A vocabulary for describing biographical information about people, both living and dead.", - "homepage": "http://purl.org/vocab/bio/0.1/", - "id": "lov.bio", - "name": "BIO: A vocabulary for biographical information", - "prefix": "bio", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocab/bio/0.1/$1" - }, - "lov.biol": { - "authority": "lov", - "description": "An RDF vocabulary for the taxonomy of all forms of life", - "homepage": "http://purl.org/NET/biol/ns#", - "id": "lov.biol", - "name": "Biological Taxonomy Vocabulary 0.2 (Core)", - "prefix": "biol", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://purl.org/NET/biol/ns#$1" - }, - "lov.biopax": { - "authority": "lov", - "description": "The goal of the BioPAX group is to develop a common exchange format for biological pathway data. More information is available at http://www.biopax.org. This ontology is freely available under the LGPL license", - "homepage": "http://www.biopax.org/release/biopax-level3.owl", - "id": "lov.biopax", - "name": "BioPAX Level 3 ontology", - "prefix": "biopax", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://www.biopax.org/release/biopax-level3.owl#$1" - }, - "lov.biotop": { - "authority": "lov", - "description": "Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network", - "homepage": "http://purl.org/biotop/biotop.owl", - "id": "lov.biotop", - "name": "BioTop", - "prefix": "biotop", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://purl.org/biotop/biotop.owl#$1" - }, - "lov.biro": { - "authority": "lov", - "description": "BiRO, the Bibliographic Reference Ontology, is an ontology structured according to the FRBR model to define bibliographic records (as subclasses of frbr:Work) and bibliographic references (as subclasses of frbr:Expression), and their compilations into bibliographic collections such as library catalogues, and into bibliographic lists such as reference lists in journal articles, respectively.", - "homepage": "http://purl.org/spar/biro", - "id": "lov.biro", - "name": "The Bibliographic Reference Ontology", - "prefix": "biro", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/biro/$1" - }, - "lov.blt": { - "authority": "lov", - "description": "Some useful terms for describing bibliographic resources that other models did not include. Version 1.4: brings the description for this schema in line with \"Metadata recommendations for Linked Open Vocabulairies\", version 1.1.; dct:license replaced by cc:license and the value changed from http://www.opendatacommons.org/licenses/pddl/1.0/ to http://creativecommons.org/publicdomain/mark/1.0/; various typos corrected. Version 1.4.1: added links to previous schema versions", - "homepage": "http://www.bl.uk/schemas/bibliographic/blterms", - "id": "lov.blt", - "name": "British Library Terms RDF schema", - "prefix": "blt", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.bl.uk/schemas/bibliographic/blterms#$1" - }, - "lov.bot": { - "authority": "lov", - "description": "A vocabulary to describe data sources in a way they can be easily reused and accessed by chatbots.", - "homepage": "http://swa.cefriel.it/ontologies/botdcat-ap", - "id": "lov.bot", - "name": "BotDCAT-AP - Data Catalogue vocabulary Application Profile for chatbots", - "prefix": "bot", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://swa.cefriel.it/ontologies/botdcat-ap#$1" - }, - "lov.botany": { - "authority": "lov", - "description": "This is a specialist botanical variant of the Biological Taxonomy Vocabulary.", - "homepage": "http://purl.org/NET/biol/botany#", - "id": "lov.botany", - "name": "Biological Taxonomy Vocabulary 0.2 (Botany)", - "prefix": "botany", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://purl.org/NET/biol/botany#$1" - }, - "lov.bperson": { - "authority": "lov", - "description": "Person ontology in Dutch", - "homepage": "http://data.vlaanderen.be/ns/persoon", - "id": "lov.bperson", - "name": "Person", - "prefix": "bperson", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.vlaanderen.be/ns/persoon#$1" - }, - "lov.br": { - "authority": "lov", - "description": "A lightweight ontology to structure e- brainstorming sessions", - "homepage": "http://vocab.deri.ie/br", - "id": "lov.br", - "name": "Brainstorm Ontology", - "prefix": "br", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.deri.ie/br#$1" - }, - "lov.brk": { - "authority": "lov", - "description": "Basisregistratie Kadaster (BRK) vocabulaire", - "homepage": "http://brk.basisregistraties.overheid.nl/def/brk", - "id": "lov.brk", - "name": "Key Register Cadastre (BRK) vocabulary", - "prefix": "brk", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://brk.basisregistraties.overheid.nl/def/brk#$1" - }, - "lov.brt": { - "authority": "lov", - "description": "Basisregistratie Topografie (BRT) vocabulaire", - "homepage": "http://brt.basisregistraties.overheid.nl/def/top10nl", - "id": "lov.brt", - "name": "Key Register Topography (BRT) vocabulary", - "prefix": "brt", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://brt.basisregistraties.overheid.nl/def/top10nl#$1" - }, - "lov.bto": { - "authority": "lov", - "description": "The Building Topology Ontology (BOT) is a simple ontology defining the core concepts of a building.\n\nIt is a simple, easy to extend ontology for the construction industry to document and exchange building data on the web.\n\nChanges since version 0.2.0 of the ontology are documented in:\nhttps://w3id.org/bot/bot.html#changes\n\nThe version 0.2.0 of the ontology is documented in:\nMads Holten Rasmussen, Pieter Pauwels, Maxime Lefran\u00e7ois, Georg Ferdinand Schneider, Christian Anker Hviid and Jan Karlsh\u00f8j (2017) Recent changes in the Building Topology Ontology, 5th Linked Data in Architecture and Construction Workshop (LDAC2017), November 13-15, 2017, Dijon, France, https://www.researchgate.net/publication/320631574_Recent_changes_in_the_Building_Topology_Ontology\n\nThe initial version 0.1.0 of the ontology was documented in:\nMads Holten Rasmussen, Pieter Pauwels, Christian Anker Hviid and Jan Karlsh\u00f8j (2017) Proposing a Central AEC Ontology That Allows for Domain Specific Extensions, Lean and Computing in Construction Congress (LC3): Volume I \u2013 Proceedings of the Joint Conference on Computing in Construction (JC3), July 4-7, 2017, Heraklion, Greece, pp. 237-244 https://doi.org/10.24928/JC3-2017/0153", - "homepage": "https://w3id.org/bot", - "id": "lov.bto", - "name": "BOT: Building Topology Ontology", - "prefix": "bto", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/bot#$1" - }, - "lov.c4n": { - "authority": "lov", - "description": "A vocabulary to describe calls, such as call for tenders, call for proposals, call for papers, etc.", - "homepage": "http://vocab.deri.ie/c4n", - "id": "lov.c4n", - "name": "Call for Anything vocabulary", - "prefix": "c4n", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "http://vocab.deri.ie/c4n#$1" - }, - "lov.c4o": { - "authority": "lov", - "description": "C4O allows the characterization of bibliographic citations in terms of their number and their context.", - "homepage": "http://purl.org/spar/c4o", - "id": "lov.c4o", - "name": "C4O, the Citation Counting and Context Characterization Ontology", - "prefix": "c4o", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/c4o/$1" - }, - "lov.cal": { - "authority": "lov", - "description": "A vocabulary for description of events and calendars", - "homepage": "http://www.w3.org/2002/12/cal/ical", - "id": "lov.cal", - "name": "Internet Calendaring and Scheduling Core Object Specification", - "prefix": "cal", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2002/12/cal/ical#$1" - }, - "lov.caresses": { - "authority": "lov", - "description": "The CARESSES Ontology encodes guidelines defined by experts in Transcultural Nursing, with the aim of offering a specific tool for endowing social assistive robots (assisting older adults) with cultural competence.", - "homepage": "http://caressesrobot.org/ontology", - "id": "lov.caresses", - "name": "CARESSES Ontology", - "prefix": "caresses", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://caressesrobot.org/ontology#$1" - }, - "lov.cart": { - "authority": "lov", - "description": "Ontology for representation of cartesian co-ordinates", - "homepage": "http://purl.org/net/cartCoord#", - "id": "lov.cart", - "name": "cartCoordOnt", - "prefix": "cart", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://purl.org/net/cartCoord#$1" - }, - "lov.caso": { - "authority": "lov", - "description": "CASO (Context Aware System Observation) is an ontology for context aware system and observation services. Its goal is to describe all the processing of the context.", - "homepage": "http://www.w3id.org/def/caso#", - "id": "lov.caso", - "name": "Context Aware System Observation Ontology", - "prefix": "caso", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3id.org/def/caso#$1" - }, - "lov.cbcm": { - "authority": "lov", - "description": "This ontology describes terms concerning companies, their cross-border movements within the European Union (EU), and associated EU company legislation.", - "homepage": "http://w3id.org/um/cbcm/eu-cm-ontology", - "id": "lov.cbcm", - "name": "The European Union Company Mobility Ontology (EUCM ontology)", - "prefix": "cbcm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://w3id.org/um/cbcm/eu-cm-ontology#$1" - }, - "lov.cbo": { - "authority": "lov", - "description": "A metadata vocabulary for describing comic books and comic book collections.", - "homepage": "http://comicmeta.org/cbo/", - "id": "lov.cbo", - "name": "Comic Book Ontology", - "prefix": "cbo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://comicmeta.org/cbo/$1" - }, - "lov.cbs": { - "authority": "lov", - "description": "Ontologie voor datasets van het CBS", - "homepage": "http://betalinkeddata.cbs.nl/def/cbs", - "id": "lov.cbs", - "name": "De Centraal Bureau voor de Statistiek (CBS) ontologie", - "prefix": "cbs", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences", - "earth and related environmental sciences" - ], - "uri_format": "http://betalinkeddata.cbs.nl/def/cbs#$1" - }, - "lov.cc": { - "authority": "lov", - "description": "The Creative Commons Rights Expression Language (CC REL) lets you describe copyright licenses in RDF", - "homepage": "http://creativecommons.org/ns", - "id": "lov.cc", - "name": "Creative Commons Rights Expression Language", - "prefix": "cc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://creativecommons.org/ns#$1" - }, - "lov.cci": { - "authority": "lov", - "description": "Ontology for Cloud Computing Instances. Instance are classes of VM that comprise varying combinations of CPU, memory, storage, and networking capacity. This ontology allows to define the instantiation model of MVs used in large cloud computing providers such as Amazon, Azure, etc.", - "homepage": "http://cookingbigdata.com/linkeddata/ccinstances", - "id": "lov.cci", - "name": "Ontology for Cloud Computing instances", - "prefix": "cci", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://cookingbigdata.com/linkeddata/ccinstances#$1" - }, - "lov.cco": { - "authority": "lov", - "description": "The Cognitive Characteristics Ontology specification provides a vocabulary for describing cognitive pattern within contexts, their temporal dynamics and their origins, on/ for the Semantic Web.", - "homepage": "http://purl.org/ontology/cco/core#", - "id": "lov.cco", - "name": "Cognitive Characteristics Ontology", - "prefix": "cco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/cco/core#$1" - }, - "lov.ccp": { - "authority": "lov", - "description": "Simple and direct pricing ontology for Cloud Computing Services. This ontology allows to define model of prices used in large cloud computing providers such as Amazon, Azure, etc., including options for regions, type of instances, prices specification, etc.", - "homepage": "http://cookingbigdata.com/linkeddata/ccpricing", - "id": "lov.ccp", - "name": "Vocabulary for prices options in Cloud Computing Services", - "prefix": "ccp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://cookingbigdata.com/linkeddata/ccpricing#$1" - }, - "lov.ccr": { - "authority": "lov", - "description": "Ontology for the definition of regions and zones of availability on CloudComputing platforms and services. This ontology allows to define model of regions used in large cloud computing providers such as Amazon, Azure, etc.", - "homepage": "http://cookingbigdata.com/linkeddata/ccregions", - "id": "lov.ccr", - "name": "Vocabulary for Regions and Zones on Cloud Computing", - "prefix": "ccr", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://cookingbigdata.com/linkeddata/ccregions#$1" - }, - "lov.ccsla": { - "authority": "lov", - "description": "Service Level Agreement for Cloud Computing Services. This ontology allows to define model of SLA/SLO used in large cloud computing providers such as Amazon, Azure, etc., including terms, claims, credit, compensations, etc", - "homepage": "http://cookingbigdata.com/linkeddata/ccsla", - "id": "lov.ccsla", - "name": "Service Level Agreement for Cloud Computing", - "prefix": "ccsla", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://cookingbigdata.com/linkeddata/ccsla#$1" - }, - "lov.cdc": { - "authority": "lov", - "description": "The Construction Dataset Context (CDC) ontology is an extension of DCAT v2.0, a W3C Recommendation ontology for describing (RDF and non-RDF) datasets published on the Web. Using this extension, it becomes possible to describe a context for construction-related datasets that are being distributed using Web technology as well as datasets that are not shared outside an organization such as local copies, work in progress and other datasets that remain internal. This dataset metadata encompasses the temporal context (period or snapshot), the type of content of the dataset (as-built, design, etc.) and relations between contextualized datasets (previous as-built, requirements related to a design, etc.). In addition, this DCAT extension also provides terminology for managing dataset distributions that are scoped to a certain (named or default) graph of an RDF file or quadstore.", - "homepage": "https://w3id.org/cdc", - "id": "lov.cdc", - "name": "CDC: Construction Dataset Context ontology", - "prefix": "cdc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/cdc#$1" - }, - "lov.cdesc": { - "authority": "lov", - "description": "The Context Description module includes models for the context of a cultural property, in a broad sense: agents (e.g.: author, collector, copyright holder), objects (e.g.: inventories, bibliography, protective measures, other cultural properties, collections etc.), activities (e.g.: surveys, conservation interventions), situations (e.g.: commission, coin issuance, estimate, legal situation) related, involved or involving the cultural property. Thus it represents attributes that do not result from a measurement of features in a cultural property, but are associated with it.", - "homepage": "https://w3id.org/arco/ontology/context-description", - "id": "lov.cdesc", - "name": "Context Description Ontology (ArCo network)", - "prefix": "cdesc", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "https://w3id.org/arco/ontology/context-description/$1" - }, - "lov.cdm": { - "authority": "lov", - "description": "An attempt to represent how universal/accepted/popular a URI is", - "homepage": "http://purl.org/twc/ontology/cdm.owl#", - "id": "lov.cdm", - "name": "Conceptual Depth and Momentum", - "prefix": "cdm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/twc/ontology/cdm.owl#$1" - }, - "lov.cdtype": { - "authority": "lov", - "description": "Types defined by the Dublin Core Collections Application Profile", - "homepage": "http://purl.org/cld/cdtype/", - "id": "lov.cdtype", - "name": "The Collection Description Type Namespace", - "prefix": "cdtype", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/cld/cdtype/$1" - }, - "lov.cem": { - "authority": "lov", - "description": "The Crime Event Model is an ontology for the representation of crime events extracted from local newspapers. It could be employed for Crime Analysis purposes: extracting crime information from newspapers and enriching them with proper machine-readable semantics is a critical task to help law enforcement agencies at preventing crime, supporting criminal investigations and evaluating the action of law enforcement agencies themselves. The model is based on the fundamental 5W1H journalistic questions, that are Who?, What?, When?, Where?, Why? and How?. Another important requirement was the attempt to exploit existing knowledge graphs and ontologies such as the Simple Event Model (SEM) Ontology and the Schema.org data model for interoperability and interconnection.", - "homepage": "https://w3id.org/CEMontology", - "id": "lov.cem", - "name": "Crime Event Model (CEM)", - "prefix": "cem", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/CEMontology/$1" - }, - "lov.ceo": { - "authority": "lov", - "description": "An Ontology for Consumer Electronics Products and Services", - "homepage": "http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1", - "id": "lov.ceo", - "name": "Consumer Electronics Ontology", - "prefix": "ceo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1#$1" - }, - "lov.cerif": { - "authority": "lov", - "description": "The Common European Research Information Format (CERIF) Ontology Specification provides basic concepts and properties for describing research information as semantic data.", - "homepage": "http://www.eurocris.org/ontologies/cerif/1.3", - "id": "lov.cerif", - "name": "CERIF Ontology 1.3", - "prefix": "cerif", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.eurocris.org/ontologies/cerif/1.3#$1" - }, - "lov.cert": { - "authority": "lov", - "description": "Ontology for Certificates and crypto stuff.", - "homepage": "http://www.w3.org/ns/auth/cert#", - "id": "lov.cert", - "name": "The Cert Ontology", - "prefix": "cert", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/auth/cert#$1" - }, - "lov.cevent": { - "authority": "lov", - "description": "The Cultural Event module models cultural events, i.e. events involving cultural properties.", - "homepage": "https://w3id.org/arco/ontology/cultural-event", - "id": "lov.cevent", - "name": "Cultural Event Ontology (ArCo network)", - "prefix": "cevent", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/arco/ontology/cultural-event/$1" - }, - "lov.cff": { - "authority": "lov", - "description": "This is an ontology representation of the generic features defined by Climate and Forecast (CF) standard names vocabulary (http://cf-pcmdi.llnl.gov/documents/cf-standard-names/), maintained by the Program for Climate Model Diagnosis and Intercomparison (http://cf-pcmdi.llnl.gov/ ) which is intended for use with climate and forecast data, in the atmosphere, surface and ocean domains.", - "homepage": "http://purl.oclc.org/NET/ssnx/cf/cf-feature", - "id": "lov.cff", - "name": "Climate and Forecast (CF) features", - "prefix": "cff", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://purl.oclc.org/NET/ssnx/cf/cf-feature#$1" - }, - "lov.cfp": { - "authority": "lov", - "description": "This is an ontology representation of the climatic data variables defined by Climate and Forecast (CF) standard names vocabulary (http://cf-pcmdi.llnl.gov/documents/cf-standard-names/), maintained by the Program for Climate Model Diagnosis and Intercomparison (http://cf-pcmdi.llnl.gov/ ) which is intended for use with climate and forecast data, in the atmosphere, surface and ocean domains.", - "homepage": "http://purl.oclc.org/NET/ssnx/cf/cf-property", - "id": "lov.cfp", - "name": "Climate and Forecast (CF) standard names parameter vocabulary", - "prefix": "cfp", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "http://purl.oclc.org/NET/ssnx/cf/cf-property#$1" - }, - "lov.cfrl": { - "authority": "lov", - "description": "The Corporate Financial Reports and Loans Ontology (CFRL).", - "homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/cfrl#", - "id": "lov.cfrl", - "name": "Corporate Financial Reports and Loans Ontology", - "prefix": "cfrl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://linkeddata.finki.ukim.mk/lod/ontology/cfrl#$1" - }, - "lov.cgov": { - "authority": "lov", - "description": "An ontology of UK central government", - "homepage": "http://reference.data.gov.uk/def/central-government", - "id": "lov.cgov", - "name": "Central Government Ontology", - "prefix": "cgov", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://reference.data.gov.uk/def/central-government/$1" - }, - "lov.chord": { - "authority": "lov", - "description": "This document describes the first draft of a chord ontology based on work from the Centre for Digital Music, Queen Mary, University of London. It has been created as part of the OMRAS2 project and is intended to provide a common, versatile vocabulary for describing chords and chord sequences in RDF.", - "homepage": "http://purl.org/ontology/chord/", - "id": "lov.chord", - "name": "The OMRAS2 Chord Ontology", - "prefix": "chord", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/chord/$1" - }, - "lov.ci": { - "authority": "lov", - "description": "This vocabulary defines a number of concepts peculiar to content strategy which are not accounted for by other vocabularies.", - "homepage": "https://privatealpha.com/ontology/content-inventory/1#", - "id": "lov.ci", - "name": "A Content Inventory Vocabulary", - "prefix": "ci", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://privatealpha.com/ontology/content-inventory/1#$1" - }, - "lov.cis": { - "authority": "lov", - "description": "The ontology aims at modelling the data on cultural institutes or sites such as data regarding the agents that play a specific role on cultural institutes or sites, the sites themselves, the contact points, all multimedia files which describe the cultural institute or site and any other information useful to the public in order to access the institute or site. Moreover, the ontology represents events that can take place in specific cultural institutes or sites.", - "homepage": "http://dati.beniculturali.it/cultural-ON/cultural-ON.owl", - "id": "lov.cis", - "name": "Cultural-ON (Cultural ONtology): Cultural Institute/Site and Cultural Event Ontology", - "prefix": "cis", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://dati.beniculturali.it/cis/$1" - }, - "lov.cito": { - "authority": "lov", - "description": "The Citation Typing Ontology enables characterization of the nature or type of citations", - "homepage": "http://purl.org/spar/cito", - "id": "lov.cito", - "name": "CiTO, the Citation Typing Ontology", - "prefix": "cito", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/cito/$1" - }, - "lov.citof": { - "authority": "lov", - "description": "CiTOFunctions is an ontology that provides a classification for citations. In particular, it classifies CiTO properties (each defining a particular citational act)", - "homepage": "http://www.essepuntato.it/2013/03/cito-functions", - "id": "lov.citof", - "name": "Functions of Citations", - "prefix": "citof", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.essepuntato.it/2013/03/cito-functions/$1" - }, - "lov.cl": { - "authority": "lov", - "description": "Le projet Advene a pour objectif de fournir un mod\u00e8le et plusieurs formats de donn\u00e9es pour partager des annotations sur des vid\u00e9os num\u00e9riques (films, cours, conf\u00e9rences...), ainsi que des outils pour \u00e9diter et visualiser les hyp\u00e9rvid\u00e9os g\u00e9n\u00e9r\u00e9es \u00e0 partir de ces vid\u00e9os et des annotations. Les enseignants, les amateurs de cin\u00e9ma, etc., peuvent les utiliser pour \u00e9changer leurs commentaires et analyse de documents audiovisuels.\n\nLe mod\u00e8le Cinelab permet non seulement de repr\u00e9senter les annotations vid\u00e9os, mais aussi d'expliciter leur structure (\u00e0 travers les notions de sch\u00e9ma et de type d'annotation), ainsi que leur pr\u00e9sentations \u00e0 l'aide de vues (mod\u00e8les appliqu\u00e9s aux donn\u00e9es pour produire des hypervid\u00e9os) et de requ\u00eates.\n\nCe mod\u00e8le a \u00e9t\u00e9 d\u00e9velopp\u00e9 par les partenaires du projet Cinelab (2007-2008, financ\u00e9 par l'ANR), et utilis\u00e9 par la suite dans plusieurs projets et applications, dont Advene (LIRIS) et Ligne de temps (IRI).", - "homepage": "http://advene.org/ns/cinelab/ld", - "id": "lov.cl", - "name": "Cinelab ontology", - "prefix": "cl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://advene.org/ns/cinelab/ld#$1" - }, - "lov.cld": { - "authority": "lov", - "description": "An expression in RDF of the application profile for collection-level description developed by the Dublin Core Collection Description Task Group.", - "homepage": "http://purl.org/cld/terms/", - "id": "lov.cld", - "name": "The Collection Description Terms", - "prefix": "cld", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/cld/terms/$1" - }, - "lov.cmo": { - "authority": "lov", - "description": "An ontology to tie classes and properties to SKOS concepts", - "homepage": "http://purl.org/twc/ontologies/cmo.owl", - "id": "lov.cmo", - "name": "Conceptual Model Ontology", - "prefix": "cmo", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://purl.org/twc/ontologies/cmo.owl#$1" - }, - "lov.cnt": { - "authority": "lov", - "description": "Representing Content in RDF as defined by http://www.w3.org/TR/Content-in-RDF/", - "homepage": "http://www.w3.org/2011/content", - "id": "lov.cnt", - "name": "Representing Content in RDF", - "prefix": "cnt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2011/content#$1" - }, - "lov.co": { - "authority": "lov", - "description": "The Counter Ontology specification provides basic concepts and properties for describing a general counter concept and some important sub counters", - "homepage": "http://purl.org/ontology/co/core#", - "id": "lov.co", - "name": "Counter Ontology", - "prefix": "co", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/co/core#$1" - }, - "lov.cochrane": { - "authority": "lov", - "description": "The Cochrane Core ontology describes the entities and concepts that exist in the domain of evidence based healthcare. It is used for the construction of the Cochrane Linked Data Vocabulary containing some 400k terms including Interventions (Drugs, Procedures etc), Populations (Age, Sex, Condition), and clinical Outcomes.", - "homepage": "http://data.cochrane.org/ontologies/core/", - "id": "lov.cochrane", - "name": "Cochrane Core Vocabulary Ontology", - "prefix": "cochrane", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://data.cochrane.org/ontologies/core/$1" - }, - "lov.cocoon": { - "authority": "lov", - "description": "Simple ontology for Cloud Computing Services. This ontology allows to define model of prices used in large cloud computing providers such as Google, Amazon, Azure, etc., including options for regions, type of instances, prices specification, etc.", - "homepage": "https://w3id.org/cocoon/v1.0", - "id": "lov.cocoon", - "name": "Cloud Computing Services Ontology", - "prefix": "cocoon", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "https://w3id.org/cocoon/v1.0#$1" - }, - "lov.cogs": { - "authority": "lov", - "description": "Vocabulary for describing ETL and data transformation activities.", - "homepage": "http://vocab.deri.ie/cogs", - "id": "lov.cogs", - "name": "COGS Vocabulary", - "prefix": "cogs", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.deri.ie/cogs#$1" - }, - "lov.cold": { - "authority": "lov", - "description": "Ontology for the description of customizable products. It models the configuration process as the traversal of a graph of partially defined products, or \"Configurations\"", - "homepage": "http://purl.org/configurationontology", - "id": "lov.cold", - "name": "'Configuration as Linked Data' ontology", - "prefix": "cold", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/configurationontology#$1" - }, - "lov.coll": { - "authority": "lov", - "description": "The Collections Ontology (CO) defines unordered collections (Set and Bag) and ordered collections (or List). This ontology has been inspired by the work \"Putting OWL in Order: Patterns for Sequences in OWL\" by Drummond et al. (OWL-ED 2006).", - "homepage": "http://purl.org/co", - "id": "lov.coll", - "name": "Collections Ontology", - "prefix": "coll", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/co/$1" - }, - "lov.comm": { - "authority": "lov", - "description": "This vocabulary is intended to describe all the aspects which are needed to communicate incident related information for fire department services", - "homepage": "http://vocab.resc.info/communication", - "id": "lov.comm", - "name": "Vocabulary related to incident communication", - "prefix": "comm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.resc.info/communication#$1" - }, - "lov.common": { - "authority": "lov", - "description": "The Delivery Context Ontology models the knowledge of the environment in which devices interact with the Web or other services", - "homepage": "http://www.w3.org/2007/uwa/context/deliverycontext.owl", - "id": "lov.common", - "name": "The Delivery Context Ontology", - "prefix": "common", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2007/uwa/context/common.owl#$1" - }, - "lov.con": { - "authority": "lov", - "description": "Utility concepts for everyday life", - "homepage": "http://www.w3.org/2000/10/swap/pim/contact", - "id": "lov.con", - "name": "Contact", - "prefix": "con", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2000/10/swap/pim/contact#$1" - }, - "lov.contax": { - "authority": "lov", - "description": "An ontology containing additional terminology for structuring and annotating RDFS/OWL taxonomies for describing constructions (components, materials, spatial zones, damages, construction tasks and properties). It also functions as an index for known taxonomies starting from root classes and properties.", - "homepage": "https://w3id.org/con-tax", - "id": "lov.contax", - "name": "ConTax ontology", - "prefix": "contax", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/con-tax#$1" - }, - "lov.conversion": { - "authority": "lov", - "description": "Ontology used to describe interpretations of tabular literals to produce RDF", - "homepage": "http://purl.org/twc/vocab/conversion/", - "id": "lov.conversion", - "name": "Conversion Ontology", - "prefix": "conversion", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/twc/vocab/conversion/$1" - }, - "lov.coo": { - "authority": "lov", - "description": "The COO provides a vocabulary for exposing available configuration options for car models. It allows indicating choices that can be made as well as compatibility, dependency, and inclusion information. The ontology imports and extends the GoodRelations ontology for e-commerce", - "homepage": "http://purl.org/coo/ns#", - "id": "lov.coo", - "name": "Car Options Ontology", - "prefix": "coo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/coo/ns#$1" - }, - "lov.core": { - "authority": "lov", - "description": "This is the core module in Materials Design Ontology.", - "homepage": "https://w3id.org/mdo/core/", - "id": "lov.core", - "name": "Materials Design Ontology - Core Module", - "prefix": "core", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/mdo/core/$1" - }, - "lov.coun": { - "authority": "lov", - "description": "Basic properties of a country as defined by ISO 3166 (code and name)", - "homepage": "http://www.daml.org/2001/09/countries/iso-3166-ont", - "id": "lov.coun", - "name": "ISO 3166 Country Codes", - "prefix": "coun", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://www.daml.org/2001/09/countries/iso-3166-ont#$1" - }, - "lov.cpa": { - "authority": "lov", - "description": "A set of annotation properties to be used for ontology design patterns", - "homepage": "http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl", - "id": "lov.cpa", - "name": "Content Pattern Annotations", - "prefix": "cpa", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl#$1" - }, - "lov.cpmeta": { - "authority": "lov", - "description": "OWL vocabulary describing metadata of two environmental research infrastructures: ICOS and SITES", - "homepage": "http://meta.icos-cp.eu/ontologies/cpmeta/", - "id": "lov.cpmeta", - "name": "Ontology of Integrated Carbon Observation System (ICOS)", - "prefix": "cpmeta", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://meta.icos-cp.eu/ontologies/cpmeta/$1" - }, - "lov.crm": { - "authority": "lov", - "description": "This is the encoding approved by CRM-SIG in the meeting 21/11/2012 as the official current version for the CIDOC CRM namespace. Note that this is NOT a definition of the CIDOC CRM, but an encoding derived from the authoritative release of the CIDOC CRM v5.0.4 on http://www.cidoc-crm.org/official_release_cidoc.html", - "homepage": "http://www.cidoc-crm.org/cidoc-crm/", - "id": "lov.crm", - "name": "CIDOC Conceptual Reference Model", - "prefix": "crm", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.cidoc-crm.org/cidoc-crm/$1" - }, - "lov.cro": { - "authority": "lov", - "description": "The Copyright Ontology is a contribution geared towards the development of copyright-aware Digital Rights Management (DRM) systems.", - "homepage": "http://rhizomik.net/ontologies/copyrightonto.owl", - "id": "lov.cro", - "name": "Copyright Ontology", - "prefix": "cro", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rhizomik.net/ontologies/copyrightonto.owl#$1" - }, - "lov.crsw": { - "authority": "lov", - "description": "The ReSIST Courseware Ontology represents the various educational courses and resources within the ReSIST project", - "homepage": "http://courseware.rkbexplorer.com/ontologies/courseware", - "id": "lov.crsw", - "name": "ReSIST Courseware Ontology", - "prefix": "crsw", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://courseware.rkbexplorer.com/ontologies/courseware#$1" - }, - "lov.cs": { - "authority": "lov", - "description": "This vocabulary defines a set of terms for describing changes to resource descriptions.", - "homepage": "http://purl.org/vocab/changeset/schema", - "id": "lov.cs", - "name": "Changeset", - "prefix": "cs", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocab/changeset/schema#$1" - }, - "lov.csp": { - "authority": "lov", - "description": "A vocabulary to represent Constraint Satisfaction Problems (CSPs) in which constraints are expressed by Boolean expressions on fluents.", - "homepage": "http://vocab.deri.ie/csp", - "id": "lov.csp", - "name": "Constraint Satisfaction Problems Vocabulary", - "prefix": "csp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.deri.ie/csp#$1" - }, - "lov.csvw": { - "authority": "lov", - "description": "This document describes the RDFS vocabulary description used in the Metadata Vocabulary for Tabular Data along with the default JSON-LD Context.", - "homepage": "http://www.w3.org/ns/csvw#", - "id": "lov.csvw", - "name": "CSV on the Web Vocabulary", - "prefix": "csvw", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/csvw#$1" - }, - "lov.ct": { - "authority": "lov", - "description": "Defines types of connectivity used in communication and bearer services accessible in certain connectivity.", - "homepage": "http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl", - "id": "lov.ct", - "name": "Connectivity types", - "prefix": "ct", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl#$1" - }, - "lov.ctag": { - "authority": "lov", - "description": "Common Tags are references to unique, well-defined concepts, complete with metadata and their own URLs.", - "homepage": "http://commontag.org/ns#", - "id": "lov.ctag", - "name": "Common Tag Vocabulary", - "prefix": "ctag", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://commontag.org/ns#$1" - }, - "lov.ctlog": { - "authority": "lov", - "description": "The Catalogue module allows the description of concepts related to the Italian General Catalogue of Cultural Heritage (ICCD-MiBAC), and in particular catalogue records, that is XML files recording all data gathered by a cataloguer on a particular cultural property.", - "homepage": "https://w3id.org/arco/ontology/catalogue", - "id": "lov.ctlog", - "name": "Catalogue Ontology (ArCo network)", - "prefix": "ctlog", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "https://w3id.org/arco/ontology/catalogue/$1" - }, - "lov.cto": { - "authority": "lov", - "description": "The Construction Tasks Ontology (CTO) describes tasks operating on construction elements, spatial zones and/or damages. The tasks are either planned or executed depending on the dataset metadata context of the dataset its used in. Five different types of tasks are defined: instalment, removal, modification, repair and inspection. \nConsequences of tasks on the dataset, i.e. added and/or deleted triples, are modeled using reified statements. The tasks can link to a reified statement using the CTO relations.", - "homepage": "https://w3id.org/cto", - "id": "lov.cto", - "name": "CTO: Construction Tasks Ontology", - "prefix": "cto", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/cto#$1" - }, - "lov.ctorg": { - "authority": "lov", - "description": "El objetivo de este vocabulario es la creaci\u00f3n de un esquema que permita definir los contenidos de la informaci\u00f3n relacionada con los \u00f3rganos de gobierno y los centros p\u00fablicos que ofrecen servicios. Se identifican ciertas variables en el dominio de los centros p\u00fablicos, que se modelan a trav\u00e9s de ciertos tipos de datos y de propiedades relacionadas entre los recursos. Se utiliza Ontologies for e-Government para modelar las principales caracter\u00edsticas.", - "homepage": "http://purl.org/ctic/infraestructuras/organizacion", - "id": "lov.ctorg", - "name": "Vocabulario de la estructura de organismos p\u00fablicos", - "prefix": "ctorg", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://purl.org/ctic/infraestructuras/organizacion#$1" - }, - "lov.ctrl": { - "authority": "lov", - "description": "CTRLont specifies concepts and relationships of control actors on a high level", - "homepage": "https://w3id.org/ibp/CTRLont", - "id": "lov.ctrl", - "name": "CTRLont - An ontology to formally specify the control domain", - "prefix": "ctrl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/ibp/CTRLont#$1" - }, - "lov.ctxdesc": { - "authority": "lov", - "description": "OWL pattern for describing activity models as abstract dependencies among classes.", - "homepage": "http://www.demcare.eu/ontologies/contextdescriptor.owl", - "id": "lov.ctxdesc", - "name": "Context Descriptor Pattern", - "prefix": "ctxdesc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.demcare.eu/ontologies/contextdescriptor.owl#$1" - }, - "lov.cwmo": { - "authority": "lov", - "description": "Creative Workshop Management Ontology (CWMO) - an ontology designed to describe the creative workshop domain, to permit reasoning on creative method and to describe resources gathered inside Creative Support System. The primary goal of the ontology is to cover all knowledge about creative workshop and creative method necessary for Creative support system. The second goal is to provide interoperability between distributed Creative Support System.", - "homepage": "http://purl.org/cwmo/#", - "id": "lov.cwmo", - "name": "Creative Workshop Management Ontology (CWMO)", - "prefix": "cwmo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/cwmo/#$1" - }, - "lov.cwork": { - "authority": "lov", - "description": "This ontology defines the terms required to describe the creative works produced by the BBC and their associated metadata.", - "homepage": "http://www.bbc.co.uk/ontologies/creativework", - "id": "lov.cwork", - "name": "Creative Work Ontology", - "prefix": "cwork", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.bbc.co.uk/ontologies/creativework/$1" - }, - "lov.cwrc": { - "authority": "lov", - "description": "L'Ontologie CWRC est l'ontologie du Collaboratoire scientifique des \u00e9crits du Canada.", - "homepage": "http://sparql.cwrc.ca/ontologies/cwrc", - "id": "lov.cwrc", - "name": "L'Ontologie CWRC", - "prefix": "cwrc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://sparql.cwrc.ca/ontologies/cwrc#$1" - }, - "lov.d2rq": { - "authority": "lov", - "description": "This document specifies the D2RQ mapping language. D2RQ is a declarative language to describe mappings between relational database schemata and OWL/RDFS ontologies.", - "homepage": "http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1", - "id": "lov.d2rq", - "name": "D2RQ - Language Specification", - "prefix": "d2rq", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#$1" - }, - "lov.dady": { - "authority": "lov", - "description": "A vocabulary that allows for coarse-grained descriptions of the data-source dynamics as well as the discovery of change notification mechanism(s).", - "homepage": "http://vocab.deri.ie/dady", - "id": "lov.dady", - "name": "Dataset Dynamics (dady) vocabulary", - "prefix": "dady", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/NET/dady#$1" - }, - "lov.daia": { - "authority": "lov", - "description": "The Document Availability Information Ontology (DAIA) describes the current availability of documents in libraries and similar institutions. Availability can be expressed in terms of specific services.", - "homepage": "http://purl.org/ontology/daia", - "id": "lov.daia", - "name": "Document Availability Information Ontology", - "prefix": "daia", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/ontology/daia/$1" - }, - "lov.daq": { - "authority": "lov", - "description": "Quality metrics can be (in principle) calculated on various forms of data (such as datasets, graphs, set of triples etc...). This vocabulary allow the owner/user of such RDF data to calculate metrics on multiple (and different) resources.", - "homepage": "http://purl.org/eis/vocab/daq#", - "id": "lov.daq", - "name": "Dataset Quality Vocabulary", - "prefix": "daq", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/eis/vocab/daq#$1" - }, - "lov.dataid": { - "authority": "lov", - "description": "DBpedia Data ID is an ontology with the goal of describing LOD datasets via RDF files in a uniform way. Established vocabularies like DCAT, VoID, Prov-O and SPARQL Service Description are used for maximum compatibility.", - "homepage": "http://dataid.dbpedia.org/ns/core#", - "id": "lov.dataid", - "name": "DataID", - "prefix": "dataid", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://dataid.dbpedia.org/ns/core#$1" - }, - "lov.date": { - "authority": "lov", - "description": "OntoMedia (Ontology for Media) Date Component has been designed to describe the different ways of marking time in media.", - "homepage": "http://contextus.net/ontology/ontomedia/misc/date#", - "id": "lov.date", - "name": "OntoMedia Date Part Representation", - "prefix": "date", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://contextus.net/ontology/ontomedia/misc/date#$1" - }, - "lov.datex": { - "authority": "lov", - "description": "This document gives URIs to all terms used within Datex II. the Datex standard was developed for information exchange between traffic management centres, traffic information centres and service providers in Europe", - "homepage": "http://vocab.datex.org/terms#", - "id": "lov.datex", - "name": "Linked Datex II", - "prefix": "datex", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://vocab.datex.org/terms#$1" - }, - "lov.dave": { - "authority": "lov", - "description": "The Data Value Vocabulary (DaVe) is an extensible core vocabulary that allows user to use custom data value dimensions and metrics to characterise data value in a specific context. This flexibility allows for the comprehensive modelling of data value. As a data value model, DaVe allows users to monitor data value as it occurs within a data exploitation or value creation process (data value chain)", - "homepage": "http://theme-e.adaptcentre.ie/dave/dave.ttl", - "id": "lov.dave", - "name": "Data Value Vocabulary (DaVe)", - "prefix": "dave", - "source": "lov.linkeddata.es", - "subjects": [ - "generic", - "mathematics", - "computer and information sciences" - ], - "uri_format": "http://theme-e.adaptcentre.ie/dave#$1" - }, - "lov.dba": { - "authority": "lov", - "description": "The ontology, presented here in a beta version, is based on the analysis of the documentation and descriptive requirements of the Intesa Sanpaolo Historical Archive and is intended to describe the content of historical banking documents and of some of the activities carried out by the bank, particularly in relation to third parties (loans, charity donations, seizures and confiscations, etc.), which involve the initiation of processes or the production of documents. The focal point of the descriptive model is the bank - an entity that initiates different types of processes, whose common feature is that they are structured into various stages/events - and the relationship between the documentation produced and the information it contains. In fact, this ontology is based on information collected from archived documents which describe various processes and activities carried out by banking institutions: the starting point for its construction were the inventories and databases of documentation stored in the Historical Archive which was produced by the various banks that over time were merged into Intesa Sanpaolo. The ontology was created to provide a sufficiently abstract representation and model for describing the processes of various banking activities from which the documentation was produced - from a company's request for financing and its outcome, to the preparation of seizure, confiscation and asset restitution filings, to charitable contributions, just to mention a few examples - reusing models that were already well established and widely used. The structure of the proposed ontology is in fact intended to adapt to the various activities, described in the archive files that a banking institution performs in relation to third parties. The proposed ontology is therefore not an ontology on banking activity in general, but on the relationship between this activity and the documents that are produced. Moreover, its objective is not to describe the documents in the strict sense of the term, for which reference is made to OAD ontology. The purpose of this project is to lay the initial, and fundamental, building blocks for describing the complexity, variety, and breadth of the domain of archiving bank records and the data they contain. Despite having data from different banks relating to different activities and having already made arrangements for the integration of third-party datasets and ontologies, before completing the project we will have to wait for the processing of representations based on other types of documents and banking institutions, including non-Italian ones.", - "homepage": "https://w3id.org/dba/ontology/", - "id": "lov.dba", - "name": "Description Banking Archives Ontology", - "prefix": "dba", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "https://w3id.org/dba/ontology/$1" - }, - "lov.dbm": { - "authority": "lov", - "description": "An ontology for the Drug Bureau of Macedonia (DBM).", - "homepage": "http://purl.org/net/dbm/ontology#", - "id": "lov.dbm", - "name": "DBM Ontology", - "prefix": "dbm", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://purl.org/net/dbm/ontology#$1" - }, - "lov.dbowl": { - "authority": "lov", - "description": "Primitive ontology for database to Semantic Web mapping which subsumes classes that represent mappings to explicit OWL constructs, such as OWL class, object property, data property, etc. Classes in this ontology are populated by individuals representing components of the database schema being mapped.", - "homepage": "http://ontology.cybershare.utep.edu/dbowl", - "id": "lov.dbowl", - "name": "Relational to Ontology Mapping Primitive", - "prefix": "dbowl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.cybershare.utep.edu/dbowl/relational-to-ontology-mapping-primitive.owl#$1" - }, - "lov.dbpedia-owl": { - "authority": "lov", - "description": "The DBpedia ontology provides the classes and properties used in the DBpedia data set.", - "homepage": "http://dbpedia.org/ontology/", - "id": "lov.dbpedia-owl", - "name": "The DBpedia Ontology", - "prefix": "dbpedia-owl", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://dbpedia.org/ontology/$1" - }, - "lov.dbug": { - "authority": "lov", - "description": "An extension of DOAP for the description of bugs", - "homepage": "http://ontologi.es/doap-bugs#", - "id": "lov.dbug", - "name": "DOAP Bugs", - "prefix": "dbug", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontologi.es/doap-bugs#$1" - }, - "lov.dcam": { - "authority": "lov", - "description": "An abstract model for Dublin Core metadata", - "homepage": "http://purl.org/dc/dcam/", - "id": "lov.dcam", - "name": "DCMI Abstract Model", - "prefix": "dcam", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://purl.org/dc/dcam/$1" - }, - "lov.dcat": { - "authority": "lov", - "description": "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web", - "homepage": "http://www.w3.org/ns/dcat", - "id": "lov.dcat", - "name": "Data Catalog Vocabulary", - "prefix": "dcat", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/dcat#$1" - }, - "lov.dce": { - "authority": "lov", - "description": "The Dublin Core Metadata Element Set is a vocabulary of fifteen properties for use in resource description. The name \"Dublin\" is due to its origin at a 1995 invitational workshop in Dublin, Ohio; \"core\" because its elements are broad and generic, usable for describing a wide range of resources.", - "homepage": "http://purl.org/dc/elements/1.1/", - "id": "lov.dce", - "name": "Dublin Core Metadata Element Set", - "prefix": "dce", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/dc/elements/1.1/$1" - }, - "lov.dcite": { - "authority": "lov", - "description": "The DataCite Ontology is an ontology written in OWL 2 DL to enable certain metadata properties of the DataCite Metadata Specification version 2.0 (http://datacite.org/schema/DataCite-MetadataKernel_v2.0.pdf) to be described in RDF.", - "homepage": "http://purl.org/spar/datacite", - "id": "lov.dcite", - "name": "The DataCite Ontology", - "prefix": "dcite", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/datacite/$1" - }, - "lov.dcndl": { - "authority": "lov", - "description": "RDF Schema declaration for Japan NDL Metadata Terms", - "homepage": "http://ndl.go.jp/dcndl/terms/", - "id": "lov.dcndl", - "name": "NDL Metadata Terms", - "prefix": "dcndl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ndl.go.jp/dcndl/terms/$1" - }, - "lov.dco": { - "authority": "lov", - "description": "domOS Common Ontology (dCO) represents a common information model to share a unified understanding for humans and machines and to ensure semantic interoperability in a heterogeneous IoT infrastructure. This ontology allows the decoupling of the infrastructure from the software services and applications.", - "homepage": "https://w3id.org/dco", - "id": "lov.dco", - "name": "domOS Common Ontology", - "prefix": "dco", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/dco#$1" - }, - "lov.dcterms": { - "authority": "lov", - "description": "an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.", - "homepage": "http://purl.org/dc/terms/", - "id": "lov.dcterms", - "name": "DCMI Metadata Terms", - "prefix": "dcterms", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/dc/terms/$1" - }, - "lov.dctype": { - "authority": "lov", - "description": "The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource.", - "homepage": "http://purl.org/dc/dcmitype/", - "id": "lov.dctype", - "name": "DCMI Type Vocabulary", - "prefix": "dctype", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://purl.org/dc/dcmitype/$1" - }, - "lov.ddesc": { - "authority": "lov", - "description": "The Denotative Description module encodes the characteristics of a cultural property, as detectable and/or detected during the cataloguing process and measurable according to a reference system. Examples include measurements e.g. length, constituting materials e.g. clay, employed techniques e.g. melting, conservation status e.g. good, decent, bad.\nIn this module are used as template the following Ontology Design Patterns:\n- http://www.ontologydesignpatterns.org/cp/owl/collectionentity.owl\n- http://www.ontologydesignpatterns.org/cp/owl/classification.owl\n- http://www.ontologydesignpatterns.org/cp/owl/descriptionandsituation.owl\n- http://www.ontologydesignpatterns.org/cp/owl/situation.owl", - "homepage": "https://w3id.org/arco/ontology/denotative-description", - "id": "lov.ddesc", - "name": "Denotative Description Ontology (ArCo network)", - "prefix": "ddesc", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "https://w3id.org/arco/ontology/denotative-description/$1" - }, - "lov.decision": { - "authority": "lov", - "description": "Decision-making is a process that can result in some decision and decision is a situation of indicating one of the considered options. Decision Ontology provides means for precise distinguishing and distinct treatment of these two aspects.", - "homepage": "https://decision-ontology.googlecode.com/svn/trunk/decision.owl", - "id": "lov.decision", - "name": "Decision ontology", - "prefix": "decision", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://decision-ontology.googlecode.com/svn/trunk/decision.owl#$1" - }, - "lov.demlab": { - "authority": "lov", - "description": "The ontology has been developed in the framework of the Dem@Care project for representing the experimentation protocol towards diagnostic support and assessment of Dementia in a controlled environment. The aim of the protocol is to provide a brief overview of their health status of the participants during consultation (cognition, behaviours and function), and to correlate the system (sensor) data with the data collected using typical dementia care assessment tools.", - "homepage": "http://www.demcare.eu/ontologies/demlab.owl", - "id": "lov.demlab", - "name": "Dem@Care Lab Ontology for Dementia Assessment", - "prefix": "demlab", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://www.demcare.eu/ontologies/demlab.owl#$1" - }, - "lov.deo": { - "authority": "lov", - "description": "The Discourse Elements Ontology is an ontology for describing the major rhetorical elements of a document such as a journal article. It is a subsidiary ontology that is imported into the Document Components Ontology, itself part of SPAR, the Semantic Publishing and Referencing Ontologies", - "homepage": "http://purl.org/spar/deo", - "id": "lov.deo", - "name": "The Discourse Elements Ontology", - "prefix": "deo", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/deo/$1" - }, - "lov.deps": { - "authority": "lov", - "description": "An extension to DOAP for describing a project's requirements", - "homepage": "http://ontologi.es/doap-deps#", - "id": "lov.deps", - "name": "DOAP Dependencies", - "prefix": "deps", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontologi.es/doap-deps#$1" - }, - "lov.dfc": { - "authority": "lov", - "description": "A common vocabulary for digital food platforms", - "homepage": "http://static.datafoodconsortium.org/ontologies/DFC_FullModel.owl", - "id": "lov.dfc", - "name": "Data Food Consortium Ontology", - "prefix": "dfc", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://static.datafoodconsortium.org/ontologies/DFC_FullModel.owl#$1" - }, - "lov.dfc-b": { - "authority": "lov", - "description": "DFC Business Ontology", - "homepage": "http://static.datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl", - "id": "lov.dfc-b", - "name": "DFC Business Ontology", - "prefix": "dfc-b", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://static.datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl#$1" - }, - "lov.dfc-p": { - "authority": "lov", - "description": "A common vocabulary for digital food platforms (Product Glossary Part)", - "homepage": "http://static.datafoodconsortium.org/ontologies/DFC_ProductGlossary.owl", - "id": "lov.dfc-p", - "name": "A common vocabulary for digital food platforms (Product Glossary Part)", - "prefix": "dfc-p", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://static.datafoodconsortium.org/ontologies/DFC_ProductGlossary.owl#$1" - }, - "lov.dfc-t": { - "authority": "lov", - "description": "A common vocabulary for digital food platforms (Technical Part)", - "homepage": "http://static.datafoodconsortium.org/ontologies/DFC_TechnicalOntology.owl", - "id": "lov.dfc-t", - "name": "A common vocabulary for digital food platforms (Technical Part)", - "prefix": "dfc-t", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://static.datafoodconsortium.org/ontologies/DFC_TechnicalOntology.owl#$1" - }, - "lov.dg": { - "authority": "lov", - "description": "The DINGO ontology (Data Integration for Grant Ontology) defines the terms of the DINGO vocabulary and provides a machine readable extensible framework to model data relative to projects, funding, project and funding actors, and, notably, funding policies. It is designed to yield high modeling power and elasticity to cope with the huge variety in funding and project practices, which makes it applicable to many areas where funding is an important aspect: first of all research, but also the arts, cultural conservation, and many others.", - "homepage": "https://w3id.org/dingo/", - "id": "lov.dg", - "name": "DINGO Ontology", - "prefix": "dg", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/dingo#$1" - }, - "lov.dicom": { - "authority": "lov", - "description": "Ontology for healthcare metadata - especially metadata found in DICOM files (Digital Imaging and Communications in Medicine, see http://dicom.nema.org/). Author: Michael Brunnbauer, Bonubase GmbH (www.bonubase.com). The author's email address is brunni@netestate.de. See http://purl.org/healthcarevocab/v1help for explanations.", - "homepage": "http://purl.org/healthcarevocab/v1", - "id": "lov.dicom", - "name": "Healthcare metadata - DICOM ontology", - "prefix": "dicom", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://purl.org/healthcarevocab/v1#$1" - }, - "lov.dio": { - "authority": "lov", - "description": "The scope of the DIO is the domain of design intent or design rationale that needs to be documented while undertaking the design of any artifact", - "homepage": "https://w3id.org/dio", - "id": "lov.dio", - "name": "The Design Intent Ontology", - "prefix": "dio", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/dio#$1" - }, - "lov.disco": { - "authority": "lov", - "description": "A metadata vocabulary for documenting research and survey data", - "homepage": "http://rdf-vocabulary.ddialliance.org/discovery", - "id": "lov.disco", - "name": "DDI-RDF Discovery Vocabulary", - "prefix": "disco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdf-vocabulary.ddialliance.org/discovery#$1" - }, - "lov.dita": { - "authority": "lov", - "description": "The DITA RDF ontology translates the semantics of a subset of the vocabulary described in the DITA 1.2 specification in a format that can be understood in the semantic Web of data. By Colin Maudry, licensed under the terms of the Unlicense (public domain).", - "homepage": "http://purl.org/dita/ns#", - "id": "lov.dita", - "name": "DITA RDF ontology", - "prefix": "dita", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/dita/ns#$1" - }, - "lov.dk": { - "authority": "lov", - "description": "The Data Knowledge Vocabulary allows for a comprehensive description of data assets and enterprise data management. It covers a business data dictionary, data quality management, data governance, the technical infrastructure and many other aspects of enterprise data management. The vocabulary represents a linked data implementation of the Data Knowledge Model which resulted from extensive applied research.", - "homepage": "http://www.data-knowledge.org/dk/", - "id": "lov.dk", - "name": "The Data Knowledge Vocabulary", - "prefix": "dk", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.data-knowledge.org/dk/$1" - }, - "lov.dm2e": { - "authority": "lov", - "description": "The DM2E model is a specialisation of the Europeana Data Model (EDM) and can be used for the description of manuscripts in the cultural heritage domain.", - "homepage": "http://onto.dm2e.eu/schemas/dm2e", - "id": "lov.dm2e", - "name": "DM2E model", - "prefix": "dm2e", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://onto.dm2e.eu/schemas/dm2e/$1" - }, - "lov.dnbt": { - "authority": "lov", - "description": "The DNB RDF Vocabulary (dnb:) is a collection of classes, properties and datatypes used within the DNB's linked data service.It complements the GND Ontology (gndo:) which is specifically geared towards authority data from the Integrated Authority File (GND), whereas this vocabulary is more general-purpose.", - "homepage": "http://d-nb.info/standards/elementset/dnb", - "id": "lov.dnbt", - "name": "DNB Metadata Terms", - "prefix": "dnbt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://d-nb.info/standards/elementset/dnb#$1" - }, - "lov.doap": { - "authority": "lov", - "description": "The Description of a Project (DOAP) vocabulary, described using W3C RDF Schema and the Web Ontology Language.", - "homepage": "http://usefulinc.com/ns/doap#", - "id": "lov.doap", - "name": "Description of a Project vocabulary", - "prefix": "doap", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://usefulinc.com/ns/doap#$1" - }, - "lov.doc": { - "authority": "lov", - "description": "Defines properties and relationships between works.", - "homepage": "http://www.w3.org/2000/10/swap/pim/doc", - "id": "lov.doc", - "name": "Works, licences, derivatives and dependencies", - "prefix": "doc", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.w3.org/2000/10/swap/pim/doc#$1" - }, - "lov.doco": { - "authority": "lov", - "description": "An ontology for describing the component parts of a bibliographic document", - "homepage": "http://purl.org/spar/doco", - "id": "lov.doco", - "name": "DoCO, the Document Components Ontology", - "prefix": "doco", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/doco/$1" - }, - "lov.docso": { - "authority": "lov", - "description": "A micro-ontology that defines a set of typical document-related services such as provided by libraries, museums and archives.", - "homepage": "http://purl.org/ontology/dso", - "id": "lov.docso", - "name": "Document Service Ontology", - "prefix": "docso", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/dso#$1" - }, - "lov.dogont": { - "authority": "lov", - "description": "The DogOnt ontology supports device/network independent description of houses, including both controllable and architectural elements.", - "homepage": "http://elite.polito.it/ontologies/dogont.owl", - "id": "lov.dogont", - "name": "Ontology Modeling for Intelligent Domotic Environments", - "prefix": "dogont", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "http://elite.polito.it/ontologies/dogont$1" - }, - "lov.donto": { - "authority": "lov", - "description": "The data.gov.au Dataset Ontology is an OWL ontology designed to describe the characteristics of datasets published on data.gov.au.\n\nThe ontology contains elements which describe the publication, update, origin, governance, spatial and temporal coverage and other contextual information about the dataset. The ontology also covers aspects of organisational custodianship and governance.\n \nBy using this ontology to describe datasets on data.gov.au publishers increase discoverability and enable the consumption of this information in other applications/systems as Linked Data. It further enables decentralised publishing of catalogs and facilitates federated dataset search across sites, e.g. in datasets that are published by the States.\n \nOther publishers of Linked Data may make assertions about data published using this ontology, e.g. they may publish information about the use of the dataset in other applications.", - "homepage": "http://reference.data.gov.au/def/ont/dataset", - "id": "lov.donto", - "name": "Dataset Ontology", - "prefix": "donto", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://reference.data.gov.au/def/ont/dataset#$1" - }, - "lov.dot": { - "authority": "lov", - "description": "- Version 0.8: \n* completed ontology metadata wrt LOV\n* added classes dot:ClassifiedDamage and dot:UnclassifiedDamage (subclasses of dot:Damage)\n* made dot:StructuralDamage and dot:Defect subclasses of dot:Damage", - "homepage": "https://w3id.org/dot#", - "id": "lov.dot", - "name": "Damage Topology Ontology", - "prefix": "dot", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/dot#$1" - }, - "lov.dpn": { - "authority": "lov", - "description": "This ontology is being developed by CSIRO under the eReefs project for describing data provider nodes, web services available and datasets that are hosted by them. This ontology features a module for describing Datasets. It does not however describe geospatial, temporal, organisational or domain concepts as these are intended to be included from other ontologies via the imports statement. Other modules complementary to the DPN ontology are http://purl.org/dpn/dataset and http://purl.org/dpn/services. This version aligns DCAT and DC terms and imports DPN services.", - "homepage": "http://purl.org/dpn", - "id": "lov.dpn", - "name": "Data Provider Node ontology", - "prefix": "dpn", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/dpn#$1" - }, - "lov.dprov": { - "authority": "lov", - "description": "This ontology is a reduced-in-scope version of the [W3C Decisions and Decision-Making Incubator Group](https://www.w3.org/2005/Incubator/decision/)'s Decision Ontology (DO) which can be found at . It has been re-worked to align entirely with the W3C's [PROV ontology](https://www.w3.org/TR/prov-o/) since it is widely recognised that analysing the elements of decisions *post hoc* is an exercise in provenance.\n\nUnlike the original DO, this ontology cannot be used for *normative* scenarios: it is only capable of recording decisions that have already been made (so-called *data-driven* use in the DO). This is because PROV, to which this ontology is completely mapped, does not have a templating system which can indicate what *should* occur in future scenarios.\n\nThis ontology introduces only one new element for decision modelling over that which was present in the DO: an Agent which allows agency in decision making to be recorded.", - "homepage": "http://promsns.org/def/decprov", - "id": "lov.dprov", - "name": "Decision Provenance ontology (DecPROV)", - "prefix": "dprov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://promsns.org/def/do#$1" - }, - "lov.dq": { - "authority": "lov", - "description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - DQ Package", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/dataquality", - "id": "lov.dq", - "name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Data quality package)", - "prefix": "dq", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/dataquality#$1" - }, - "lov.dqc": { - "authority": "lov", - "description": "This RDF document contains a library of data quality constraints represented as SPARQL query templates based on the SPARQL Inferencing Framework (SPIN). The data quality constraint templates are especially useful for the identification of data quality problems during data entry and for periodic quality checks during data usage.", - "homepage": "http://semwebquality.org/ontologies/dq-constraints", - "id": "lov.dqc", - "name": "The Data Quality Constraints Library", - "prefix": "dqc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semwebquality.org/ontologies/dq-constraints#$1" - }, - "lov.dqm": { - "authority": "lov", - "description": "The Data Quality Management Vocabulary - An Ontology for Data Requirements Management, Data Quality Monitoring, Data Quality Assessment, and Data Cleansing", - "homepage": "http://purl.org/dqm-vocabulary/v1/dqm", - "id": "lov.dqm", - "name": "The Data Quality Management Vocabulary", - "prefix": "dqm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/dqm-vocabulary/v1/dqm#$1" - }, - "lov.dqv": { - "authority": "lov", - "description": "The Data Quality Vocabulary (DQV) is seen as an extension to DCAT to cover the quality of the data, how frequently is it updated, whether it accepts user corrections, persistence commitments etc. When used by publishers, this vocabulary will foster trust in the data amongst developers.", - "homepage": "http://www.w3.org/ns/dqv", - "id": "lov.dqv", - "name": "Data Quality Vocabulary", - "prefix": "dqv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/dqv#$1" - }, - "lov.dr": { - "authority": "lov", - "description": "Relationships without range and domains meant to be reused in different contexts", - "homepage": "http://purl.org/swan/2.0/discourse-relationships/", - "id": "lov.dr", - "name": "Discourse relationships vocabulary", - "prefix": "dr", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/swan/2.0/discourse-relationships/$1" - }, - "lov.drama": { - "authority": "lov", - "description": "Designed with the goals to describe and encode the core dramatic qualities and to serve as a knowledge base underlying a number of applications, Drammar is a comprehensive ontology of drama, realized through a collaboration of computer scientists and drama scholars. It makes the knowledge about drama available as a vocabulary for the linked interchange of drama encodings and readily usable by automatic reasoners.\nBy avoinding references to style and artistic qualities Drammar aims at representing the elements shared by different, cross-media manifestations of drama, the so\u2013called intangible elements of drama as an intangible cultural heritage form.", - "homepage": "http://www.purl.org/drammar", - "id": "lov.drama", - "name": "Drammar: a comprehensive ontology of drama", - "prefix": "drama", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.purl.org/drammar#$1" - }, - "lov.drm": { - "authority": "lov", - "description": "A metamodel for government data", - "homepage": "http://vocab.data.gov/def/drm", - "id": "lov.drm", - "name": "Data Reference Model", - "prefix": "drm", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://vocab.data.gov/def/drm#$1" - }, - "lov.ds": { - "authority": "lov", - "description": "Este vocabulario se utiliza para modelar los cat\u00e1logos de conjuntos de datos y las relaciones con los datasets", - "homepage": "http://purl.org/ctic/dcat#", - "id": "lov.ds", - "name": "Dataset Catalog Vocabulary", - "prefix": "ds", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/ctic/dcat#$1" - }, - "lov.dsd": { - "authority": "lov", - "description": "To ensure comparability between schemas from different data models, the Description of a Data Source (DSD) vocabulary has been developed.", - "homepage": "https://w3id.org/dsd", - "id": "lov.dsd", - "name": "Description of a Data Source", - "prefix": "dsd", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/dsd#$1" - }, - "lov.dsn": { - "authority": "lov", - "description": "DSNotify Eventsets is a vocabulary for events that change resources in linked data sources.", - "homepage": "http://purl.org/dsnotify/vocab/eventset/", - "id": "lov.dsn", - "name": "DSNotify Eventsets: A vocabulary for change events in linked data sources", - "prefix": "dsn", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/dsnotify/vocab/eventset/$1" - }, - "lov.dso": { - "authority": "lov", - "description": "This ontology offers OWL-Lite definition for object list. It is a restricted version of OWL-S ObjectList", - "homepage": "http://inference-web.org/2.0/ds.owl", - "id": "lov.dso", - "name": "Data Structure Ontology", - "prefix": "dso", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://inference-web.org/2.0/ds.owl#$1" - }, - "lov.dtx_srti": { - "authority": "lov", - "description": "An RDF/OWL vocabulary to represent SRTI DATEX II profile (according the Commission Delegated Regulation (EU) No 886/2013) within the European LOD-RoadTran18 action \"Supporting the cross-border use of Road Traffic Data with Linked Open Data based on DATEX II (LOD-RoadTran18)\" (Agreement No: INEA/CEF/ICT/A2018/1803421, Action No: 2018-EU-IA-0088). The vocabulary is used for mapping between DATEX II and LOD formats.", - "homepage": "http://cef.uv.es/lodroadtran18/def/transporte/dtx_srti", - "id": "lov.dtx_srti", - "name": "LOD SRTI DATEX II", - "prefix": "dtx_srti", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://cef.uv.es/lodroadtran18/def/transporte/dtx_srti#$1" - }, - "lov.dtype": { - "authority": "lov", - "description": "The ontology 'dtype' provides a specification of simple data types such as enumerations. These are needed in support of the conversion of XML Schemas and UML Models to OWL. Codelists are also defined in 'dtype'.", - "homepage": "http://www.linkedmodel.org/schema/dtype", - "id": "lov.dtype", - "name": "Datatype Ontology", - "prefix": "dtype", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.linkedmodel.org/schema/dtype#$1" - }, - "lov.dul": { - "authority": "lov", - "description": "The DOLCE+DnS Ultralite ontology. It is a simplification of some parts of the DOLCE Lite-Plus library (cf. http://www.ontologydesignpatterns.org/ont/dul/DLP397.owl)", - "homepage": "http://www.ontologydesignpatterns.org/ont/dul/DUL.owl", - "id": "lov.dul", - "name": "DOLCE+DnS Ultralite", - "prefix": "dul", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.ontologydesignpatterns.org/ont/dul/DUL.owl#$1" - }, - "lov.duv": { - "authority": "lov", - "description": "The Dataset Usage Vocabulary (DUV) is used to describe consumer experiences, citations, and feedback about datasets from the human perspective.", - "homepage": "http://www.w3.org/ns/duv", - "id": "lov.duv", - "name": "Dataset Usage Vocabulary", - "prefix": "duv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/duv#$1" - }, - "lov.dvia": { - "authority": "lov", - "description": "dvia is an RDF vocabulary designed to facilitate interoperability between visualization applications published on the Web.", - "homepage": "http://purl.org/ontology/dvia", - "id": "lov.dvia", - "name": "The visualization vocabulary for LOD applications", - "prefix": "dvia", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/ontology/dvia#$1" - }, - "lov.eac-cpf": { - "authority": "lov", - "description": "Derive from the EAC-CPF original XML schema. Encoded Archival Context for Corporate Bodies, Persons, and Families provides a grammar for encoding names of creators of archival materials and related information.", - "homepage": "http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/", - "id": "lov.eac-cpf", - "name": "EAC-CPF Descriptions Ontology for Linked Archival Data:", - "prefix": "eac-cpf", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/$1" - }, - "lov.earl": { - "authority": "lov", - "description": "EARL is a vocabulary, the terms of which are defined across a set of specifications and technical notes, and that is used to describe test results. The primary motivation for developing this vocabulary is to facilitate the exchange of test results between Web accessibility evaluation tools in a vendor-neutral and platform-independent format. It also provides reusable terms for generic quality assurance and validation purposes.", - "homepage": "http://www.w3.org/ns/earl", - "id": "lov.earl", - "name": "Evaluation and Report Language", - "prefix": "earl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/earl#$1" - }, - "lov.earth": { - "authority": "lov", - "description": "The Linked Earth Ontology aims to provide a common vocabulary for annotating paleoclimatology data", - "homepage": "http://linked.earth/ontology#", - "id": "lov.earth", - "name": "The Linked Earth Ontology", - "prefix": "earth", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://linked.earth/ontology#$1" - }, - "lov.ebg": { - "authority": "lov", - "description": "The euBusinessGraph (`ebg:`) ontology represents companies, type/status/economic classification, addresses, identifiers, company officers (e.g., directors and CEOs), and dataset offerings.\n\nIt uses `schema:domainIncludes/rangeIncludes` (which are polymorphic) to describe which properties are applicable to a class, \nrather than `rdfs:domain/range` (which are monomorphic) to prescribe what classes must be applied to each node using a property.\nWe find that this enables more flexible reuse and combination of different ontologies.\nWe reuse the following ontologies and nomenclatures, and extend them where appropriate with classes and properties:\n\n- W3C Org, W3C RegOrg (basic company data), \n\n- W3C Time (officer membership), \n\n- W3C Locn (addresses),\n\n- schema.org (domain/rangeIncludes and various properties)\n\n- DBpedia ontology (jurisdiction)\n\n- NGEO and Spatial (NUTS administrative divisions)\n\n- ADMS (identifiers), \n\n- FOAF, SIOC (blog posts),\n\n- RAMON, SKOS (NACE economic classifications and various nomenclatures),\n\n- VOID (dataset descriptions).\n\nThis is only a reference. See more detail in the [EBG Semantic Model](https://docs.google.com/document/d/1dhMOTlIOC6dOK_jksJRX0CB-GIRoiYY6fWtCnZArUhU/edit) google document, which includes an informative description of classes and properties, gives examples and data provider rules, and provides more schema and instance diagrams.", - "homepage": "http://data.businessgraph.io/ontology#", - "id": "lov.ebg", - "name": "euBusinessGraph ontology", - "prefix": "ebg", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.businessgraph.io/ontology#$1" - }, - "lov.ebucore": { - "authority": "lov", - "description": "Combined with the EBU Class Conceptual Data Model (CCDM) of simple business objects, EBUCore provides the appropriate framework for descriptive and technical metadata for use in Service Oriented Architectures and also in audiovisual ontologies for semantic web and linked data developments.", - "homepage": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore", - "id": "lov.ebucore", - "name": "EBU Ontology", - "prefix": "ebucore", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#$1" - }, - "lov.eccrev": { - "authority": "lov", - "description": "A vocabulary & data model for describing RDF changes and revisions. It defines the Commit & Revision classes together with their expected properties.", - "homepage": "https://vocab.eccenca.com/revision/", - "id": "lov.eccrev", - "name": "RDF changes and revisions vocabulary", - "prefix": "eccrev", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://vocab.eccenca.com/revision/$1" - }, - "lov.ecfo": { - "authority": "lov", - "description": "This ontology defines a vocabulary for describing carbon emission conversion factors (CF). These are values typically used to calculate carbon emissions where the CF multiplies a quantified estimate of the energy (e.g., kWh of electricity, litters of fuel, etc.) used by a particular activity.", - "homepage": "https://w3id.org/ecfo", - "id": "lov.ecfo", - "name": "The Emission Conversion Factor Ontology", - "prefix": "ecfo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/ecfo#$1" - }, - "lov.eclap": { - "authority": "lov", - "description": "The ECLAP vocabulary provide classes and properties for the description of multimedia content related with performing arts.", - "homepage": "http://www.eclap.eu/schema/eclap/", - "id": "lov.eclap", - "name": "ECLAP, Performing Arts Vocabulary", - "prefix": "eclap", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.eclap.eu/schema/eclap/$1" - }, - "lov.ecpo": { - "authority": "lov", - "description": "Defines the common bibliographic terms for the description of enumeration and chronology of periodicals", - "homepage": "http://purl.org/ontology/ecpo", - "id": "lov.ecpo", - "name": "Enumeration and Chronology of Periodicals Ontology", - "prefix": "ecpo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/ecpo#$1" - }, - "lov.ecrm": { - "authority": "lov", - "description": "Erlangen CRM / OWL - An OWL DL 1.0 implementation of the CIDOC Conceptual Reference Model, based on: Nick Crofts, Martin Doerr, Tony Gill, Stephen Stead, Matthew Stiff (eds.): Definition of the CIDOC Conceptual Reference Model (http://cidoc-crm.org/).\nThis implementation has been originally created by Bernhard Schiemann, Martin Oischinger and G\u00fcnther G\u00f6rz at the Friedrich-Alexander-University of Erlangen-Nuremberg, Department of Computer Science, Chair of Computer Science 8 (Artificial Intelligence) in cooperation with the Department of Museum Informatics of the Germanisches Nationalmuseum Nuremberg and the Department of Biodiversity Informatics of the Zoologisches Forschungsmuseum Alexander Koenig Bonn.\nThe Erlangen CRM / OWL implementation of the CIDOC Conceptual Reference Model is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.", - "homepage": "http://erlangen-crm.org/current/", - "id": "lov.ecrm", - "name": "Erlangen CRM / OWL", - "prefix": "ecrm", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://erlangen-crm.org/current/$1" - }, - "lov.edac": { - "authority": "lov", - "description": "The ELSEWeb EDAC ontology describes datasets published by EDAC. This project provides foundational support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu", - "homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl", - "id": "lov.edac", - "name": "ELSEWeb EDAC Ontology", - "prefix": "edac", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl#$1" - }, - "lov.edm": { - "authority": "lov", - "description": "The Europeana Data Model (EDM) is aimed at being an integration medium for collecting, connecting and enriching the descriptions provided by Europeana data providers.", - "homepage": "http://www.europeana.eu/schemas/edm/", - "id": "lov.edm", - "name": "Europeana Data Model vocabulary", - "prefix": "edm", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.europeana.eu/schemas/edm/$1" - }, - "lov.edu": { - "authority": "lov", - "description": "Ontoloogia kirjeldab hariduse valdkonna peamised m?isted ja seosed nende vahel. Praeguses versioonis on r?hk pandud ?ppematerjali, ?piv?ljundite ja ?ppekavaga seotud detailidele.", - "homepage": "https://schema.edu.ee/", - "id": "lov.edu", - "name": "Education Ontology", - "prefix": "edu", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "https://schema.edu.ee/$1" - }, - "lov.edupro": { - "authority": "lov", - "description": "The EduProgression ontology formalizes the educational progressions of the French educational system, making possible to represent the existing progressions in a standard formal model, searchable and understandable by machines (OWL).", - "homepage": "http://ns.inria.fr/semed/eduprogression/", - "id": "lov.edupro", - "name": "EduProgression Ontology", - "prefix": "edupro", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://ns.inria.fr/semed/eduprogression#$1" - }, - "lov.eem": { - "authority": "lov", - "description": "This vocabulary is based on the EPC Information Services Specification http://www.gs1.org/sites/default/files/docs/epc/epcis_1_0_1-standard-20070921.pdf", - "homepage": "http://purl.org/eem", - "id": "lov.eem", - "name": "The EPCIS Event Model", - "prefix": "eem", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/eem#$1" - }, - "lov.eeo": { - "authority": "lov", - "description": "An ontology to describe experiments, evaluations and their relation.", - "homepage": "https://w3id.org/eeo", - "id": "lov.eeo", - "name": "Experimental Evaluation Ontology", - "prefix": "eeo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/eeo#$1" - }, - "lov.ei2a": { - "authority": "lov", - "description": "The initiative Arag\u00f3n Open Data was initiated by agreement of 17 of July of 2012 of the Government of Aragon. Under the same was ordered the start of the project to open public data and on February 6, 2013 was implemented through the Portal opendata.aragon.es .\n\nThroughout this time there have been numerous works to achieve automation in the publication of information to ensure that third parties can reuse it in the best way. Given the volume of data that begins to exist, within the line of work of automation in information management, all those elements that help in the improvement of the structuring of information and the standardization of the data contained in the databases are beginning to have a special relevance.\n\nBased on this, within the General Directorate of Electronic Administration and Information Society, the idea arises of generating a set of technical and legal rules that allow to deepen in that standardization and that lead to think in the creation of the Interoperable Information Scheme Of Aragon (E2IA). The E2IA thus emerges as the framework in which the open data and in general the information of the Government of Aragon can begin to be automated in a much more profound way. The E2IA has to have a number of technical, organizational and legal elements that need to be developed.\n\nFor this reason, the Technological Institute of Aragon (ITAINNOVA) has been entrusted with carrying out actions consisting in identifying, studying and analyzing current research trends and technological development in relation to ontologies and dictionaries of data interoperability, defining the ontological proposal, performing The necessary tests to validate the ontological proposal and generate the text and web versions of the ontology.", - "homepage": "https://opendata.aragon.es/def/ei2a/ei2a.owl", - "id": "lov.ei2a", - "name": "Aragon Interoperable Information Structure Ontology\nEI2A", - "prefix": "ei2a", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://opendata.aragon.es/def/ei2a#$1" - }, - "lov.elec": { - "authority": "lov", - "description": "El objetivo de este vocabulario es la creaci\u00f3n de un esquema que permita definir los contenidos de informaci\u00f3n relacionada con procesos electorales y sus resultados. \t\t\tSe identifican ciertas variables en el dominio de las elecciones, que se modelan a trav\u00e9s de ciertos tipos de datos y de propiedades relacionadas entre los recursos.", - "homepage": "http://purl.org/ctic/sector-publico/elecciones", - "id": "lov.elec", - "name": "Vocabulario de Resultados Electorales", - "prefix": "elec", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://purl.org/ctic/sector-publico/elecciones#$1" - }, - "lov.eli": { - "authority": "lov", - "description": "Transposition of the ELI metadata fields into an OWL ontology", - "homepage": "http://data.europa.eu/eli/ontology", - "id": "lov.eli", - "name": "The European Legislation Identifier", - "prefix": "eli", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities", - "law" - ], - "uri_format": "http://data.europa.eu/eli/ontology#$1" - }, - "lov.emotion": { - "authority": "lov", - "description": "EmOCA is used to contextualize dimensionnal emotion and to categorize it for human readability.", - "homepage": "http://ns.inria.fr/emoca", - "id": "lov.emotion", - "name": "Emotion Ontology for Context Awareness", - "prefix": "emotion", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/emoca#$1" - }, - "lov.emp": { - "authority": "lov", - "description": "El objetivo de este vocabulario es la creaci\u00f3n de un esquema que permita definir los contenidos de la informaci\u00f3n relacionada con la oferta de empleo p\u00fablico. \t\t\tSe identifican ciertas variables en el dominio de la oferta de empleo p\u00fablico, que se modelan a trav\u00e9s de ciertos tipos de datos y de propiedades relacionadas entre los recursos.", - "homepage": "http://purl.org/ctic/empleo/oferta", - "id": "lov.emp", - "name": "Vocabulario de Ofertas de Empleo", - "prefix": "emp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ctic/empleo/oferta#$1" - }, - "lov.ends": { - "authority": "lov", - "description": "Endpoint Status vocabulary intends to describe endpoint availability", - "homepage": "http://labs.mondeca.com/vocab/endpointStatus", - "id": "lov.ends", - "name": "Vocabulary of endpoint status (availability, responseTime)", - "prefix": "ends", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://labs.mondeca.com/vocab/endpointStatus#$1" - }, - "lov.ep": { - "authority": "lov", - "description": "Describes the main classes and properties which EPrints adds to voID, DC, BIBO and SKOS etc", - "homepage": "http://eprints.org/ontology/", - "id": "lov.ep", - "name": "EPrints Ontology", - "prefix": "ep", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://eprints.org/ontology/$1" - }, - "lov.eppl": { - "authority": "lov", - "description": "PROV extension for linking Plans and parts of plans to their respective executions.", - "homepage": "https://w3id.org/ep-plan", - "id": "lov.eppl", - "name": "The EP-Plan ontology", - "prefix": "eppl", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/ep-plan#$1" - }, - "lov.eqp": { - "authority": "lov", - "description": "Defines aircraft models, aircraft systems / subsystems, and aircraft characteristics", - "homepage": "https://data.nasa.gov/ontologies/atmonto/equipment#", - "id": "lov.eqp", - "name": "Aircraft Equipment Vocabulary", - "prefix": "eqp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://data.nasa.gov/ontologies/atmonto/equipment#$1" - }, - "lov.era": { - "authority": "lov", - "description": "This is the human and machine readable Vocabulary/Ontology governed by the European Union Agency for Railways. It represents the concepts and relationships linked to the sectorial legal framework and the use cases under the Agency\u00b4s remit. Currently, this vocabulary covers the European railway infrastructure and the vehicles authorized to operate over it. It is a semantic/browsable representation of the [RINF](https://www.era.europa.eu/sites/default/files/registers/docs/rinf_application_guide_for_register_en.pdf) and [ERATV](https://www.era.europa.eu/sites/default/files/registers/docs/iu-eratv_application_guide_for_register_2016-797_en.pdf) application guides that were built by domain experts in the RINF and ERATV working parties.\nSince version 2.6.0, the ontology includes the routebook concepts described in appendix D2 \\\"Elements the infrastructure manager has to provide to the railway undertaking for the Route Book\\\" (https://eur-lex.europa.eu/eli/reg_impl/2019/773/oj) and the appendix D3 \\\"ERTMS trackside engineering information relevant to operation that the infrastructure manager shall provide to the railway undertaking\\\".", - "homepage": "http://data.europa.eu/949/", - "id": "lov.era", - "name": "ERA vocabulary", - "prefix": "era", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.europa.eu/949/$1" - }, - "lov.esco": { - "authority": "lov", - "description": "The ontology of the taxonomy \"European Skills, Competences, qualifications and Occupations\".\n\nThe ontology considers three ESCO pillars (or taxonomy) and 2 registers.\nThe three pillars are:\n- Occupation\n- Skill (and competences)\n- Qualification\n\nFor the construction and use of the ESCO pillars, the following modelling artefacts are used:\n- Facetting support to specialize ESCO pillar concepts based on bussiness relevant Concept Groups (e.g. species, languages, ...)\n- Conept Groups, Thesaurus array and Compound terms (as detailed in ISO 25964) to organize faceted concepts\n- SKOS mapping properties to relate ESCO pillar concepts to concepts in other (external) taxonomies (e.g. FoET, ISCO88 and ISCO08. More mappings can be added in the future.)\n- Tagging ESCO pillar concepts by other (external) taxonomies (NUTS, EQF, NACE, ...)\n- Capture gender specifics on the labels of the ESCO pillar concepts\n- Rich ESCO concept relationships holding a description and other specific characteristics of the relation between two ESCO pillar concepts.\n\nESCO maintains two additional registers:\n- Awarding Body\n- Work Context\nAwarding Bodies typically are referenced by ESCO qualifications.\nOccupations can have one or more work context.", - "homepage": "http://data.europa.eu/esco/model", - "id": "lov.esco", - "name": "The ESCO ontology", - "prefix": "esco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.europa.eu/esco/model#$1" - }, - "lov.essglobal": { - "authority": "lov", - "description": "Un vocabulario para la Economia Social y Solid\u00e1ria (ESS). Este vocabulario es concebido para ser conjugado con los esquemas de metadados/vocabularios/ontologias: dcterms, good relations, foaf, vcard, organization e schema.org - esto esta definido em el Perfil de Aplicaci\u00f3n Dublin Core de la ESS. Vocabulario desarollado por el grupo ESSGlobal de la Red Intercontinental para la promoci\u00f3n de Economia Social y Solidaria (RIPESS).", - "homepage": "http://purl.org/essglobal/vocab/", - "id": "lov.essglobal", - "name": "ESSGlobal Vocabulary", - "prefix": "essglobal", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/essglobal/vocab/$1" - }, - "lov.eupont": { - "authority": "lov", - "description": "EUPont is an ontology to model high level rules for Internet of Things End User Programming (IoT-EUP).", - "homepage": "http://elite.polito.it/ontologies/eupont.owl", - "id": "lov.eupont", - "name": "EUPont: an ontology for End User Programming of the IoT", - "prefix": "eupont", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://elite.polito.it/ontologies/eupont.owl#$1" - }, - "lov.event": { - "authority": "lov", - "description": "This ontology deals with the notion of reified events - events seen as first-class objects.", - "homepage": "http://purl.org/NET/c4dm/event.owl", - "id": "lov.event", - "name": "The Event Ontology", - "prefix": "event", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/NET/c4dm/event.owl#$1" - }, - "lov.ex": { - "authority": "lov", - "description": "\u30b9\u30ad\u30fc\u30de\u306b\u30b5\u30f3\u30d7\u30eb\u30b3\u30fc\u30c9\u3092\u57cb\u3081\u8fbc\u3080\u305f\u3081\u306e\u8a9e\u5f59\u3002XSLT\u3092\u4f7f\u3063\u3066\u3001XHTML\u306e\u4e2d\u3067\u4f8b\u3092\u8868\u793a\u3055\u305b\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u3002", - "homepage": "http://purl.org/net/ns/ex", - "id": "lov.ex", - "name": "Example vocabulary", - "prefix": "ex", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/ns/ex#$1" - }, - "lov.exif": { - "authority": "lov", - "description": "Vocabulary to describe an Exif format picture data. All Exif 2.2 tags are defined as RDF properties, as well as several terms to help this schema.", - "homepage": "http://www.w3.org/2003/12/exif/ns", - "id": "lov.exif", - "name": "Exif data description vocabulary", - "prefix": "exif", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2003/12/exif/ns#$1" - }, - "lov.ext": { - "authority": "lov", - "description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - EX Package", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/extent", - "id": "lov.ext", - "name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Extent package)", - "prefix": "ext", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/extent#$1" - }, - "lov.fabio": { - "authority": "lov", - "description": "FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web bibliographic records of scholarly endeavours. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies.", - "homepage": "http://purl.org/spar/fabio", - "id": "lov.fabio", - "name": "FRBR-aligned Bibliographic Ontology", - "prefix": "fabio", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/fabio/$1" - }, - "lov.faldo": { - "authority": "lov", - "description": "Used to describe a location that consists of a number of Regions but where the order is not known. e.g. the oddly named order() keyword in a INSDC file.", - "homepage": "http://biohackathon.org/resource/faldo", - "id": "lov.faldo", - "name": "Feature Annotation Location Description Ontology", - "prefix": "faldo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://biohackathon.org/resource/faldo#$1" - }, - "lov.fea": { - "authority": "lov", - "description": "To facilitate efforts to transform the Federal Government to one that is citizen-centered, results-oriented, and market-based, the Office of Management and Budget (OMB) is developing the Federal Enterprise Architecture (FEA), a business-based framework for Governmentwide improvement.", - "homepage": "http://vocab.data.gov/def/fea", - "id": "lov.fea", - "name": "Federal Enterprise Architecture Vocabulary", - "prefix": "fea", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://vocab.data.gov/def/fea#$1" - }, - "lov.fel": { - "authority": "lov", - "description": "This RDF vocabulary can be use to describe and categorize annotations involving entity mentions (sub-strings of text) that link to knowledgebase identifiers", - "homepage": "http://w3id.org/vcb/fel#", - "id": "lov.fel", - "name": "A Fine-grained Entity Linking vocabulary", - "prefix": "fel", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://w3id.org/vcb/fel#$1" - }, - "lov.fiesta-iot": { - "authority": "lov", - "description": "The FIESTA-IoT ontology takes inspiration from the well-known Noy et al. methodology for reusing and interconnecting existing ontologies. To build the ontology, we leverage a number of core concepts from various mainstream ontologies and taxonomies, such as Semantic Sensor Network (SSN), M3-lite (a lite version of M3 ontology), WGS84, IoT-lite, Time, and DUL ontology.", - "homepage": "http://purl.org/iot/ontology/fiesta-iot", - "id": "lov.fiesta-iot", - "name": "FIESTA-IoT Ontology", - "prefix": "fiesta-iot", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/iot/ontology/fiesta-iot#$1" - }, - "lov.fiesta-priv": { - "authority": "lov", - "description": "FIESTA-Priv Ontology", - "homepage": "http://purl.org/iot/ontology/fiesta-priv#", - "id": "lov.fiesta-priv", - "name": "FIESTA-Priv Ontology", - "prefix": "fiesta-priv", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/iot/ontology/fiesta-iot#$1" - }, - "lov.foaf": { - "authority": "lov", - "description": "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked.", - "homepage": "http://xmlns.com/foaf/0.1/", - "id": "lov.foaf", - "name": "Friend of a Friend vocabulary", - "prefix": "foaf", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://xmlns.com/foaf/0.1/$1" - }, - "lov.fog": { - "authority": "lov", - "description": "The File Ontology for Geometry formats (FOG) describes meaningful relations towards geometry snippets in RDF literals, geometry files on relative or absolute URLs and ontology-based geometry descriptions. The defined properties in this ontology are related towards each other and additional metadata is provided, such as file extension and related specifications/sources (incl. entries in dbpedia and Wikidata). \n\nThe initial version of the ontology (v0.0.1) was documented in:\n\nBonduel, Mathias, Wagner, Anna, Pauwels, Pieter, Vergauwen, Maarten, & Klein, Ralf (2019). Including Widespread Geometry Formats in Semantic Graphs Using RDF Literals. In Proceedings of the European Conference on Computing in Construction (EC3 2019). Chania, Greece.", - "homepage": "https://w3id.org/fog", - "id": "lov.fog", - "name": "FOG: File Ontology for Geometry formats", - "prefix": "fog", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "https://w3id.org/fog#$1" - }, - "lov.foio": { - "authority": "lov", - "description": "This ontology defines feature of interest and their properties, as an extension of the core classes of the SSN ontology (https://www.w3.org/ns/ssn/).\n\nA feature of interest is an abstraction of a real world phenomena (thing, person, event, etc). A feature of interest is then defined in terms of its properties, which are qualifiable, quantifiable, observable or operable qualities of the feature of interest. \n\nAlignments to other ontologies are proposed in external documents: \n\n- [SSNAlignment](https://w3id.org/seas/SSNAlignment) proposes an alignment to the [SSN ontology](http://www.w3.org/ns/ssn/).\n- [QUDTAlignment](https://w3id.org/seas/QUDTAlignment) proposes an alignment to the [QUDT ontology](http://qudt.org/).", - "homepage": "https://w3id.org/seas/FeatureOfInterestOntology", - "id": "lov.foio", - "name": "The SEAS Feature of Interest ontology.", - "prefix": "foio", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/seas/FeatureOfInterestOntology/$1" - }, - "lov.food": { - "authority": "lov", - "description": "This ontology models the Food domain. It allows to describe ingredients and food products. Ontology used by the Open Food Facts dataset", - "homepage": "http://data.lirmm.fr/ontologies/food", - "id": "lov.food", - "name": "Food Ontology", - "prefix": "food", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://data.lirmm.fr/ontologies/food#$1" - }, - "lov.fowl": { - "authority": "lov", - "description": "Along with Wine Ontology, was used as example in the first OWL Recommendation (February 2004)", - "homepage": "http://www.w3.org/TR/2003/PR-owl-guide-20031215/food", - "id": "lov.fowl", - "name": "Food Ontology in OWL", - "prefix": "fowl", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://www.w3.org/TR/2003/PR-owl-guide-20031209/food#$1" - }, - "lov.frad": { - "authority": "lov", - "description": "This is the element set of native RDF classes and properties described in the Functional Requirements for Authority Data model. The model also uses elements previously described in the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model.", - "homepage": "http://iflastandards.info/ns/fr/frad/", - "id": "lov.frad", - "name": "FRAD model", - "prefix": "frad", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://iflastandards.info/ns/fr/frad/$1" - }, - "lov.frapo": { - "authority": "lov", - "description": "FRAPO, the Funding, Research Administration and Projects Ontology, is a CERIF-compliant ontology written in OWL 2 DL for describing research project administrative information.", - "homepage": "http://purl.org/cerif/frapo/", - "id": "lov.frapo", - "name": "Funding, Research Administration and Projects Ontology", - "prefix": "frapo", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://purl.org/cerif/frapo/$1" - }, - "lov.frappe": { - "authority": "lov", - "description": "FraPPE is a vocabulary to enable Visual Analytics operations on geo-spatial time varying data. By enabling Visual Analytics instruments FraPPE ease the capture, correlation and comparison operations on geo-spatial data from different sources evolving over time", - "homepage": "http://streamreasoning.org/ontologies/frappe#", - "id": "lov.frappe", - "name": "FraPPE: Frame, Pixel, Place, Event vocabulary", - "prefix": "frappe", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://streamreasoning.org/ontologies/frappe#$1" - }, - "lov.frbr": { - "authority": "lov", - "description": "An expression in RDF of the concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR)", - "homepage": "http://purl.org/vocab/frbr/core", - "id": "lov.frbr", - "name": "Expression of Core FRBR Concepts in RDF", - "prefix": "frbr", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/vocab/frbr/core#$1" - }, - "lov.frbre": { - "authority": "lov", - "description": "Expression of Extended FRBR Concepts in RDF", - "homepage": "http://purl.org/vocab/frbr/extended", - "id": "lov.frbre", - "name": "Extended FRBR", - "prefix": "frbre", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/vocab/frbr/extended#$1" - }, - "lov.frbrer": { - "authority": "lov", - "description": "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model.", - "homepage": "http://iflastandards.info/ns/fr/frbr/frbrer/", - "id": "lov.frbrer", - "name": "FRBRer model", - "prefix": "frbrer", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://iflastandards.info/ns/fr/frbr/frbrer/$1" - }, - "lov.fresnel": { - "authority": "lov", - "description": "OWL Full vocabulary for defining lenses and formats on RDF models.", - "homepage": "http://www.w3.org/2004/09/fresnel", - "id": "lov.fresnel", - "name": "Fresnel Lens and Format Core Vocabulary", - "prefix": "fresnel", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2004/09/fresnel#$1" - }, - "lov.g50k": { - "authority": "lov", - "description": "A vocabulary developed to describe the Ordance Survey 50k Gazetteer linked data", - "homepage": "http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/", - "id": "lov.g50k", - "name": "50K Gazetteer Vocabulary", - "prefix": "g50k", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/$1" - }, - "lov.game": { - "authority": "lov", - "description": "This schema describes games with a known state, and few or no random elements.", - "homepage": "http://data.totl.net/game/", - "id": "lov.game", - "name": "TotL Game Ontology", - "prefix": "game", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.totl.net/game/$1" - }, - "lov.gc": { - "authority": "lov", - "description": "The Government Core Ontology establishes a foundation for all oegov ontologies.", - "homepage": "http://www.oegov.org/core/owl/gc", - "id": "lov.gc", - "name": "oeGOV Government Core Ontology", - "prefix": "gc", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://www.oegov.org/core/owl/gc#$1" - }, - "lov.gci": { - "authority": "lov", - "description": "Global City Indicator Foundation Ontology developed by the Information Engineering Group, Mechanical & Industrial Engineering, University of Toronto. Contains the foundation ontologies required to represent ISO 37120 city indicators, including Placenames, Time, Measurement, Provenance, Statistics, Validity and Trust. See: Fox, M.S., (2013), \"A Foundation Ontology for Global City Indicators\", Global City Institute Working Paper, Vol. 1, No.4, pp. 1-45. Global Cities Institute, University of Toronto. Updated 24 June 2014: http://www.eil. Based on the Global City Indicators Facility, University of Toronto: http://www.cityindicators.org/Deliverables/Core%20and%20Supporting%20Indicators%20Table%20SEPTEMBER%202011.pdf.\n\nContact: Mark S. Fox, msf@eil.utoronto.ca", - "homepage": "http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl", - "id": "lov.gci", - "name": "Global City Indicator Foundation Ontology", - "prefix": "gci", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl#$1" - }, - "lov.gcon": { - "authority": "lov", - "description": "GConsent provides concepts and relationships for defining consent and its associated information or metadata with a view towards GDPR compliance. It is the outcome of an analysis of consent and requirements associated with obtaining, using, and changes in consent as per the GDPR. The ontology also provides an approach to using its terms in various scenarios and use-cases (see more information in the documentation) which is intended to assist in its adoption.", - "homepage": "https://w3id.org/GConsent", - "id": "lov.gcon", - "name": "GConsent - a consent ontology based on the GDPR", - "prefix": "gcon", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/GConsent#$1" - }, - "lov.gd": { - "authority": "lov", - "description": "A RDF Schema that defines concepts and relationships common to all Open Government Data", - "homepage": "http://vocab.data.gov/gd", - "id": "lov.gd", - "name": "Government Data Vocabulary", - "prefix": "gd", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://reference.data.gov/def/govdata/$1" - }, - "lov.gdprov": { - "authority": "lov", - "description": "GDPRov is an OWL2 ontology to express provenance metadata of consent and data lifecycles towards documenting compliance for GDPR.", - "homepage": "https://w3id.org/GDPRov", - "id": "lov.gdprov", - "name": "The GDPR Provenance ontology", - "prefix": "gdprov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/GDPRov#$1" - }, - "lov.gdprt": { - "authority": "lov", - "description": "The General Data Protection Regulation (GDPR) is comprised of several articles, each with points that refer to specific concepts. The general convention of referring to these points and concepts is to quote the specific article or point using a human-readable reference. This ontology provides a way to refer to the points within the GDPR using the EurLex ontology published by the European Publication Office. It also defines the concepts defined, mentioned, and requried by the GDPR using the Simple Knowledge Organization System (SKOS) ontology.", - "homepage": "https://w3id.org/GDPRtEXT", - "id": "lov.gdprt", - "name": "GDPR text EXTensions", - "prefix": "gdprt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/GDPRtEXT#$1" - }, - "lov.gen": { - "authority": "lov", - "description": "A simple RDF vocabulary containing terms to facilitate the linking of genealogical data.", - "homepage": "http://purl.org/gen/0.1#", - "id": "lov.gen", - "name": "Vocabulary for Linked Genealogical Data", - "prefix": "gen", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/gen/0.1#$1" - }, - "lov.geo": { - "authority": "lov", - "description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum.", - "homepage": "http://www.w3.org/2003/01/geo/wgs84_pos", - "id": "lov.geo", - "name": "WGS84 Geo Positioning", - "prefix": "geo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1" - }, - "lov.geod": { - "authority": "lov", - "description": "Vocabulary describing the administrative subdivision of Norway", - "homepage": "http://vocab.lenka.no/geo-deling", - "id": "lov.geod", - "name": "Landinndelingen i Norge", - "prefix": "geod", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://vocab.lenka.no/geo-deling#$1" - }, - "lov.geof": { - "authority": "lov", - "description": "This ontology contains geographic feature classes and associated properties including classes and properties for describing the spatial location of the geographic feature. The classes and properties have been defined based on an ESRI dataset.", - "homepage": "http://www.mindswap.org/2003/owl/geo/geoFeatures20040307.owl", - "id": "lov.geof", - "name": "Geo Features", - "prefix": "geof", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://www.mindswap.org/2003/owl/geo/geoFeatures20040307.owl#$1" - }, - "lov.geofla": { - "authority": "lov", - "description": "Ontologie d\u00e9crivant le d\u00e9coupage administratif de la France m\u00e9tropolitaine, des d\u00e9partements d'outre mer, ou de la collectivit\u00e9 d\u00e9partementale de Mayotte, repr\u00e9sent\u00e9e comme une hi\u00e9rarchie de classes OWL", - "homepage": "http://data.ign.fr/def/geofla", - "id": "lov.geofla", - "name": "Ontologie des unit\u00e9s administratives de l'IGN", - "prefix": "geofla", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://data.ign.fr/def/geofla#$1" - }, - "lov.geom": { - "authority": "lov", - "description": "Ontologie des primitives g\u00e9om\u00e9triques repr\u00e9sentant la forme et la localisation d'entit\u00e9s topographiques.", - "homepage": "http://data.ign.fr/def/geometrie", - "id": "lov.geom", - "name": "Ontologie des primitives g\u00e9om\u00e9triques", - "prefix": "geom", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://data.ign.fr/def/geometrie#$1" - }, - "lov.geop": { - "authority": "lov", - "description": "FAO's geopolitical ontology version 1.1 was populated with FAO, UN and internationally recognized data sources.", - "homepage": "http://aims.fao.org/aos/geopolitical.owl", - "id": "lov.geop", - "name": "FAO Geopolitical Ontology", - "prefix": "geop", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://aims.fao.org/aos/geopolitical.owl#$1" - }, - "lov.geosp": { - "authority": "lov", - "description": "The GeoSpecies Ontology is used to describe geographical distribution of living species.", - "homepage": "http://rdf.geospecies.org/ont/geospecies", - "id": "lov.geosp", - "name": "GeoSpecies Ontology", - "prefix": "geosp", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://rdf.geospecies.org/ont/geospecies#$1" - }, - "lov.gf": { - "authority": "lov", - "description": "An OWL representation of part of the General Feature Model described in ISO 19109 and the General Feature Instance model described in Annex C of ISO 19156:2011.", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19109/2005/feature", - "id": "lov.gf", - "name": "OWL representation of ISO 19109 (General Feature Model)", - "prefix": "gf", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19109/2005/feature#$1" - }, - "lov.gleif-base": { - "authority": "lov", - "description": "Ontology defining generic concepts for reuse by other Global Legal Entity Identifier Foundation (GLEIF) ontologies. It defines generic classes for (legal) Entities and their relationships and statuses; and generic properties for different types of name and address. It makes use of the OMG Languages Countries and Codes (LCC) ontology (based on the ISO 3166 standard) for country and region information.", - "homepage": "https://www.gleif.org/ontology/Base/", - "id": "lov.gleif-base", - "name": "Global Legal Entity Identifier Foundation Base Ontology", - "prefix": "gleif-base", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://www.gleif.org/ontology/Base/$1" - }, - "lov.gleif-elf": { - "authority": "lov", - "description": "Ontology defining concepts for Entity Legal Forms and their abbreviations by jurisdiction, based on ISO 20275. Though used by Global Legal Entity Identifier Foundation (GLEIF) for Legal Entity Identifier registration, it is more broadly applicable.", - "homepage": "https://www.gleif.org/ontology/EntityLegalForm/", - "id": "lov.gleif-elf", - "name": "Entity Legal Form Ontology", - "prefix": "gleif-elf", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "https://www.gleif.org/ontology/EntityLegalForm/$1" - }, - "lov.gleif-geo": { - "authority": "lov", - "description": "Ontology defining concepts for Geocoding of addresses. It is based on the geocoding used in the Global Legal Entity Identifier Foundation (GLEIF) Golden Copy Data, but is more broadly applicable.", - "homepage": "https://www.gleif.org/ontology/Geocoding/", - "id": "lov.gleif-geo", - "name": "Global Legal Entity Identifier Foundation Geocoding Ontology", - "prefix": "gleif-geo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://www.gleif.org/ontology/Geocoding/$1" - }, - "lov.gleif-l1": { - "authority": "lov", - "description": "Ontology for legal entity identifier registration. It was designed for Global Legal Entity Identifier Foundation (GLEIF) Level 1 data corresponding to the Common Data Format version 2.1. It covers key reference data for a legal entity identifiable with an LEI. The ISO 17442 standard developed by the International Organization for Standardization defines a set of attributes or LEI reference data that comprises the most essential elements of identification. It specifies the minimum reference data, which must be supplied for each LEI: The official name of the legal entity as recorded in the official registers. The registered address of that legal entity. The country of formation. The codes for the representation of names of countries and their subdivisions. The date of the first LEI assignment; the date of last update of the LEI information; and the date of expiry, if applicable.", - "homepage": "https://www.gleif.org/ontology/L1/", - "id": "lov.gleif-l1", - "name": "Global Legal Entity Identifier Foundation Level 1 Ontology - Who Is Who", - "prefix": "gleif-L1", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://www.gleif.org/ontology/L1/$1" - }, - "lov.gleif-l2": { - "authority": "lov", - "description": "Ontology for legal entity parent relationships. It was designed for Global Legal Entity Identifier Foundation (GLEIF) Level 2 data corresponding to the Relationship Record format, version 1.1. Legal entities that have or acquire an LEI report their \u2018direct accounting consolidating parent\u2019 as well as their \u2018ultimate accounting consolidating parent\u2019, or for International Branches \u2018is an International Branch of'. Otherwise they must provide a Reporting Exception.", - "homepage": "https://www.gleif.org/ontology/L2/", - "id": "lov.gleif-l2", - "name": "Global Legal Entity Identifier Foundation Level 2 Ontology - Who Owns Whom", - "prefix": "gleif-L2", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://www.gleif.org/ontology/L2/$1" - }, - "lov.gleif-ra": { - "authority": "lov", - "description": "Ontology defining concepts for Business Registries, including the jurisdictions served. This is based on the Registration Authority Code List (RAL) used for Global Legal Entity Identifier Foundation (GLEIF) registration, but is more broadly applicable.", - "homepage": "https://www.gleif.org/ontology/RegistrationAuthority/", - "id": "lov.gleif-ra", - "name": "Global Legal Entity Identifier Foundation Registration Authority Ontology", - "prefix": "gleif-ra", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "https://www.gleif.org/ontology/RegistrationAuthority/$1" - }, - "lov.gleif-repex": { - "authority": "lov", - "description": "Ontology for representing exceptions to reporting of parents, for entities registered with a Legal Entity Identifier. The Global Legal Identifier System (GLEIS) requires that legal entities with an LEI provide information on their ultimate and direct accounting consolidating parents. Relationship reporting is mandatory with exceptions allowed for certain well-defined reasons. This ontology provides a simple structure for recording reasons for each exception by LEI.", - "homepage": "https://www.gleif.org/ontology/ReportingException/", - "id": "lov.gleif-repex", - "name": "Global Legal Entity Identifier Foundation Reporting Exception Ontology", - "prefix": "gleif-repex", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://www.gleif.org/ontology/ReportingException/$1" - }, - "lov.gm": { - "authority": "lov", - "description": "An OWL representation of part of the model for geometry and space from ISO 19107:2003 Geographic Information - Spatial Schema", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry", - "id": "lov.gm", - "name": "OWL representation of ISO 19107 (Geographic Information)", - "prefix": "gm", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry#$1" - }, - "lov.gml": { - "authority": "lov", - "description": "A specialization of GeoSPARQL defining specific subtypes of Geometry", - "homepage": "http://www.opengis.net/ont/gml", - "id": "lov.gml", - "name": "OGC Geometry", - "prefix": "gml", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://www.opengis.net/ont/gml#$1" - }, - "lov.gn": { - "authority": "lov", - "description": "The Geonames ontology provides elements of description for geographical features defined in the geonames.org data base", - "homepage": "http://www.geonames.org/ontology", - "id": "lov.gn", - "name": "The Geonames ontology", - "prefix": "gn", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://www.geonames.org/ontology#$1" - }, - "lov.gndo": { - "authority": "lov", - "description": "GND stands for \"Gemeinsame Normdatei\" (Integrated Authority File) and offers a broad range of elements to describe authorities. The GND originates from the German library community and aims to solve the name ambiguity problem in the library world.", - "homepage": "http://d-nb.info/standards/elementset/gnd#", - "id": "lov.gndo", - "name": "GND Ontology", - "prefix": "gndo", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://d-nb.info/standards/elementset/gnd#$1" - }, - "lov.gold": { - "authority": "lov", - "description": "The General Ontology for Linguistic Description (GOLD) was created primarily for applications involving descriptive linguistics.", - "homepage": "http://purl.org/linguistics/gold", - "id": "lov.gold", - "name": "General Ontology for Linguistic Description", - "prefix": "gold", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/linguistics/gold/$1" - }, - "lov.gom": { - "authority": "lov", - "description": "- Version 0.0.1: initial version", - "homepage": "https://w3id.org/gom", - "id": "lov.gom", - "name": "GOM: Geometry Metadata Ontology", - "prefix": "gom", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "https://w3id.org/gom#$1" - }, - "lov.gov": { - "authority": "lov", - "description": "The Genealogisches Orts-Verzeichnis (GOV) contains information about current and historical political, ecclesiastical and legal administrative affiliations of settlements and administrative units. In addition several time-dependent values (such as names, population numbers, postal codes etc.) are given.", - "homepage": "http://gov.genealogy.net/ontology.owl", - "id": "lov.gov", - "name": "Ontology for modelling historic administrative information.", - "prefix": "gov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://gov.genealogy.net/ontology.owl#$1" - }, - "lov.gr": { - "authority": "lov", - "description": "The GoodRelations ontology provides the vocabulary for annotating e-commerce offerings (1) to sell, lease, repair, dispose, or maintain commodity products and (2) to provide commodity services.", - "homepage": "http://purl.org/goodrelations/v1", - "id": "lov.gr", - "name": "The GoodRelations Ontology for Semantic Web-based E-Commerce", - "prefix": "gr", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/goodrelations/v1#$1" - }, - "lov.grddl": { - "authority": "lov", - "description": "Gleaning Resource Descriptions from Dialects of Languages Vocabulary", - "homepage": "http://www.w3.org/2003/g/data-view", - "id": "lov.grddl", - "name": "Gleaning Resource Descriptions from Dialects of Languages Vocabulary", - "prefix": "grddl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2003/g/data-view#$1" - }, - "lov.gso": { - "authority": "lov", - "description": "Ontology for Relating Generic and Specific Information Resources", - "homepage": "http://www.w3.org/2006/gen/ont", - "id": "lov.gso", - "name": "Generic Specific Ontology", - "prefix": "gso", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2006/gen/ont#$1" - }, - "lov.gsp": { - "authority": "lov", - "description": "A Geographic Query Language for RDF Data OGC 11-052r5", - "homepage": "http://www.opengis.net/ont/geosparql", - "id": "lov.gsp", - "name": "OGC GeoSPARQL", - "prefix": "gsp", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://www.opengis.net/ont/geosparql#$1" - }, - "lov.gtfs": { - "authority": "lov", - "description": "This ontology is a translation of the General Transit Feed Specification towards URIs. Its intended use is creating an exchange platform where the Linked GTFS model can be used as a start to get the right data into the right format.", - "homepage": "http://vocab.gtfs.org/terms#", - "id": "lov.gtfs", - "name": "General Transit Feed Specification", - "prefix": "gtfs", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.gtfs.org/terms#$1" - }, - "lov.gts": { - "authority": "lov", - "description": "This is an RDF/OWL representation of the GeoSciML Geologic Timescale model, which has been adapted from the model described in Cox, S.J.D, & Richard, S.M. (2005) A formal model for the geologic timescale and GSSP, compatible with geospatial information transfer standards, Geosphere, Geological Society of America 1/3, 119\u2013137.", - "homepage": "http://resource.geosciml.org/ontology/timescale/gts", - "id": "lov.gts", - "name": "Geologic Timescale model", - "prefix": "gts", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://resource.geosciml.org/ontology/timescale/gts#$1" - }, - "lov.gufo": { - "authority": "lov", - "description": "The objective of gUFO is to provide a lightweight implementation of the Unified Foundational Ontology (UFO) [1-5] suitable for Semantic Web OWL 2 DL applications. \n\nIntended users are those implementing UFO-based lightweight ontologies that reuse gUFO by specializing and instantiating its elements.\n\nThere are three implications of the use of the term lightweight. First of all, we have employed little expressive means in an effort to retain computational properties for the resulting OWL ontology. Second, we have selected a subset of UFO-A [1, 2] and UFO-B [3] to include here. In particular, there is minimalistic support for UFO-B (only that which is necessary to establish the participation of objects in events and to capture historical dependence between events). Third, a lightweight ontology, differently from a reference ontology, is designed with the purpose of providing an implementation artifact to structure a knowledge base (or knowledge graph). This has driven a number of pragmatic implementation choices which are discussed in comments annotated to the various elements of this implementation. \n\nThe 'g' in gUFO stands for gentle. At the same time, \"gufo\" is the Italian word for \"owl\".\n\n\nFor the source repository, see: ", - "homepage": "http://purl.org/nemo/gufo#", - "id": "lov.gufo", - "name": "gUFO: A Lightweight Implementation of the Unified Foundational Ontology (UFO)", - "prefix": "gufo", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://purl.org/nemo/gufo#$1" - }, - "lov.gvp": { - "authority": "lov", - "description": "The GVP Ontology defines classes, properties and values (skos:Concepts) used in GVP LOD. It is complete regarding AAT and TGN (as of version 2.0), and will be extended in time with more elements needed for the other GVP vocabularies (ULAN, CONA).", - "homepage": "http://vocab.getty.edu/ontology", - "id": "lov.gvp", - "name": "Getty Vocabulary Program ontology", - "prefix": "gvp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.getty.edu/ontology#$1" - }, - "lov.h2o": { - "authority": "lov", - "description": "This ontology establishes classes corresponding to stereotypes used in ISO-conformant models, as used in the rules for conversion of the ISO TC 211 Harmonized Model from the UML to OWL representations", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic", - "id": "lov.h2o", - "name": "Ontology for conversion of ISO/TC 211", - "prefix": "h2o", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic#$1" - }, - "lov.ha": { - "authority": "lov", - "description": "An ontology to detect activity in a smart home", - "homepage": "http://sensormeasurement.appspot.com/ont/home/homeActivity#", - "id": "lov.ha", - "name": "Home Activity", - "prefix": "ha", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sensormeasurement.appspot.com/ont/home/homeActivity#$1" - }, - "lov.hctl": { - "authority": "lov", - "description": "Ontology designed to provide an RDF representation of Hypermedia Controls, in particular links and forms.", - "homepage": "https://www.w3.org/2019/wot/hypermedia#", - "id": "lov.hctl", - "name": "Hypermedia Controls Ontology", - "prefix": "hctl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://www.w3.org/2019/wot/hypermedia#$1" - }, - "lov.hdo": { - "authority": "lov", - "description": "Simple ontology developed for integration purposes. Describe helpdesk entities used to record support tickets for diagnosis and resolve purpuses. The ontology re-uses a) W3C ORG and REGORG ontologies, b) DUL upper ontology, and c) GoodRelations ontology.", - "homepage": "http://www.samos.gr/ontologies/helpdeskOnto.owl", - "id": "lov.hdo", - "name": "HelpDesk support Ontology", - "prefix": "hdo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.samos.gr/ontologies/helpdeskOnto.owl#$1" - }, - "lov.hifm": { - "authority": "lov", - "description": "An ontology for describing brand-name drugs.", - "homepage": "http://purl.org/net/hifm/ontology#", - "id": "lov.hifm", - "name": "HIFM Ontology", - "prefix": "hifm", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences", - "health sciences" - ], - "uri_format": "http://purl.org/net/hifm/ontology#$1" - }, - "lov.holding": { - "authority": "lov", - "description": "A vocabulary to express (library) holdings in RDF", - "homepage": "http://purl.org/ontology/holding", - "id": "lov.holding", - "name": "Holding Ontology", - "prefix": "holding", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/ontology/holding#$1" - }, - "lov.holy": { - "authority": "lov", - "description": "This is the Hydrogen Ontology (HOLY). HOLY is a domain ontology for describing the complex structure of hydrogen-based markets. HOLY contributes to the systemic modeling of the hydrogen domain with a focus on its value chain. Hence, it provides a foundation for retrieval, storage, and delivery of market insights.", - "homepage": "http://purl.org/holy/ns#", - "id": "lov.holy", - "name": "Hydrogen Ontology", - "prefix": "holy", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://purl.org/holy/ns#$1" - }, - "lov.hosp": { - "authority": "lov", - "description": "A RDF Schema that defines concepts and relationships used for Hospital data.", - "homepage": "http://vocab.data.gov/hosp", - "id": "lov.hosp", - "name": "Hospital Vocabulary", - "prefix": "hosp", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://health.data.gov/def/hospital/$1" - }, - "lov.hpont": { - "authority": "lov", - "description": "The Heat Pump Ontology (HPOnt) aims to formalize and represent all the relevant information of Heat Pumps.\n\nThe HPOnt has been developed as part of the REACT project which has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement no. 824395.", - "homepage": "https://w3id.org/hpont", - "id": "lov.hpont", - "name": "The Heat Pump Ontology (HPOnt).", - "prefix": "hpont", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/hpont#$1" - }, - "lov.hr": { - "authority": "lov", - "description": "hRESTS is a vocabulary for describing RESTful Web services", - "homepage": "http://iserve.kmi.open.ac.uk/ns/hrests", - "id": "lov.hr", - "name": "hRESTS Ontology", - "prefix": "hr", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://iserve.kmi.open.ac.uk/ns/hrests#$1" - }, - "lov.hto": { - "authority": "lov", - "description": "The Haystack Tagging Ontology is an OWL ontology for Project Haystack, a domain vocabulary for Building Automation Systems.", - "homepage": "http://vcharpenay.github.io/hto/hto.xml", - "id": "lov.hto", - "name": "Haystack Tagging Ontology", - "prefix": "hto", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vcharpenay.github.io/hto/hto.xml#$1" - }, - "lov.http": { - "authority": "lov", - "description": "A namespace for describing HTTP messages (http://www.w3.org/Protocols/rfc2616/rfc2616.html)", - "homepage": "http://www.w3.org/2011/http", - "id": "lov.http", - "name": "HTTP in RDF", - "prefix": "http", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/2011/http#$1" - }, - "lov.hw": { - "authority": "lov", - "description": "Smart home ontology for weather phenomena and exterior conditions", - "homepage": "https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl", - "id": "lov.hw", - "name": "Home Weather", - "prefix": "hw", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl$1" - }, - "lov.hydra": { - "authority": "lov", - "description": "A lightweight vocabulary for hypermedia-driven Web APIs", - "homepage": "http://www.w3.org/ns/hydra/core", - "id": "lov.hydra", - "name": "The Hydra Core Vocabulary", - "prefix": "hydra", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/hydra/core#$1" - }, - "lov.iadopt": { - "authority": "lov", - "description": "The I-ADOPT Framework ontology", - "homepage": "https://w3id.org/iadopt/ont", - "id": "lov.iadopt", - "name": "I-ADOPT Framework ontology", - "prefix": "iadopt", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences", - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/iadopt/ont/$1" - }, - "lov.ibis": { - "authority": "lov", - "description": "This document specifies a vocabulary for describing an IBIS (issue-based information system).", - "homepage": "https://privatealpha.com/ontology/ibis/1#", - "id": "lov.ibis", - "name": "IBIS Vocabulary", - "prefix": "ibis", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://privatealpha.com/ontology/ibis/1#$1" - }, - "lov.ic": { - "authority": "lov", - "description": "This ontology provides basic classes and more detailed properties for representating international street addresses, phone numbers and emails. Rather than using existing ontologies, such as vcard, it was decided to create a new one as the vcard and foaf ignore the details of international addresses, phone numbers, etc.", - "homepage": "http://ontology.eil.utoronto.ca/icontact.owl", - "id": "lov.ic", - "name": "International Contact Ontology: Addresses, phone numbers and emails.", - "prefix": "ic", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.eil.utoronto.ca/icontact.owl#$1" - }, - "lov.iddo": { - "authority": "lov", - "description": "The interconnected data dictionary ontology maps the data model of the ISO 23386 for the describing, creating, and maintenance of properties in interconnected data dictionaries.", - "homepage": "https://w3id.org/iddo", - "id": "lov.iddo", - "name": "The Interconnected Data Dictionary Ontology (IDDO)", - "prefix": "iddo", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "https://w3id.org/iddo#$1" - }, - "lov.idemo": { - "authority": "lov", - "description": "Ontologie des classes et propri\u00e9t\u00e9s utilis\u00e9es pour la d\u00e9mographie, notamment le recensement de la population", - "homepage": "http://rdf.insee.fr/def/demo", - "id": "lov.idemo", - "name": "Ontologie d\u00e9mographique de l'INSEE", - "prefix": "idemo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdf.insee.fr/def/demo#$1" - }, - "lov.identity": { - "authority": "lov", - "description": "v.2.0 based on P3P1.0 Specification http://www.w3.org/TR/P3P/", - "homepage": "http://www.identity.org/ontologies/identity.owl", - "id": "lov.identity", - "name": "Ontology of digital identity.", - "prefix": "identity", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.identity.org/ontologies/identity.owl#$1" - }, - "lov.ids": { - "authority": "lov", - "description": "This ontology defines classes and properties for describing participants, infrastructure, data and services of the International Data Spaces (formerly known as Industrial Data Space).", - "homepage": "https://w3id.org/idsa/core", - "id": "lov.ids", - "name": "IDS Information Model", - "prefix": "ids", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities", - "law", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/idsa/core/$1" - }, - "lov.ifc": { - "authority": "lov", - "description": "OWL ontology for the IFC conceptual data schema and exchange file format for Building Information Model (BIM) data", - "homepage": "https://w3id.org/ifc/IFC4_ADD1", - "id": "lov.ifc", - "name": "IFC4_ADD1", - "prefix": "ifc", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/ifc/IFC4_ADD1#$1" - }, - "lov.igeo": { - "authority": "lov", - "description": "Ontologie des objets g\u00e9ographiques de l'INSEE, en particulier des territoires administratifs de la France", - "homepage": "http://rdf.insee.fr/def/geo", - "id": "lov.igeo", - "name": "Ontologie g\u00e9ographique de l'INSEE", - "prefix": "igeo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://rdf.insee.fr/def/geo#$1" - }, - "lov.ignf": { - "authority": "lov", - "description": "Codes for describing coordinates reference systems consistently with ISO TC/211. French translations of terms and definitions are mainly taken from the multilingual glossary of ISO/TC 211 available online: http://www.isotc211.org/Terminology.htm", - "homepage": "http://data.ign.fr/def/ignf", - "id": "lov.ignf", - "name": "Ontologie des syst\u00e8mes de coordonn\u00e9es de r\u00e9f\u00e9rence", - "prefix": "ignf", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://data.ign.fr/def/ignf#$1" - }, - "lov.imo": { - "authority": "lov", - "description": "La Ontologia de IMGpedia provee terminos para referirse a descriptores visuales y relaciones de similitud entre imagenes", - "homepage": "http://imgpedia.dcc.uchile.cl/ontology", - "id": "lov.imo", - "name": "The IMGpedia Ontology", - "prefix": "imo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://imgpedia.dcc.uchile.cl/ontology#$1" - }, - "lov.incident": { - "authority": "lov", - "description": "Vocabulary to describe the response to a incident by emergency services.\nThis is NOT intended to describe the incident itself, it describes the response", - "homepage": "http://vocab.resc.info/incident", - "id": "lov.incident", - "name": "Vocabulary to describe incident response by emergency services", - "prefix": "incident", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.resc.info/incident#$1" - }, - "lov.infor": { - "authority": "lov", - "description": "Allows designers to model information objects and their realizations. This allows to reason about physical objects and the information they realize, by keeping them distinguished.", - "homepage": "http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl", - "id": "lov.infor", - "name": "Information Realization", - "prefix": "infor", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl#$1" - }, - "lov.inno": { - "authority": "lov", - "description": "One key use case for this ontology is to facilitate the matching of needs and innovations.", - "homepage": "http://purl.org/innovation/ns", - "id": "lov.inno", - "name": "Ontology for Innovation", - "prefix": "inno", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/innovation/ns#$1" - }, - "lov.interval": { - "authority": "lov", - "description": "An ontology for time intervals", - "homepage": "http://reference.data.gov.uk/def/intervals", - "id": "lov.interval", - "name": "Intervals Ontology", - "prefix": "interval", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://reference.data.gov.uk/def/intervals/$1" - }, - "lov.iol": { - "authority": "lov", - "description": "An ontology of information objects, encodings and realizations, as a plugin to DOLCE-Ultralite", - "homepage": "http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl", - "id": "lov.iol", - "name": "Information Objects ontology", - "prefix": "iol", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl#$1" - }, - "lov.iot-lite": { - "authority": "lov", - "description": "iot-lite is a lightweight ontology based on SSN to describe Internet of Things (IoT) concepts and relationships.", - "homepage": "http://purl.oclc.org/NET/UNIS/fiware/iot-lite#", - "id": "lov.iot-lite", - "name": "Iot-lite ontology", - "prefix": "iot-lite", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "http://purl.oclc.org/NET/UNIS/fiware/iot-lite#$1" - }, - "lov.iot-tta": { - "authority": "lov", - "description": "The Internet of Things taxonomy is extended with semantic ontologies for IoT layers, containing classes, properties, individuals, and rules specific to IoT technologies, tools, and applications", - "homepage": "https://w3id.org/iot-tta", - "id": "lov.iot-tta", - "name": "Ontology for Internet of Things Technologies, Tools, and Applications", - "prefix": "iot-tta", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/iot-tta#$1" - }, - "lov.ioto": { - "authority": "lov", - "description": "IoT-O is a core domain Internet of Things ontology. It is intended to model horizontal knowledge about IoT systems and applications, and to be extended with vertical, application specific knowledge.\nIt is constituted of different modules : \n - A sensing module, based on W3C's SSN (http://purl.oclc.org/NET/ssnx/ssn)\n - An acting module, based on SAN (http://www.irit.fr/recherches/MELODI/ontologies/SAN)\n - A service module, based on MSM (http://iserve.kmi.open.ac.uk/ns/msm/msm-2014-09-03.rdf) and hRest (http://www.wsmo.org/ns/hrests)\n - A lifecycle module, based on a lifecycle vocabulary (http://vocab.org/lifecycle/schema-20080603.rdf) and an iot-specific extension (http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle)\n - An energy module, based on powerOnt (ttp://elite.polito.it/ontologies/poweront.owl)\n\nIoT-O developping team also contributes to the oneM2M IoT interoperability standard.", - "homepage": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-O", - "id": "lov.ioto", - "name": "IoT-O", - "prefix": "ioto", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-O#$1" - }, - "lov.iottaxolite": { - "authority": "lov", - "description": "The IoT-Taxonomy-lite is adapted from M3-lite taxonomy. This taxonomy is refactored and defines many other concepts such as subclasses of Feature-of-Interest and Quality-of-Observation.", - "homepage": "http://purl.org/iot/vocab/iot-taxonomy-lite#", - "id": "lov.iottaxolite", - "name": "The IoTTaxonomy-lite Taxonomy", - "prefix": "iottaxolite", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/iot/vocab/iot-taxonomy-lite#$1" - }, - "lov.ipo": { - "authority": "lov", - "description": "Vocabulary for describing issues (or problems) and corresponding symptoms and solutions to a broad variety of contexts. It is intended to provide a generic, reusable core ontology that can be extended or specialized for use in domain-specific situations, aimed at supporting linked data publishing. The solutions are represented by procedures, which are possible workflows for solving corresponding issues.", - "homepage": "http://purl.org/ipo/core", - "id": "lov.ipo", - "name": "IPO - Issue Procedure Ontology", - "prefix": "ipo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ipo/core#$1" - }, - "lov.irao": { - "authority": "lov", - "description": "Informatics Research Artifacts Ontology, described using W3C RDF Schema and the Web Ontology Language OWL.", - "homepage": "http://ontology.ethereal.cz/irao", - "id": "lov.irao", - "name": "Informatics Research Artifacts Ontology", - "prefix": "irao", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities", - "computer and information sciences" - ], - "uri_format": "http://ontology.ethereal.cz/irao/$1" - }, - "lov.irw": { - "authority": "lov", - "description": "This ontology is an evolution of IRE ontology. It describes identification of resources on the Web, through the definition of relationships between resources and their representations on the Web. The requirement is to describe what can be identified by URIs and how this is handled e.g. in form of HTTP requests and reponds.", - "homepage": "http://www.ontologydesignpatterns.org/ont/web/irw.owl", - "id": "lov.irw", - "name": "The Identity of Resources on the Web ontology", - "prefix": "irw", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/ont/web/irw.owl#$1" - }, - "lov.is": { - "authority": "lov", - "description": "The Information Service Ontology specification provides basic concepts and properties for describing different information services, e.g. Wikipedia, MusicBrainz, Freebase", - "homepage": "http://purl.org/ontology/is/core#", - "id": "lov.is", - "name": "Info Service Ontology", - "prefix": "is", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/is/core#$1" - }, - "lov.isbd": { - "authority": "lov", - "description": "This is a registration of classes and properties from International Standard Bibliographic Description (ISBD), consolidated edition, published by De Gruyter Saur in July 2011 (ISBN 978-3-11-026379-4).", - "homepage": "http://iflastandards.info/ns/isbd/elements/", - "id": "lov.isbd", - "name": "ISBD elements", - "prefix": "isbd", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://iflastandards.info/ns/isbd/elements/$1" - }, - "lov.iso-thes": { - "authority": "lov", - "description": "This vocabulary aims at providing interoperability between SKOS and ISO 25964 \u2010 1:2011, the new standard for thesauri", - "homepage": "http://purl.org/iso25964/skos-thes", - "id": "lov.iso-thes", - "name": "ISO 25964 SKOS extension", - "prefix": "iso-thes", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/iso25964/skos-thes#$1" - }, - "lov.iso37120": { - "authority": "lov", - "description": "ISO 37120 \u2013 Sustainable Development and Resilience of Communities \u2013 Indicators for City Services and Quality of Life (under TC268)\n\nhttp://ontology.eil.utoronto.ca/ISO37120.html\n\nThis OWL file defines a class for each indicator defined in the ISO 37120 standard. Names for each indicator are provided. Text definitions are provided only for Economy, Education and Energy indicators, due to copyright restrictions imposed by ISO. This file is meant to provide a single URI for each indicator.\n\nAn ontology for representing an indicator's supporting data plus meta information such as provenance, validity and trust can be found in:\nhttp://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl\n\nDocumentation of the ontology can be found in:\nhttp://eil.utoronto.ca/smartcities/papers/GCI-Foundation-Ontology.pdf", - "homepage": "http://ontology.eil.utoronto.ca/ISO37120.owl", - "id": "lov.iso37120", - "name": "ISO 37120 indicator URIs", - "prefix": "iso37120", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://ontology.eil.utoronto.ca/ISO37120.owl#$1" - }, - "lov.isoadr": { - "authority": "lov", - "description": "This ontology is a version of the ISO TC211, Group for Ontology Management (GOM)'s OWL ontology interpretation of the ISO19160-1:2015 \"Addressing -- Part 1: Conceptual model\" standard (see https://www.iso.org/standard/61710.html) taken from that ontology's source code, published at https://github.com/ISO-TC211/GOM/tree/master/isotc211_GOM_harmonizedOntology/19160-1/2015.", - "homepage": "http://reference.data.gov.au/def/ont/iso19160-1-address", - "id": "lov.isoadr", - "name": "ISO19160-1:2015 Address ontology", - "prefix": "isoadr", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://reference.data.gov.au/def/ont/iso19160-1-address#$1" - }, - "lov.ispra": { - "authority": "lov", - "description": "L'ontologia ISPRA nasce dall'esigenza di pubblicazione dei dataset LOD ed \u00e8 finalizzata alla descrizione dei processi e delle attivit\u00e0 dell'Istituto negli ambiti circoscritti dai primi dataset pubblicati. Al momento sono descritte in modo analitico le classi e le propriet\u00e0 che insistono sul dominio specifico della rete ondametrica nazionale, della rete mareografica, del consumo del suolo e degli interventi di dissesto idrogeologico, ma l'obiettivo \u00e8 di estenderla parallelamente alla pubblicazione di nuovi dataset.", - "homepage": "http://dati.isprambiente.it/ontology/core#", - "id": "lov.ispra", - "name": "Ispra Ontology", - "prefix": "ispra", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities", - "earth and related environmental sciences" - ], - "uri_format": "http://dati.isprambiente.it/ontology/core#$1" - }, - "lov.istex": { - "authority": "lov", - "description": "ISTEX est une plateforme qui a pour ambition d\u2019offrir, \u00e0 l\u2019ensemble de la communaut\u00e9 de l\u2019enseignement sup\u00e9rieur et de la recherche fran\u00e7aise qui le souhaite, un acc\u00e8s en ligne aux collections r\u00e9trospectives de la litt\u00e9rature scientifique dans toutes les disciplines. \u00c0 ce r\u00e9servoir in\u00e9gal\u00e9 en ressources multidisciplinaires s\u2019ajoute un nombre important de services \u00e0 valeur ajout\u00e9e permettant d\u2019en optimiser l\u2019exploitation gr\u00e2ce \u00e0 des outils de fouille de contenus (TDM) et de valorisation interactive.", - "homepage": "https://data.istex.fr/ontology/istex#", - "id": "lov.istex", - "name": "Ontologie du projet Istex pour la diffusion de la litt\u00e9rature scientifique", - "prefix": "istex", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "https://data.istex.fr/ontology/istex#$1" - }, - "lov.itm": { - "authority": "lov", - "description": "A partir del estudio de las caracter\u00edsticas de las herramientas de gesti\u00f3n de tareas o issue tracking systems, se ha elaborado este vocabulario.", - "homepage": "http://spi-fm.uca.es/spdef/models/genericTools/itm/1.0", - "id": "lov.itm", - "name": "Issue Tracking tool Model", - "prefix": "itm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://spi-fm.uca.es/spdef/models/genericTools/itm/1.0#$1" - }, - "lov.itsmo": { - "authority": "lov", - "description": "IT Service Management Ontology (ITSMO) provides the vocabulary for annotating resources related to IT Service Management. ITSMO tries to be consistent with 2011 ITIL glossary.", - "homepage": "http://ontology.it/itsmo/v1", - "id": "lov.itsmo", - "name": "IT Service Management Ontology", - "prefix": "itsmo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.it/itsmo/v1#$1" - }, - "lov.ivoam": { - "authority": "lov", - "description": "A vocabulary of particles used for observations in astronomy.\nThis list started its existence as the controlled vocabulary for\nVODataService's vs:Waveband type; the machine-readable identifiers are in\nupper case for backwards compatibility.", - "homepage": "http://www.ivoa.net/rdf/messenger", - "id": "lov.ivoam", - "name": "Messengers", - "prefix": "ivoam", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ivoa.net/rdf/messenger#$1" - }, - "lov.jsonsc": { - "authority": "lov", - "description": "Module for data schema specifications, part of the W3C Web of Things (WoT) Thing Description model", - "homepage": "https://www.w3.org/2019/wot/json-schema#", - "id": "lov.jsonsc", - "name": "JSON Schema in RDF", - "prefix": "jsonsc", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://www.w3.org/2019/wot/json-schema#$1" - }, - "lov.jup": { - "authority": "lov", - "description": "Slovnik prisupnosti budov vznikl v ramci projektu Mapy bez barier, ktery realizuje Nadace Charty 77 - Konto Bariery. Vychazi z Metodiky kategorizace pristupnosti objektu, je vsak doplnen i o entity vyplyvajici z pozadavku projektu. Tento slovnik je i tematem diplomove prace Ontologie pristupnosti budov. Projekt je spolufinancovan z prostredku Evropske unie, Evropskeho fondu pro regionalni rozvoj.", - "homepage": "http://w3id.org/charta77/jup", - "id": "lov.jup", - "name": "Ontology of Building Accessibility", - "prefix": "jup", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://w3id.org/charta77/jup/$1" - }, - "lov.juso": { - "authority": "lov", - "description": "Juso Ontology is a Web vocabulary for describing geographical addresses and features.", - "homepage": "http://rdfs.co/juso/", - "id": "lov.juso", - "name": "Juso Ontology", - "prefix": "juso", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://rdfs.co/juso/$1" - }, - "lov.juso.kr": { - "authority": "lov", - "description": "South Korea Extension to Juso Ontology is a Web vocabulary that extends Juso Ontology to describe geographical addresses and features in South Korea.", - "homepage": "http://rdfs.co/juso/kr/", - "id": "lov.juso.kr", - "name": "South Korea Extension to Juso Ontology", - "prefix": "juso.kr", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://rdfs.co/juso/kr/$1" - }, - "lov.kdo": { - "authority": "lov", - "description": "The Knowledge Diversity Ontology aims at providing a vocabulary that describes different dimensions of knowledge diversity of the Web. To support the representation of diversity information, the conceptual model of the Knowledge Diversity Ontology includes concepts and relations that were identified and modelled by focusing on real world scenarios in context of customer feedback, news, and Wikipedia opinion mining as well as content and sentiment analysis.", - "homepage": "http://kdo.render-project.eu/kdo#", - "id": "lov.kdo", - "name": "The Knowledge Diversity Ontology", - "prefix": "kdo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://kdo.render-project.eu/kdo#$1" - }, - "lov.kees": { - "authority": "lov", - "description": "KEES (Knowledge Exchange Engine Schema ) ontology describes a knowledge base configuration in terms of ABox and TBox statements together with their accrual and reasoning policies. This vocabulary is designed to drive automatic data ingestion in a graph database according KEES and Linked (Open) Data principles.", - "homepage": "http://linkeddata.center/kees/v1", - "id": "lov.kees", - "name": "KEES Ontology", - "prefix": "kees", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://linkeddata.center/kees/v1#$1" - }, - "lov.keys": { - "authority": "lov", - "description": "A vocabulary for musical keys and notes", - "homepage": "http://purl.org/NET/c4dm/keys.owl", - "id": "lov.keys", - "name": "Keys Ontology", - "prefix": "keys", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/NET/c4dm/keys.owl#$1" - }, - "lov.km4c": { - "authority": "lov", - "description": "A Knowledge Model to describe a smart city, that interconnect data from infomobility service, Open Data and other source", - "homepage": "http://www.disit.org/km4city/schema", - "id": "lov.km4c", - "name": "km4city, the DISIT Knowledge Model for City and Mobility", - "prefix": "km4c", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://www.disit.org/km4city/schema#$1" - }, - "lov.label": { - "authority": "lov", - "description": "Term definitions for singular and plural label properties", - "homepage": "http://purl.org/net/vocab/2004/03/label", - "id": "lov.label", - "name": "label", - "prefix": "label", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/vocab/2004/03/label#$1" - }, - "lov.lawd": { - "authority": "lov", - "description": "The goal of LAWD is to fill in the cracks between the data used and published by projects with a focus on the ancient world and the standard Linked Data vocablary schemes, like Dublin Core, the Open Annotation Collaboration, and CIDOC-CRM.", - "homepage": "http://lawd.info/ontology/", - "id": "lov.lawd", - "name": "Linking Ancient World Data Ontology", - "prefix": "lawd", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://lawd.info/ontology/$1" - }, - "lov.lc": { - "authority": "lov", - "description": "This ontology provides the predicates necessary to describe a connection or hop from one transit stop to another.", - "homepage": "http://semweb.mmlab.be/ns/linkedconnections#Ontology", - "id": "lov.lc", - "name": "The Linked Connections ontology", - "prefix": "lc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semweb.mmlab.be/ns/linkedconnections#$1" - }, - "lov.lcy": { - "authority": "lov", - "description": "The Lifecycle Schema provides classes and properties that allow the specification of a lifecycle that any resource may pass through.", - "homepage": "http://purl.org/vocab/lifecycle/schema", - "id": "lov.lcy", - "name": "Lifecycle Schema", - "prefix": "lcy", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocab/lifecycle/schema#$1" - }, - "lov.ldp": { - "authority": "lov", - "description": "A set of best practices and simple approach for a read-write Linked Data architecture, based on HTTP access to web resources that describe their state using the RDF data model.", - "homepage": "http://www.w3.org/ns/ldp#", - "id": "lov.ldp", - "name": "Linked Data Platform", - "prefix": "ldp", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/ns/ldp#$1" - }, - "lov.ldr": { - "authority": "lov", - "description": "The Linked Data Rights ontology provides the vocabulary for creating rights expressions for Linked Data resources.", - "homepage": "http://purl.oclc.org/NET/ldr/ns#", - "id": "lov.ldr", - "name": "Linked Data Rights (LDR)", - "prefix": "ldr", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "http://purl.oclc.org/NET/ldr/ns#$1" - }, - "lov.ldvm": { - "authority": "lov", - "description": "Vocabulary for Linked Data Visualization Model (LDVM) serves for description and configuration of components and pipelines according to LDVM", - "homepage": "http://linked.opendata.cz/ontology/ldvm/", - "id": "lov.ldvm", - "name": "Vocabulary for Linked Data Visualization Model", - "prefix": "ldvm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://linked.opendata.cz/ontology/ldvm/$1" - }, - "lov.lemon": { - "authority": "lov", - "description": "Lemon: The lexicon model for ontologies is designed to allow for descriptions of lexical information regarding ontological elements and other RDF resources. Lemon covers mapping of lexical decomposition, phrase structure, syntax, variation, morphology, and lexicon-ontology mapping.", - "homepage": "http://lemon-model.net/lemon", - "id": "lov.lemon", - "name": "LExicon Model for ONtologies", - "prefix": "lemon", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://lemon-model.net/lemon#$1" - }, - "lov.lexdcp": { - "authority": "lov", - "description": "A model for the representation of lexical information relative to ontologies. Decomposition module.", - "homepage": "http://www.w3.org/ns/lemon/decomp", - "id": "lov.lexdcp", - "name": "Lexicon Model for Ontologies - Decomp", - "prefix": "lexdcp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/lemon/decomp#$1" - }, - "lov.lexinfo": { - "authority": "lov", - "description": "Version 2.0 of LexInfo Ontology, based on Lemon", - "homepage": "http://www.lexinfo.net/ontology/2.0/lexinfo", - "id": "lov.lexinfo", - "name": "LexInfo Ontology", - "prefix": "lexinfo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.lexinfo.net/ontology/2.0/lexinfo#$1" - }, - "lov.lgdo": { - "authority": "lov", - "description": "LinkedGeoData ontology has been derived from concepts defined by Open Street Map", - "homepage": "http://linkedgeodata.org/ontology", - "id": "lov.lgdo", - "name": "LinkedGeoData ontology", - "prefix": "lgdo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://linkedgeodata.org/ontology/$1" - }, - "lov.lh": { - "authority": "lov", - "description": "An ontology for metadata about legal texts represented using the LegalHTML format", - "homepage": "https://w3id.org/legalhtml/ov", - "id": "lov.lh", - "name": "LegalHTML Ontology", - "prefix": "lh", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/legalhtml/ov#$1" - }, - "lov.li": { - "authority": "lov", - "description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - LI Package", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/lineage", - "id": "lov.li", - "name": "OWL representation of ISO 19115 (Geographic Information - Metadata - Lineage package)", - "prefix": "li", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/lineage#$1" - }, - "lov.lib": { - "authority": "lov", - "description": "Experimental \"library\" extension vocabulary for use with Schema.org", - "homepage": "http://purl.org/library/", - "id": "lov.lib", - "name": "Library extension of schema.org", - "prefix": "lib", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/library/$1" - }, - "lov.lifecycle": { - "authority": "lov", - "description": "This ontology is a specialization of the lifecycle vocabulary (http://purl.org/vocab/lifecycle/schema) meant to be used in the context of IoT. It is used as a module in the IoT core domain ontology IoT-O (www.irit.fr/recherches/MELODI/ontologies/IoT-O). \n\nIoT-Lifecycle adds a specific state definition (ParametrizedState) and a specific transition (Update) that is useful to model actuators.", - "homepage": "http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle", - "id": "lov.lifecycle", - "name": "IoT-Lifecycle", - "prefix": "lifecycle", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocab/lifecycle/schema#$1" - }, - "lov.lime": { - "authority": "lov", - "description": "LIME (LInguistic MEtadata) is a vocabulary for expressing linguistic metadata about linguistic resources and linguistically grounded datasets.", - "homepage": "http://www.w3.org/ns/lemon/lime", - "id": "lov.lime", - "name": "Lexicon Model for Ontologies - LIngusitic MEtadata (LIME)", - "prefix": "lime", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.w3.org/ns/lemon/lime#$1" - }, - "lov.limo": { - "authority": "lov", - "description": "A Vocabulary for Incorporating Predictive Models into the Linked Data Web", - "homepage": "http://purl.org/limo-ontology/limo/", - "id": "lov.limo", - "name": "Linked Statistical Models Vocabulary", - "prefix": "limo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/limo-ontology/limo#$1" - }, - "lov.limoo": { - "authority": "lov", - "description": "A vocabulary to describe licenses", - "homepage": "http://purl.org/LiMo/0.1#", - "id": "lov.limoo", - "name": "License Model Ontology", - "prefix": "limoo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/LiMo/0.1#$1" - }, - "lov.lingvo": { - "authority": "lov", - "description": "An ontology for using languages as resources", - "homepage": "https://w3id.org/vocab/lingvoj", - "id": "lov.lingvo", - "name": "The Lingvoj Ontology", - "prefix": "lingvo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/vocab/lingvoj#$1" - }, - "lov.lio": { - "authority": "lov", - "description": "A Lightweight Ontology for Describing Images", - "homepage": "http://purl.org/net/lio", - "id": "lov.lio", - "name": "Lightweight Image Ontology", - "prefix": "lio", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/lio#$1" - }, - "lov.llont": { - "authority": "lov", - "description": "LinkLion - the Link Discovery Portal", - "homepage": "http://www.linklion.org/ontology", - "id": "lov.llont", - "name": "LinkLion - the Link Discovery Portal", - "prefix": "llont", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.linklion.org/ontology#$1" - }, - "lov.lmm1": { - "authority": "lov", - "description": "This ontology is a composition of some content design patterns for the semiotic triangle. Its structure is extracted from DOLCE-Ultralite (DOLCE+c.DnS), but it uses a different terminology,", - "homepage": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl", - "id": "lov.lmm1", - "name": "Lexical MetaModel Level 1", - "prefix": "lmm1", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl#$1" - }, - "lov.lmm2": { - "authority": "lov", - "description": "An ontology for aligning existing linguistic ontologies, and for describing the research objects of NLP.", - "homepage": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl", - "id": "lov.lmm2", - "name": "Lexical MetaModel Level 2", - "prefix": "lmm2", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl#$1" - }, - "lov.loc": { - "authority": "lov", - "description": "Este vocabulario se utiliza para modelar las localizaciones f\u00edsicas de lugares p\u00fablicos. \t\t\tUtiliza elementos de Geonames para identificar las distintas caracter\u00edsticas geogr\u00e1ficas.", - "homepage": "http://purl.org/ctic/infraestructuras/localizacion", - "id": "lov.loc", - "name": "Vocabulario de Localizaciones", - "prefix": "loc", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://purl.org/ctic/infraestructuras/localizacion#$1" - }, - "lov.locah": { - "authority": "lov", - "description": "This vocabulary derived from the Encoded Archival Description standard has been developed in 2010-2011 by the LOCAH project.", - "homepage": "http://data.archiveshub.ac.uk/def/", - "id": "lov.locah", - "name": "The LOCAH RDF Vocabulary", - "prefix": "locah", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://data.archiveshub.ac.uk/def/$1" - }, - "lov.locn": { - "authority": "lov", - "description": "The ISA Programme Location Core Vocabulary provides a minimum set of classes and properties for describing any place in terms of its name, address or geometry. The vocabulary is specifically designed to aid the publication of data that is interoperable with EU INSPIRE Directive.", - "homepage": "http://www.w3.org/ns/locn", - "id": "lov.locn", - "name": "ISA Programme Location Core Vocabulary", - "prefix": "locn", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://www.w3.org/ns/locn#$1" - }, - "lov.lode": { - "authority": "lov", - "description": "An ontology for publishing descriptions of historical events as Linked Data, and for mapping between other event-related vocabularies and ontologies.", - "homepage": "http://linkedevents.org/ontology/", - "id": "lov.lode", - "name": "Linking Open Descriptions of Events", - "prefix": "lode", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://linkedevents.org/ontology/$1" - }, - "lov.log": { - "authority": "lov", - "description": "An historical ontology used by the cwm command-line tool back in the very early days of the semantic web (~ 2000- 2003 ?)", - "homepage": "http://www.w3.org/2000/10/swap/log", - "id": "lov.log", - "name": "SWAP Logic Ontology", - "prefix": "log", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2000/10/swap/log#$1" - }, - "lov.lom": { - "authority": "lov", - "description": "An ontology and vocabulary used for exposing IEEE LOM, a metadata standard for educational contents, as Linked Data. \nIt is intended as a bridge for linkage of educational metadata into Linked Open Data (LOD). In this ontology, we designed a mapping of IEEE LOM elements to RDF based on Linked Data principles.", - "homepage": "http://data.opendiscoveryspace.eu/lom_ontology_ods.owl", - "id": "lov.lom", - "name": "Learning Object Metadata Ontology", - "prefix": "lom", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.opendiscoveryspace.eu/lom_ontology_ods.owl#$1" - }, - "lov.losp": { - "authority": "lov", - "description": "Ontology Specialties describes all possible specialties (directions) in the RF, in which the UGNS they are composed, as well as information about their old codes / groups / names.", - "homepage": "http://sparql.sstu.ru:3030/speciality/", - "id": "lov.losp", - "name": "Linked open specialities RF", - "prefix": "losp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://sparql.sstu.ru:3030/speciality/$1" - }, - "lov.loted": { - "authority": "lov", - "description": "A vocabulary for European Calls for Tenders (in english, german, and french)", - "homepage": "http://loted.eu/ontology", - "id": "lov.loted", - "name": "LOTED ontology", - "prefix": "loted", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "http://loted.eu/ontology#$1" - }, - "lov.lsc": { - "authority": "lov", - "description": "LSC, the Linked Science Core Vocabulary, is a lightweight vocabulary providing terms to enable publishers and researchers to relate things in science to time, space, and themes.", - "homepage": "http://linkedscience.org/lsc/ns#", - "id": "lov.lsc", - "name": "Linked Science Core Vocabulary", - "prefix": "lsc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://linkedscience.org/lsc/ns#$1" - }, - "lov.lslife": { - "authority": "lov", - "description": "The ELSEWeb Lifemapper ontology provides classes for describing biodiversity modelling services provided by Lifemapper. This project provides support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu", - "homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl", - "id": "lov.lslife", - "name": "ELSEWeb Lifemapper Ontology", - "prefix": "lslife", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl#$1" - }, - "lov.lsmap": { - "authority": "lov", - "description": "The ELSEWeb mappings ontology imports related upper level ontologies and vocabularies and aligns ELSEWeb ontologies to importec classes. This ontology provides support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu", - "homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/mappings/elseweb-mappings.owl", - "id": "lov.lsmap", - "name": "ELSEWeb Mappings Ontology", - "prefix": "lsmap", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl#$1" - }, - "lov.lsq": { - "authority": "lov", - "description": "The Linked SPARQL Queries Vocabulary (LSQ(V)), defined using RDF(S) and OWL, provides a machine readable vocabulary to help describe queries in SPARQL logs and their statistics. The vocabulary builds upon the SPIN vocabulary and the Service Description vocabulary.", - "homepage": "http://lsq.aksw.org/vocab", - "id": "lov.lsq", - "name": "The Linked SPARQL Queries Vocabulary (LSQ(V))", - "prefix": "lsq", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://lsq.aksw.org/vocab#$1" - }, - "lov.lsweb": { - "authority": "lov", - "description": "The ELSEWeb Data ontology provides simple classes for describing datasets. This project provides foundational support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu", - "homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl", - "id": "lov.lsweb", - "name": "ELSEWeb Data Ontology", - "prefix": "lsweb", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl#$1" - }, - "lov.lswmo": { - "authority": "lov", - "description": "The ELSEWeb Modelling ontology provides simple classes for describing data models. This project provides foundational support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu", - "homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl", - "id": "lov.lswmo", - "name": "ELSEWeb Modelling Ontology", - "prefix": "lswmo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl#$1" - }, - "lov.lswpm": { - "authority": "lov", - "description": "The ELSEWeb Lifemapper parameters ontology provides auxiliary classes and instances that describe input parameters of Lifemapper modelling services. This ontology provides support for the ELSEWeb project(http://elseweb.cybershare.utep.edu/).\nwebsite: http://elseweb.cybershare.utep.edu/ontologies\nemail: nvillanuevarosales@utep.edu", - "homepage": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl", - "id": "lov.lswpm", - "name": "ELSEWeb Lifemapper Parameters Ontology", - "prefix": "lswpm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl#$1" - }, - "lov.ludo": { - "authority": "lov", - "description": "Ludo is an ontology created to enable the description and representation of Serious Games that use structured data published on the Web through the Linked Data as a knowledge base. From the representation of the players\u2019 profile and their contextual information whithin the game, it is possible to generate personalized recommendations of related educational resources in order to stimulate the learning process while playing.", - "homepage": "http://ns.inria.fr/ludo", - "id": "lov.ludo", - "name": "Ludo Ontology", - "prefix": "ludo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/ludo$1" - }, - "lov.ludo-gm": { - "authority": "lov", - "description": "Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics.", - "homepage": "http://ns.inria.fr/ludo/v1/gamemodel#", - "id": "lov.ludo-gm", - "name": "Ludo Game Model Ontology", - "prefix": "ludo-gm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/ludo/v1/gamemodel#$1" - }, - "lov.ludo-gp": { - "authority": "lov", - "description": "Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics.", - "homepage": "http://ns.inria.fr/ludo/v1/gamepresentation#", - "id": "lov.ludo-gp", - "name": "Ludo - Game Presentation", - "prefix": "ludo-gp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/ludo/v1/gamepresentation#$1" - }, - "lov.ludo-vc": { - "authority": "lov", - "description": "Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics.", - "homepage": "http://ns.inria.fr/ludo/v1/virtualcontext#", - "id": "lov.ludo-vc", - "name": "Ludo - Virtual Context", - "prefix": "ludo-vc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/ludo/v1/virtualcontext#$1" - }, - "lov.ludo-xapi": { - "authority": "lov", - "description": "This is an OWL formalization of the statements defined in the Experience API (xAPI) specification. It is a module of the LUDO ontology.", - "homepage": "http://ns.inria.fr/ludo/v1/xapi", - "id": "lov.ludo-xapi", - "name": "Experience API (xAPI)", - "prefix": "ludo-xapi", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://ns.inria.fr/ludo/v1/xapi#$1" - }, - "lov.lv": { - "authority": "lov", - "description": "Under this name space new properties and classes needed for the lobid.org service are defined . Already existing properties and classes which are (re)used in lobid.org aren't documented here.", - "homepage": "http://purl.org/lobid/lv", - "id": "lov.lv", - "name": "lobid vocab", - "prefix": "lv", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/lobid/lv#$1" - }, - "lov.lvont": { - "authority": "lov", - "description": "An ontology for natural language terms description, including scripts, languages and meanings. The Lexvo.org ontology is still under development and may not be able to address all needs. Please also consider using the Lingvoj Ontology and the GOLD ontology, whereever appropriate.", - "homepage": "http://lexvo.org/ontology", - "id": "lov.lvont", - "name": "Lexvo.org Ontology", - "prefix": "lvont", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://lexvo.org/ontology#$1" - }, - "lov.lyou": { - "authority": "lov", - "description": "Vocabulary for describing common webpages provided by an organisation", - "homepage": "http://purl.org/linkingyou/", - "id": "lov.lyou", - "name": "Linking-you vocabulary", - "prefix": "lyou", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/linkingyou/$1" - }, - "lov.m3lite": { - "authority": "lov", - "description": "M3 lite taxonomy is designed for the FIESTA-IOT H2020 EU project. We refactor, clean and simplify the M3 ontology designed by Eurecom (Amelie Gyrard). M3 ontology lite is currently aligned with the quantity taxonomy used by several testbeds: SmartSantander (Spain), University of Surrey (United Kingdom), KETI (Korea) and Com4Innov (France).", - "homepage": "http://purl.org/iot/vocab/m3-lite#", - "id": "lov.m3lite", - "name": "The Machine-to-Machine Measurement (M3) Lite Ontology", - "prefix": "m3lite", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/iot/vocab/m3-lite#$1" - }, - "lov.m4i": { - "authority": "lov", - "description": "Metadata4Ing defines classes and properties or reuses such classes and properties from other ontologies to describe research processes and research data management in NFDI4Ing. \nNew concepts and properties are located in the namespace of Metadata4Ing.\nMetadata4Ing does not import complete ontologies for the sake of relevance, readability, understandability and usability by and for engineers.\nInstead, it tries to make re-use of existing identifiers for classes and properties by re-using all or a relevant subset of the axioms from the original ontology.\nThese statements have been extracted in different ways, e.g. by using Prot\u00e9g\u00e9 tools importing an ontology and copying axioms of relevant items to Metadata4Ing or by download from data services or raw files of ontologies and manual copypasting.\nIn some cases there was a need to extend or modify the original set of statements about an entity, e.g. because labels and definitions were expressed with a different owl:AnnotationProperty than the rest of Metadata4Ing, or because a skos:preflabel or a skos:definition in any of the languages we would like to support was missing.\nAny editorial changes on elements from external ontologies are declared in Metadata4Ing by an annotation with skos:editorialNote at item-level.\nTo get the original set of statements we encourage to visit the original namespace of the respective item.\nMetadata4Ing reuses elements from the following ontologies:\n- BIBO = Bibliographic Ontology \n- BIRO = Bibliographic Reference Ontology \n- DCAT = Data Catalog \n- DCTERMS = Dublin Core Terms \n- FOAF = Friend of a Friend \n- OWL = Web Ontology Language \n- PROV = Provenance Namespace \n- QUDT = Quantities, Units, Dimensions and Types \n- RDF = Resource Description Framework \n- RDFS = RDF Schema \n- SCHEMA = schema.org \n- SKOS = Simple Knowledge Organization System \n- SSN = Semantic Sensor Network Ontology \n- VANN = Vocabulary for Annotating vocabulary descriptions \n- XSD = XML Schema Definition \n- EMMO = European Materials and Modelling Ontology \n- BFO = Basic Formal Ontology \n- RO = Relation Ontology \n- PIMS-II = PIMS Interoperability Infrastructure \n- D-SI = Digital System of Units", - "homepage": "http://w3id.org/nfdi4ing/metadata4ing#", - "id": "lov.m4i", - "name": "Metadata4Ing: An ontology for describing the generation of research data within a scientific activity.", - "prefix": "m4i", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://w3id.org/nfdi4ing/metadata4ing#$1" - }, - "lov.ma-ont": { - "authority": "lov", - "description": "The Ontology for Media Resources 1.0 describes a core vocabulary of properties and a set of mappings between different metadata formats of media resources hat describe media resources published on the Web (as opposed to local archives, museums, or other non-web related and non-shared collections of media resources).", - "homepage": "http://www.w3.org/ns/ma-ont", - "id": "lov.ma-ont", - "name": "Ontology for Media Resources", - "prefix": "ma-ont", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/ma-ont#$1" - }, - "lov.mads": { - "authority": "lov", - "description": "MADS/RDF (Metadata Authority Description Schema in RDF) is a knowledge organization system (KOS) designed for use with controlled values for names (personal, corporate, geographic, etc.), thesauri, taxonomies, subject heading systems, and other controlled value lists", - "homepage": "http://www.loc.gov/mads/rdf/v1", - "id": "lov.mads", - "name": "Metadata Authority Description Schema", - "prefix": "mads", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.loc.gov/mads/rdf/v1#$1" - }, - "lov.marl": { - "authority": "lov", - "description": "Marl is a standardised data schema designed to annotate and describe subjective opinions expressed on the web or in particular Information Systems.", - "homepage": "http://www.gsi.dit.upm.es/ontologies/marl/ns", - "id": "lov.marl", - "name": "Marl Ontology Specification", - "prefix": "marl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.gsi.dit.upm.es/ontologies/marl/ns#$1" - }, - "lov.maso": { - "authority": "lov", - "description": "Ontologie pour le domaine de la s\u00e9curit\u00e9: application aux agents mobiles", - "homepage": "http://securitytoolbox.appspot.com/MASO", - "id": "lov.maso", - "name": "S\u00e9curit\u00e9 Agents Mobiles", - "prefix": "maso", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://securitytoolbox.appspot.com/MASO#$1" - }, - "lov.md": { - "authority": "lov", - "description": "An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - MD Package.", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/metadata", - "id": "lov.md", - "name": "OWL representation of ISO 19115", - "prefix": "md", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19115/2003/metadata#$1" - }, - "lov.mdi": { - "authority": "lov", - "description": "An RDF vocabulary to describe and facilitate the usage of a Multidimensional Interface.", - "homepage": "https://w3id.org/multidimensional-interface/ontology", - "id": "lov.mdi", - "name": "RDF vocabulary to describe a Multidimensional Interface.", - "prefix": "mdi", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/multidimensional-interface/ontology#$1" - }, - "lov.mdo": { - "authority": "lov", - "description": "This is the Materials Design Ontology.", - "homepage": "https://w3id.org/mdo/full/", - "id": "lov.mdo", - "name": "Materials Design Ontology - Full", - "prefix": "mdo", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "https://w3id.org/mdo/full/$1" - }, - "lov.mdo-calc": { - "authority": "lov", - "description": "This is the calculation module of Materials Design Ontology.", - "homepage": "https://w3id.org/mdo/calculation/", - "id": "lov.mdo-calc", - "name": "Materials Design Ontology - Calculation Module", - "prefix": "mdo-calc", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "https://w3id.org/mdo/calculation/$1" - }, - "lov.mdo-struc": { - "authority": "lov", - "description": "This is the structure module in Materials Design Ontology.", - "homepage": "https://w3id.org/mdo/structure/", - "id": "lov.mdo-struc", - "name": "Materials Design Ontology - Structure Module", - "prefix": "mdo-struc", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "https://w3id.org/mdo/structure/$1" - }, - "lov.mdoprov": { - "authority": "lov", - "description": "This is the provenance module of Materials Design Ontology.", - "homepage": "https://w3id.org/mdo/provenance/", - "id": "lov.mdoprov", - "name": "Materials Design Ontology - Provenance Module", - "prefix": "mdoprov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/mdo/provenance/$1" - }, - "lov.mdr": { - "authority": "lov", - "description": "An application profile of DCAT combining it with other metadata vocabularies (e.g. VoID, DCTERMS, LIME)\n to meet requirements elicited in various use cases of the Semantic Web platform Semantic Turkey", - "homepage": "http://semanticturkey.uniroma2.it/ns/mdr", - "id": "lov.mdr", - "name": "The Semantic Turkey metadata registry ontology", - "prefix": "mdr", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semanticturkey.uniroma2.it/ns/mdr#$1" - }, - "lov.meb": { - "authority": "lov", - "description": "This ontology provides the base elements required by myExperiment for content management, social networking and object annotation.", - "homepage": "http://rdf.myexperiment.org/ontologies/base/", - "id": "lov.meb", - "name": "The myExperiment Base Ontology", - "prefix": "meb", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://rdf.myexperiment.org/ontologies/base/$1" - }, - "lov.media": { - "authority": "lov", - "description": "In order to enable and encourage the sharing, distribution, syndication, and aggregation of media content, the authors propose the Media RDF vocabulary, an open standard for distributed media metadata.", - "homepage": "http://purl.org/media", - "id": "lov.media", - "name": "The Media RDF Vocabulary", - "prefix": "media", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/media#$1" - }, - "lov.medred": { - "authority": "lov", - "description": "This ontology aims to model generic Medical Data Acquisition Instruments, which can be interoperable across different clinical data management systems. The ontology is developed in the context of the MedRed project (https://www.hevs.ch/en/rad-institutes/institute-of-information-systems/projects/medical-research-data-acquisition-platform-14092)", - "homepage": "http://w3id.org/medred/medred#", - "id": "lov.medred", - "name": "MedRed ontology: clinical data acquisition model", - "prefix": "medred", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences", - "health sciences" - ], - "uri_format": "http://w3id.org/medred/medred#$1" - }, - "lov.mexalgo": { - "authority": "lov", - "description": "MEX is an RDF vocabulary designed to facilitate interoperability between published machine learning experiments results on the Web. The mex-algo layer represents the algorithm information existing into a basic machine learning experiment.", - "homepage": "http://mex.aksw.org/mex-algo", - "id": "lov.mexalgo", - "name": "MEX Algorithm Ontology", - "prefix": "mexalgo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://mex.aksw.org/mex-algo#$1" - }, - "lov.mexcore": { - "authority": "lov", - "description": "MEX e um vocabulario modelado para facilitar a interoperabilidade entre resultados de experimentos de aprendizado de maquinas publicados na Web. A camada mex-core representa a principal informacao obtida de um experimento de aprendizado de maquina.", - "homepage": "http://mex.aksw.org/mex-core", - "id": "lov.mexcore", - "name": "MEX Core Vocabulary", - "prefix": "mexcore", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://mex.aksw.org/mex-core#$1" - }, - "lov.mexperf": { - "authority": "lov", - "description": "MEX e um vocabulario modelado para facilitar a interoperabilidade entre resultados de experimentos de aprendizado de maquinas publicados na Web. A camada mex-perf e o 3o. nivel na abordagem MEX para representar performances de algoritmos de aprendizado de maquinas", - "homepage": "http://mex.aksw.org/mex-perf", - "id": "lov.mexperf", - "name": "MEX Performance Ontology", - "prefix": "mexperf", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://mex.aksw.org/mex-perf#$1" - }, - "lov.mil": { - "authority": "lov", - "description": "The Muninn Military Ontology marks up information about military people, organizations and events.", - "homepage": "http://rdf.muninn-project.org/ontologies/military", - "id": "lov.mil", - "name": "Military Ontology Specification", - "prefix": "mil", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdf.muninn-project.org/ontologies/military#$1" - }, - "lov.mls": { - "authority": "lov", - "description": "ML-Schema is a collaborative, community effort with a mission to develop, maintain, and promote standard schemas for data mining and machine learning algorithms, datasets, and experiments", - "homepage": "http://www.w3.org/ns/mls", - "id": "lov.mls", - "name": "Machine Learning Schema", - "prefix": "mls", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/mls#$1" - }, - "lov.mo": { - "authority": "lov", - "description": "The Music Ontology Specification provides main concepts and properties fo describing music (i.e. artists, albums and tracks) on the Semantic Web", - "homepage": "http://purl.org/ontology/mo/", - "id": "lov.mo", - "name": "Music Ontology", - "prefix": "mo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/mo/$1" - }, - "lov.moac": { - "authority": "lov", - "description": "MOAC, the Management of a Crisis Vocabulary, is a lightweight vocabulary aiming to provide terms to enable practitioners to relate different \"things\" in crisis management activities together as Linked Data. The initial MOAC terms originated from the Inter Agency Standing Committee (IASC), Emergency Shelter Cluster in Haiti, UNOCHA 3W Who What Where Contact Database", - "homepage": "http://www.observedchange.com/moac/ns#", - "id": "lov.moac", - "name": "Management of a Crisis Vocabulary", - "prefix": "moac", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://observedchange.com/moac/ns#$1" - }, - "lov.moat": { - "authority": "lov", - "description": "An ontology that let users define relationships between Tag objects and URIs of Semantic Web resources", - "homepage": "http://moat-project.org/ns#", - "id": "lov.moat", - "name": "Meaning of a Tag Ontology", - "prefix": "moat", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://moat-project.org/ns#$1" - }, - "lov.mod": { - "authority": "lov", - "description": "This specification describes MOD, a metadata vocabulary to describe and publish ontologies", - "homepage": "http://www.isibang.ac.in/ns/mod", - "id": "lov.mod", - "name": "MOD: Metadata for Ontology Description and publication", - "prefix": "mod", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.isibang.ac.in/ns/mod#$1" - }, - "lov.modsci": { - "authority": "lov", - "description": "ModSci is a reference ontology for modelling different types of modern sciences and related entities, such as scientific discoveries, renowned scientists, instruments, phenomena ... etc.", - "homepage": "https://w3id.org/skgo/modsci#", - "id": "lov.modsci", - "name": "ModSci, Modern Science Ontology.", - "prefix": "modsci", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "https://w3id.org/skgo/modsci#$1" - }, - "lov.mrel": { - "authority": "lov", - "description": "MARC relators are defined as both RDF properties and SKOS concepts", - "homepage": "http://id.loc.gov/vocabulary/relators", - "id": "lov.mrel", - "name": "MARC Code List for Relators", - "prefix": "mrel", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://id.loc.gov/vocabulary/relators/$1" - }, - "lov.msm": { - "authority": "lov", - "description": "A simple RDF(S) ontology able to capture (part of) the semantics of both Web services and Web APIs", - "homepage": "http://iserve.kmi.open.ac.uk/ns/msm", - "id": "lov.msm", - "name": "Minimal Service Model", - "prefix": "msm", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://iserve.kmi.open.ac.uk/ns/msm#$1" - }, - "lov.msr": { - "authority": "lov", - "description": "The Measurement Ontology is an ontology in which measurements may be rendered", - "homepage": "http://www.telegraphis.net/ontology/measurement/measurement#", - "id": "lov.msr", - "name": "Measurement Ontology", - "prefix": "msr", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.telegraphis.net/ontology/measurement/measurement#$1" - }, - "lov.mtlo": { - "authority": "lov", - "description": "MarineTLO is a top-level ontology for the marine domain (also applicable to the terrestrial domain).", - "homepage": "http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl", - "id": "lov.mtlo", - "name": "MarineTLO Ontology", - "prefix": "mtlo", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl#$1" - }, - "lov.munc": { - "authority": "lov", - "description": "An OWL vocabulary for describing uncertainty metadata.", - "homepage": "http://ns.inria.fr/munc/", - "id": "lov.munc", - "name": "Meta-Uncertainty", - "prefix": "munc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/munc#$1" - }, - "lov.mus": { - "authority": "lov", - "description": "DOREMUS is an extension of the FRBRoo model for describing the music.", - "homepage": "http://data.doremus.org/ontology#", - "id": "lov.mus", - "name": "DOREMUS is an extension of the FRBRoo model for describing the music.", - "prefix": "mus", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://data.doremus.org/ontology#$1" - }, - "lov.music": { - "authority": "lov", - "description": "A vocabulary, or music ontology, to describe classical music and performances. Classes (categories) for musical works, events, instruments and performers, as well as related properties are defined. Make sure to distinguish musical works (e.g. Opera) from performance events (Opera_Event), or works (String_Quartette) from performer (StringQuartetEnsemble in this vocab), whose natural language terms are used interchangeblly. The present version experiments more precise model to describe a musical work, its representations (performances, scores, etc) and a musical event to present a representation (a concert). Includes 30 keys as individuals.", - "homepage": "http://www.kanzaki.com/ns/music", - "id": "lov.music", - "name": "Music Vocabulary", - "prefix": "music", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.kanzaki.com/ns/music#$1" - }, - "lov.muto": { - "authority": "lov", - "description": "The Modular and Unified Tagging Ontology (MUTO) is an ontology for tagging and folksonomies. It is based on a thorough review of earlier tagging ontologies and unifies core concepts in one consistent schema. It supports different forms of tagging, such as common, semantic, group, private, and automatic tagging, and is easily extensible.", - "homepage": "http://purl.org/muto/core", - "id": "lov.muto", - "name": "Modular Unified Tagging Ontology (MUTO)", - "prefix": "muto", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/muto/core#$1" - }, - "lov.mv": { - "authority": "lov", - "description": "Our goal is to significantly improve the data mobility between all stakeholders by providing a standardized vocabulary using Semantic Web technologies and ontologies. For the open vocabulary covering various mobility aspects we use RDF (Resource Description Framework) - a recommended specification of the World Wide Web Consortium (W3C) and the so-called lingua franca for the integration of data and web. We invite everyone who is interested to join our MobiVoc initiative and to participate in the development of the Open Mobility Vocabulary.", - "homepage": "http://schema.mobivoc.org/", - "id": "lov.mv", - "name": "MobiVoc: Open Mobility Vocabulary", - "prefix": "mv", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://schema.mobivoc.org/$1" - }, - "lov.mvco": { - "authority": "lov", - "description": "The Media Value Chain Ontology (MVCO) is an ontology for formalizing the representation of the Media Value Chain. It couples naturally with the MPEG-21 multimedia framework, and its standardization as Part 19 of this ISO/IEC standard is underway (at the editing time of this document).", - "homepage": "http://purl.oclc.org/NET/mvco.owl", - "id": "lov.mvco", - "name": "Media Value Chain Ontology", - "prefix": "mvco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.oclc.org/NET/mvco.owl#$1" - }, - "lov.nao": { - "authority": "lov", - "description": "The NEPOMUK Annotation Ontology is an ontology for annotation, providing vocabulary which is commonly required to annotate resources on the semantic desktop.", - "homepage": "http://www.semanticdesktop.org/ontologies/2007/08/15/nao", - "id": "lov.nao", - "name": "NEPOMUK Annotation Ontology", - "prefix": "nao", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1" - }, - "lov.nas": { - "authority": "lov", - "description": "Defines concepts related to the structure of the US National Airspace System (NAS)", - "homepage": "https://data.nasa.gov/ontologies/atmonto/NAS#", - "id": "lov.nas", - "name": "US National Airspace System (NAS) vocabulary", - "prefix": "nas", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://data.nasa.gov/ontologies/atmonto/NAS#$1" - }, - "lov.ncal": { - "authority": "lov", - "description": "The NEPOMUK Calendaring Ontology intends to provide vocabulary for describing calendaring data (events, tasks, journal entries) which is an important part of the body of information usually stored on a desktop. It is an adaptation of the ICALTZD ontology created by the W3C RDF Calendar Task Force of the Semantic Web Interest Group in the Semantic Web Activity.", - "homepage": "http://www.semanticdesktop.org/ontologies/2007/04/02/ncal", - "id": "lov.ncal", - "name": "NEPOMUK Calendar Ontology", - "prefix": "ncal", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.semanticdesktop.org/ontologies/2007/04/02/ncal#$1" - }, - "lov.nco": { - "authority": "lov", - "description": "NEPOMUK Contact Ontology describes contact information, common in many places on the desktop. It evolved from the VCARD specification (RFC 2426) and has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is much broader though. This document gives an overview of the classes, properties and intended use cases of the NCO ontology.", - "homepage": "http://www.semanticdesktop.org/ontologies/2007/03/22/nco", - "id": "lov.nco", - "name": "NEPOMUK Contact Ontology", - "prefix": "nco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1" - }, - "lov.nen2660": { - "authority": "lov", - "description": "Ontology which is a normative part of the Dutch NEN 2660-2 standard", - "homepage": "https://w3id.org/nen2660/", - "id": "lov.nen2660", - "name": "NEN 2660-2:2022 'Rules for information modelling of the built environment - Part 2: Practical configuration, extension and implementation of NEN 2660-1''", - "prefix": "nen2660", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/nen2660/def#$1" - }, - "lov.nfo": { - "authority": "lov", - "description": "Part of Nepomuk Information Element Ontology Framework", - "homepage": "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo", - "id": "lov.nfo", - "name": "NEPOMUK File Ontology", - "prefix": "nfo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#$1" - }, - "lov.ngeo": { - "authority": "lov", - "description": "A vocabulary for specifying geographical regions in RDF", - "homepage": "http://geovocab.org/geometry", - "id": "lov.ngeo", - "name": "NeoGeo Geometry Ontology", - "prefix": "ngeo", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://geovocab.org/geometry#$1" - }, - "lov.nie": { - "authority": "lov", - "description": "The Core Ontology of the NEPOMUK suite defines basic elements such as Data Object, Information Element ...", - "homepage": "http://www.semanticdesktop.org/ontologies/2007/01/19/nie", - "id": "lov.nie", - "name": "NEPOMUK Information Element Core Ontology", - "prefix": "nie", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.semanticdesktop.org/ontologies/2007/01/19/nie#$1" - }, - "lov.nif": { - "authority": "lov", - "description": "The NLP Interchange Format (NIF) is an RDF/OWL-based format that aims to achieve interoperability between Natural Language Processing (NLP) tools, language resources and annotations.", - "homepage": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#", - "id": "lov.nif", - "name": "NLP Interchange Format", - "prefix": "nif", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#$1" - }, - "lov.nlon": { - "authority": "lov", - "description": "This specification describes National Library of Korea Ontology vocaburaries using W3C's RDF and OWL technology.", - "homepage": "http://lod.nl.go.kr/ontology/", - "id": "lov.nlon", - "name": "National Library of Korea Ontology", - "prefix": "nlon", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://lod.nl.go.kr/ontology/$1" - }, - "lov.nno": { - "authority": "lov", - "description": "This is the Neural Network Ontology. Designed by the AIFB (http://www.aifb.kit.edu/web/Web_Science)", - "homepage": "https://w3id.org/nno/ontology", - "id": "lov.nno", - "name": "The Neural Network Ontology", - "prefix": "nno", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/nno/ontology#$1" - }, - "lov.noria": { - "authority": "lov", - "description": "The NORIA-O project is a data model for IT networks, events and operations information.\nThe ontology is developed using web technologies (e.g. RDF, OWL, SKOS) and is intended as a structure for realizing an IT Service Management (ITSM) Knowledge Graph (KG) for Anomaly Detection (AD) and Risk Management applications.\nThe model has been developed in collaboration with operational teams, and in connection with third parties linked vocabularies.\n\nAlignment with third parties vocabularies is implemented on a per class or per property basis when relevant (e.g. with `rdfs:subClassOf`, `owl:equivalentClass`).\nDirections for direct instanciation of these vocabularies are provided for cases where implementing a class/property alignment is redundant.\nAlignment holds for the following vocabulary releases:\n- [BBO](https://hal.archives-ouvertes.fr/hal-02365012/) 1.0.0\n- [BOT](https://w3id.org/bot/) 0.3.2\n- [DevOps-Infra](https://oeg-upm.github.io/devops-infra/) 1.0.0\n- [FOLIO](https://github.com/IBCNServices/Folio-Ontology) 1.0.0\n- [ORG](https://www.w3.org/TR/vocab-org/) 0.8\n- [PEP](https://w3id.org/pep/) 1.1\n- [SEAS](https://w3id.org/seas/) 1.1\n- [SLOGERT](https://sepses.ifs.tuwien.ac.at/ns/log/index-en.html) 1.1.0\n- [UCO](https://github.com/ucoProject/uco) Release-0.8.0", - "homepage": "https://w3id.org/noria/ontology/", - "id": "lov.noria", - "name": "The NORIA Ontology", - "prefix": "noria", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/noria/ontology/$1" - }, - "lov.np": { - "authority": "lov", - "description": "The nanopub ontology", - "homepage": "http://www.nanopub.org/nschema", - "id": "lov.np", - "name": "Nano publication ontology", - "prefix": "np", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.nanopub.org/nschema#$1" - }, - "lov.npg": { - "authority": "lov", - "description": "The Core Ontology is a formal model providing definitions for the key concepts of interest to content publishing at Macmillan Science and Education.", - "homepage": "http://ns.nature.com/terms/", - "id": "lov.npg", - "name": "Nature.com Core Ontology", - "prefix": "npg", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.nature.com/terms/$1" - }, - "lov.nrl": { - "authority": "lov", - "description": "Designed on top of RDF, it addresses certain limitations on the part of RDF/S. In particular it includes support for Named Graphs", - "homepage": "http://www.semanticdesktop.org/ontologies/2007/08/15/nrl", - "id": "lov.nrl", - "name": "NEPOMUK Representational Language", - "prefix": "nrl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.semanticdesktop.org/ontologies/2007/08/15/nrl#$1" - }, - "lov.nrv": { - "authority": "lov", - "description": "An OWL vocabulary for describing normative requirements.", - "homepage": "http://ns.inria.fr/nrv", - "id": "lov.nrv", - "name": "Normative Requirements Vocabulary", - "prefix": "nrv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/nrv#$1" - }, - "lov.nsl": { - "authority": "lov", - "description": "The News Storyline Ontology is a generic model for describing and organising the stories news organisations tell. The ontology is intended to be flexible to support any given news or media publisher's approach to handling news stories. At the heart of the ontology, is the concept of Storyline.", - "homepage": "http://purl.org/ontology/storyline", - "id": "lov.nsl", - "name": "A News Storyline Ontology", - "prefix": "nsl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/storyline/$1" - }, - "lov.ntag": { - "authority": "lov", - "description": "NiceTag Ontology is an ontology which describes as generally as possible tags or rather tag actions understood as a speech acts occurring on the Web", - "homepage": "http://ns.inria.fr/nicetag/2010/09/09/voc", - "id": "lov.ntag", - "name": "Nice Tag Ontology", - "prefix": "ntag", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/nicetag/2010/09/09/voc#$1" - }, - "lov.oa": { - "authority": "lov", - "description": "The Open Annotation Core Data Model specifies an interoperable framework for creating associations between related resources, annotations, using a methodology that conforms to the Architecture of the World Wide Web. This ontology is a non-normative OWL formalization of the textual OA specification at http://www.openannotation.org/spec/core/20130208/index.html", - "homepage": "http://www.w3.org/ns/oa#", - "id": "lov.oa", - "name": "Open Annotation Data Model", - "prefix": "oa", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/oa#$1" - }, - "lov.oad": { - "authority": "lov", - "description": "An ontology for the description of archival data (OAD, \u201cOntology of Archival Description\u201d) using the Web Ontology Language (OWL). This ontology represents the classes and properties needed to expose the archival resources as linked data.", - "homepage": "http://culturalis.org/oad#", - "id": "lov.oad", - "name": "Ontology for archival description", - "prefix": "oad", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://culturalis.org/oad#$1" - }, - "lov.oae": { - "authority": "lov", - "description": "The Open NEE Model defines an extension of the Open Annotation Data Model (http://www.openannotation.org/spec/core) that allows describing in RDF the result of a Named Entity Extraction (NEE) process, enabling thereby an application to run advanced (SPARQL) queries over the annotated data. The model also exploits the Open NEE Configuration Model (http://www.ics.forth.gr/isl/oncm) for relating the output of a NEE process with an applied configuration (serving provenance information to the output of the entire NEE process).", - "homepage": "http://www.ics.forth.gr/isl/oae/core", - "id": "lov.oae", - "name": "Open NEE Model", - "prefix": "oae", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ics.forth.gr/isl/oae/core#$1" - }, - "lov.oan": { - "authority": "lov", - "description": "Description of French National Assembly", - "homepage": "http://data.lirmm.fr/ontologies/oan", - "id": "lov.oan", - "name": "Ontologie de l'Assembl\u00e9e Nationale", - "prefix": "oan", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://data.lirmm.fr/ontologies/oan/$1" - }, - "lov.obo": { - "authority": "lov", - "description": "The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.", - "homepage": "http://purl.obolibrary.org/obo/obi.owl", - "id": "lov.obo", - "name": "Ontology for Biomedical Investigation", - "prefix": "obo", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences", - "health sciences" - ], - "uri_format": "http://purl.obolibrary.org/obo/$1" - }, - "lov.obsm": { - "authority": "lov", - "description": "This is a taxonomy of some observation methods. It is incomplete", - "homepage": "http://rdf.geospecies.org/methods/observationMethod.rdf", - "id": "lov.obsm", - "name": "Observation Method Ontology", - "prefix": "obsm", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://rdf.geospecies.org/methods/observationMethod#$1" - }, - "lov.obws": { - "authority": "lov", - "description": "Ontology including the content ontology design pattern for modelling objects with states.", - "homepage": "http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl", - "id": "lov.obws", - "name": "Object with states ontology", - "prefix": "obws", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl#$1" - }, - "lov.oc": { - "authority": "lov", - "description": "OntoMedia (Ontology for Media) has been designed to describe the interactions occurring in multimedia.", - "homepage": "http://contextus.net/ontology/ontomedia/core/expression#", - "id": "lov.oc", - "name": "OntoMedia Core", - "prefix": "oc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://contextus.net/ontology/ontomedia/core/expression#$1" - }, - "lov.ocd": { - "authority": "lov", - "description": "L'ontologia Camera dei deputati \u00e8 stata creata per descrivere tutte le risorse (persone, eventi, documenti) sia storiche che correnti, connesse alla Camera e alla sua attivit\u00e0", - "homepage": "http://dati.camera.it/ocd/", - "id": "lov.ocd", - "name": "Ontologia Camera dei Deputati", - "prefix": "ocd", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://dati.camera.it/ocd/$1" - }, - "lov.ocds": { - "authority": "lov", - "description": "The OCDS is a data model that aims at structuring and publishing contracting data (tenders, procurements, awards, transactions, etc.). It got international adoption and is one of the leading models in this domain.", - "homepage": "http://purl.org/onto-ocds/ocds", - "id": "lov.ocds", - "name": "Schema for an Open Contracting Release (OCDS)", - "prefix": "ocds", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "http://purl.org/onto-ocds/ocds#$1" - }, - "lov.odapp": { - "authority": "lov", - "description": "This is an early version of a vocabulary to describe \"open data applications\" i.e. applications built using open data. Examples of such applications are listed on government open data catalogues and participant on open data competitions.", - "homepage": "http://vocab.deri.ie/odapp", - "id": "lov.odapp", - "name": "Open Data Applications Vocabulary", - "prefix": "odapp", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://vocab.deri.ie/odapp#$1" - }, - "lov.odapps": { - "authority": "lov", - "description": "odapps is an RDF vocabulary defined to facilitate the description of Open-Data-based ideas and applications published on the Web.", - "homepage": "http://semweb.mmlab.be/ns/odapps", - "id": "lov.odapps", - "name": "The vocabulary for (L)OD ideas and applications", - "prefix": "odapps", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semweb.mmlab.be/ns/odapps#$1" - }, - "lov.odpart": { - "authority": "lov", - "description": "The basic participation pattern, without temporal indexing. It clones equivalent elements from DOLCE-UltraLite.", - "homepage": "http://www.ontologydesignpatterns.org/cp/owl/participation.owl", - "id": "lov.odpart", - "name": "Ontology Design Pattern Participation", - "prefix": "odpart", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/cp/owl/participation.owl#$1" - }, - "lov.odrl": { - "authority": "lov", - "description": "The Open Digital Rights Language (ODRL) provides flexible and interoperable mechanisms to support transparent and innovative use of digital content in publishing, distribution, and consumption of of digital media across all sectors and communities. The ODRL Policy model is broad enough to support traditional rights expressions for commercial transaction, open access expressions for publicly distributed content, and privacy expressions for social media.", - "homepage": "http://www.w3.org/ns/odrl/2/", - "id": "lov.odrl", - "name": "The Open Digital Rights Language (ODRL) Ontology", - "prefix": "odrl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/odrl/2/$1" - }, - "lov.odrs": { - "authority": "lov", - "description": "A vocabulary that supports the publication of Open Data by providing the means to capture machine-readable \"rights statements\", e.g. the licensing information, copyright notices and attribution requirements that are associated with the publication and re-use of a dataset.", - "homepage": "http://schema.theodi.org/odrs", - "id": "lov.odrs", - "name": "Open Data Rights Statement Vocabulary", - "prefix": "odrs", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://schema.theodi.org/odrs#$1" - }, - "lov.odv": { - "authority": "lov", - "description": "Extension of data cube for civil service junior posts", - "homepage": "http://reference.data.gov.uk/def/organogram", - "id": "lov.odv", - "name": "Organogram Data Vocabulary", - "prefix": "odv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://reference.data.gov.uk/def/organogram/$1" - }, - "lov.oecc": { - "authority": "lov", - "description": "Creative Commons Ontology, extending RDF file at http://creativecommons.org/schema.rdf", - "homepage": "http://www.oegov.org/core/owl/cc", - "id": "lov.oecc", - "name": "Extended Creative Commons Ontology", - "prefix": "oecc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.oegov.org/core/owl/cc#$1" - }, - "lov.of": { - "authority": "lov", - "description": "Ontology for Open Fridge project", - "homepage": "http://owlrep.eu01.aws.af.cm/fridge", - "id": "lov.of", - "name": "Open Fridge vocabulary", - "prefix": "of", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://owlrep.eu01.aws.af.cm/fridge#$1" - }, - "lov.ofo": { - "authority": "lov", - "description": "The aim of the Occupant Feedback Ontology is to semantically describe passive and active occupant feedback and to enable integration of this feedback with linked building data.", - "homepage": "https://w3id.org/ofo#", - "id": "lov.ofo", - "name": "Occupant Feedback Ontology", - "prefix": "ofo", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/ofo#$1" - }, - "lov.ofrd": { - "authority": "lov", - "description": "Vocabulary to describe fridges and freezers", - "homepage": "http://purl.org/opdm/refrigerator#", - "id": "lov.ofrd", - "name": "Fridge and Freezer Vocabulary", - "prefix": "ofrd", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/opdm/refrigerator#$1" - }, - "lov.og": { - "authority": "lov", - "description": "The Open Graph protocol enables any web page to become a rich object in a social graph. For instance, this is used on Facebook to enable any web page to have the same functionality as a Facebook Page.", - "homepage": "http://ogp.me/ns", - "id": "lov.og", - "name": "Open Graph Protocol Vocabulary", - "prefix": "og", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://ogp.me/ns#$1" - }, - "lov.oh": { - "authority": "lov", - "description": "A vocabulary to describe opening hours using calendars (recommended: iCal, RDFCal or schema.org) published on the Web.", - "homepage": "http://semweb.mmlab.be/ns/oh", - "id": "lov.oh", - "name": "The Opening Hours vocabulary", - "prefix": "oh", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semweb.mmlab.be/ns/oh#$1" - }, - "lov.olca": { - "authority": "lov", - "description": "A vocabulary defining annotations enabling loose coupling between classes and properties in ontologies. Those annotations define with some accuracy the expected use of properties, in particular across vocabularies, without the formal constraints entailed by the use of OWL or RDFS constructions", - "homepage": "https://w3id.org/vocab/olca", - "id": "lov.olca", - "name": "Ontology Loose Coupling Annotation", - "prefix": "olca", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/vocab/olca#$1" - }, - "lov.olo": { - "authority": "lov", - "description": "The Ordered List Ontology Specification provides basic concepts and properties for describing ordered lists as semantic graphs.", - "homepage": "http://purl.org/ontology/olo/core#", - "id": "lov.olo", - "name": "Ordered List Ontology", - "prefix": "olo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/olo/core#$1" - }, - "lov.om": { - "authority": "lov", - "description": "An OWL representation of the Observation Schema described in clause 6 of ISO 19156:2011 Geographic Information - Observations and Measurements", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/observation", - "id": "lov.om", - "name": "ISO 19156 Observation Model", - "prefix": "om", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/observation#$1" - }, - "lov.omg": { - "authority": "lov", - "description": "The Ontology for Managing Geometry (OMG) is an ontology for describing geometry descriptions of objects. It provides means to support the application of multiple geometry descriptions of the same object as well as the description of the geometry evolution over time. The OMG is based the concepts introduced in the Ontology for Property Management (OPM) ontology. \n\nThis ontology was created within the research project SCOPE, funded by the German Federal Ministry for Economic Affairs and Energy (BMWi).\n\nThe initial version of the ontology (v0.0.1) is documented in:\nWagner, Anna, Bonduel, Mathias, Pauwels, Pieter & R\u00fcppel, Uwe(2019). Relating Geometry Descroptions to its Derivatives on the Web. In Proceedings of the European Conference on Computing in Construction (EC3 2019). Chania, Greece.", - "homepage": "https://w3id.org/omg", - "id": "lov.omg", - "name": "OMG: Ontology for Managing Geometry", - "prefix": "omg", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "https://w3id.org/omg#$1" - }, - "lov.oml": { - "authority": "lov", - "description": "An OWL representation of the Observation Schema described in clauses 7-8 of ISO 19156:2011 Geographic Information - Observations and Measurements / OGC Abstract Specification - Topic 20.", - "homepage": "http://def.seegrid.csiro.au/ontology/om/om-lite", - "id": "lov.oml", - "name": "OWL for Observations", - "prefix": "oml", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://def.seegrid.csiro.au/ontology/om/om-lite#$1" - }, - "lov.omn": { - "authority": "lov", - "description": "This ontology defines the most abstract concepts and properties that are needed to semantically manage resource within federated infrastructures", - "homepage": "http://open-multinet.info/ontology/omn", - "id": "lov.omn", - "name": "Open-Multinet Upper Ontology", - "prefix": "omn", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://open-multinet.info/ontology/omn#$1" - }, - "lov.omnfed": { - "authority": "lov", - "description": "This ontology defines concepts related to federation of internet infrastructures.", - "homepage": "http://open-multinet.info/ontology/omn-federation", - "id": "lov.omnfed", - "name": "Open-Multinet Upper Federation Ontology", - "prefix": "omnfed", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://open-multinet.info/ontology/omn-federation#$1" - }, - "lov.omnlc": { - "authority": "lov", - "description": "This ontology defines generic concepts related to the life cycle of resource or service.", - "homepage": "http://open-multinet.info/ontology/omn-lifecycle", - "id": "lov.omnlc", - "name": "Open-Multinet Upper Lifecycle Ontology", - "prefix": "omnlc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://open-multinet.info/ontology/omn-lifecycle#$1" - }, - "lov.onc": { - "authority": "lov", - "description": "The Open NEE Configuration Model defines a Linked Data-based model for describing a configuration supported by a Named Entity Extraction (NEE) service. It is based on the model proposed in \"Configuring Named Entity Extraction through Real-Time Exploitation of Linked Data\" (http://dl.acm.org/citation.cfm?doid=2611040.2611085) for configuring such services, and allows a NEE service to describe and publish as Linked Data its entity mining capabilities, but also to be dynamically configured.", - "homepage": "http://www.ics.forth.gr/isl/oncm/core", - "id": "lov.onc", - "name": "Open NEE Configuration Model", - "prefix": "onc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ics.forth.gr/isl/oncm/core#$1" - }, - "lov.ont": { - "authority": "lov", - "description": "Vocabulary to define some annotation properties as subproperties of common Dublin Core terms", - "homepage": "http://purl.org/net/ns/ontology-annot", - "id": "lov.ont", - "name": "Ontology annotation DLiser vocabulary", - "prefix": "ont", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/ns/ontology-annot#$1" - }, - "lov.ontolex": { - "authority": "lov", - "description": "A model for the representation of lexical information relative to ontologies. Core module.", - "homepage": "http://www.w3.org/ns/lemon/ontolex", - "id": "lov.ontolex", - "name": "Lexicon Model for Ontologies - Core", - "prefix": "ontolex", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/lemon/ontolex#$1" - }, - "lov.ontopic": { - "authority": "lov", - "description": "An ontology of topics as used in thesauri, subject directories, etc.", - "homepage": "http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl", - "id": "lov.ontopic", - "name": "Ontopic Ontology", - "prefix": "ontopic", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl#$1" - }, - "lov.ontosec": { - "authority": "lov", - "description": "This ontology covers the domain of security in the field of mobile applications.", - "homepage": "http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl", - "id": "lov.ontosec", - "name": "Ontology Security", - "prefix": "ontosec", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl#$1" - }, - "lov.ontouml": { - "authority": "lov", - "description": "A reference implementation of the OntoUML metamodel in OWL.", - "homepage": "https://w3id.org/ontouml", - "id": "lov.ontouml", - "name": "OntoUML Metamodel Vocabulary", - "prefix": "ontouml", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/ontouml#$1" - }, - "lov.onyx": { - "authority": "lov", - "description": "Onyx is a vovabulary designed designed to annotate and describe the emotions expressed by user-generated content on the web or in particular Information Systems.", - "homepage": "http://www.gsi.dit.upm.es/ontologies/onyx/ns", - "id": "lov.onyx", - "name": "Onyx Emotion Ontology", - "prefix": "onyx", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.gsi.dit.upm.es/ontologies/onyx/ns#$1" - }, - "lov.oo": { - "authority": "lov", - "description": "This vocabulary provides supplementary terms for organisations wishing to publish open data about themselves.", - "homepage": "http://purl.org/openorg/", - "id": "lov.oo", - "name": "Open Organisations", - "prefix": "oo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/openorg/$1" - }, - "lov.op": { - "authority": "lov", - "description": "A general purpose ontology for observable properties. The ontology supports description of both qualitative and quantitative properties. The allowed scale or units of measure may be specified. A property may be linked to substances-or-taxa and to features or realms, if they play a role in the definition.", - "homepage": "http://environment.data.gov.au/def/op", - "id": "lov.op", - "name": "Observable properties", - "prefix": "op", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://environment.data.gov.au/def/op#$1" - }, - "lov.open311": { - "authority": "lov", - "description": "Open 311 Ontology\n\nThis ontology generalizes the concepts that appear in 311 open data files published by several cities (Toronto, New York, Chicago, Vancouver) across North America. It provides a generis representation of 311 data that other cities can map their data onto and be used as a means of achieving interoperability.", - "homepage": "http://ontology.eil.utoronto.ca/open311.owl", - "id": "lov.open311", - "name": "Open 311 Ontology: An Ontology for publishing a city's non-emergency events.", - "prefix": "open311", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontology.eil.utoronto.ca/open311#$1" - }, - "lov.opm": { - "authority": "lov", - "description": "The Ontology for Property Management (OPM) extends the concepts introduced in the Smart Energy Aware Systems (SEAS) Evaluations ontology.", - "homepage": "https://w3id.org/opm", - "id": "lov.opm", - "name": "OPM: Ontology for Property Management", - "prefix": "opm", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/opm#$1" - }, - "lov.opmo": { - "authority": "lov", - "description": "The Open Provenance Model is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any 'thing', whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.", - "homepage": "http://openprovenance.org/model/opmo", - "id": "lov.opmo", - "name": "Open Provenance Model", - "prefix": "opmo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://openprovenance.org/model/opmo#$1" - }, - "lov.opmv": { - "authority": "lov", - "description": "OPMV, the Open Provenance Model Vocabulary, provides terms to enable practitioners of data publishing to publish their data responsibly.", - "homepage": "http://purl.org/net/opmv/ns#", - "id": "lov.opmv", - "name": "Open Provenance Model Vocabulary", - "prefix": "opmv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/opmv/ns#$1" - }, - "lov.opmw": { - "authority": "lov", - "description": "OPMW is a OPMV profile to model the executions and definitions of scientific workflows.", - "homepage": "http://www.opmw.org/ontology/", - "id": "lov.opmw", - "name": "The OPMW Ontology", - "prefix": "opmw", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.opmw.org/ontology/$1" - }, - "lov.opo": { - "authority": "lov", - "description": "Ontology for representing Online Presence", - "homepage": "http://online-presence.net/opo/ns#", - "id": "lov.opo", - "name": "Online Presence Ontology", - "prefix": "opo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://online-presence.net/opo/ns#$1" - }, - "lov.opus": { - "authority": "lov", - "description": "This file specifies in RDF Schema format the classes and properties for SwetoDblp. These classes and properties are based on the internal LSDIS Library portal engine.", - "homepage": "http://lsdis.cs.uga.edu/projects/semdis/opus#", - "id": "lov.opus", - "name": "SwetoDblp Ontology of Computer Science Publications", - "prefix": "opus", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://lsdis.cs.uga.edu/projects/semdis/opus#$1" - }, - "lov.orca": { - "authority": "lov", - "description": "orca, the Ontology of Reasoning, Certainty and Attribution, is an ontology for characterizing the certainty of information, how it is known, and its source", - "homepage": "http://vocab.deri.ie/orca", - "id": "lov.orca", - "name": "orca, the Ontology of Reasoning, Certainty and Attribution", - "prefix": "orca", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.deri.ie/orca#$1" - }, - "lov.ore": { - "authority": "lov", - "description": "Open Archives Initiative Object Reuse and Exchange (OAI-ORE) defines standards for the description and exchange of aggregations of Web resources.", - "homepage": "http://www.openarchives.org/ore/terms/", - "id": "lov.ore", - "name": "The OAI ORE terms vocabulary", - "prefix": "ore", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.openarchives.org/ore/terms/$1" - }, - "lov.org": { - "authority": "lov", - "description": "Vocabulary for describing organizational structures, specializable to a broad variety of types of organization.", - "homepage": "http://www.w3.org/ns/org#", - "id": "lov.org", - "name": "Core organization ontology", - "prefix": "org", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/org#$1" - }, - "lov.orges": { - "authority": "lov", - "description": "Extensi\u00f3n de la ontolog\u00eda de Organizaciones para adecuarla al Directorio Com\u00fan de entidades p\u00fablicas en Espa\u00f1a.", - "homepage": "http://datos.gob.es/def/sector-publico/organizacion#", - "id": "lov.orges", - "name": "Ontology about Spanish public organizations", - "prefix": "orges", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://datos.gob.es/def/sector-publico/organizacion#$1" - }, - "lov.osadm": { - "authority": "lov", - "description": "An ontology describing the administrative and voting area geography of Great Britain", - "homepage": "http://data.ordnancesurvey.co.uk/ontology/admingeo/", - "id": "lov.osadm", - "name": "The administrative geography and civil voting area ontology", - "prefix": "osadm", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://data.ordnancesurvey.co.uk/ontology/admingeo/$1" - }, - "lov.osgeom": { - "authority": "lov", - "description": "A provisional small geometry vocabulary used by Ordnance Survey vocabularies and datasets. Likely to change when some standard way of representing geometries in RDF is agreed.", - "homepage": "http://data.ordnancesurvey.co.uk/ontology/geometry/", - "id": "lov.osgeom", - "name": "Ordnance Survey Geometry Ontology", - "prefix": "osgeom", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://data.ordnancesurvey.co.uk/ontology/geometry/$1" - }, - "lov.oslc": { - "authority": "lov", - "description": "The Open Services for Lifecycle Collaboration (OSLC) initiative is creating a family of web services specifications for products, services and other tools that support all phases of the software and product lifecycle. This OSLC Core Specification sets out the common features that every OSLC Service can be expected to support", - "homepage": "http://open-services.net/ns/core#", - "id": "lov.oslc", - "name": "OSLC Core Vocabulary", - "prefix": "oslc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://open-services.net/ns/core#$1" - }, - "lov.oslo": { - "authority": "lov", - "description": "This version of the OSLO Exchange Standard provides a minimum set of classes and properties for describing a natural person, i.e. the individual as opposed to any role they may play in society or the relationships they have to other people, organisations and property; all of which contribute significantly to the broader concept of identity. The vocabulary is closely integrated with the Person, Organisation and Location Vocabularies published by the W3C in the Gov Linked Data Project. The OSLO specification is the result of a public-private partnership initiated by V-ICT-OR, the Flemish Organization for ICT in Local Government.", - "homepage": "http://purl.org/oslo/ns/localgov", - "id": "lov.oslo", - "name": "OSLO Exchange Standard", - "prefix": "oslo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/oslo/ns/localgov#$1" - }, - "lov.osp": { - "authority": "lov", - "description": "Ontologie d'une organisation publique, plus particuli\u00e8rement d'un tribunal, d'une organisation internationale ou d'un pays.", - "homepage": "http://data.lirmm.fr/ontologies/osp", - "id": "lov.osp", - "name": "Ontologie du Service Public", - "prefix": "osp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.lirmm.fr/ontologies/osp#$1" - }, - "lov.osr": { - "authority": "lov", - "description": "The OntoMedia Space representation denotes areas of landscape. Expands on the AKT location ontology", - "homepage": "http://contextus.net/ontology/ontomedia/core/space#", - "id": "lov.osr", - "name": "OntoMedia Space Representation", - "prefix": "osr", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://contextus.net/ontology/ontomedia/core/space#$1" - }, - "lov.osspr": { - "authority": "lov", - "description": "An ontology describing basic spatial relations.", - "homepage": "http://data.ordnancesurvey.co.uk/ontology/spatialrelations/", - "id": "lov.osspr", - "name": "Spatial Relations Ontology", - "prefix": "osspr", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://data.ordnancesurvey.co.uk/ontology/spatialrelations/$1" - }, - "lov.ostop": { - "authority": "lov", - "description": "The general purpose of this ontology is to provide a library of high level concepts that are used by the other modules within the whole OS Topographic ontology. The ontology also describes the relationships and instances common to more than one module.", - "homepage": "http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl", - "id": "lov.ostop", - "name": "Ordnance Survey Topography Ontology", - "prefix": "ostop", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl#$1" - }, - "lov.otl": { - "authority": "lov", - "description": "This ontology provides the terms necessary to describe the status of traffic lights.", - "homepage": "https://w3id.org/opentrafficlights", - "id": "lov.otl", - "name": "The Open Traffic Lights ontology", - "prefix": "otl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/opentrafficlights#$1" - }, - "lov.oum": { - "authority": "lov", - "description": "The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions.", - "homepage": "http://www.ontology-of-units-of-measure.org/resource/om-2/", - "id": "lov.oum", - "name": "Ontology of units of Measure (OM)", - "prefix": "oum", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1" - }, - "lov.ov": { - "authority": "lov", - "description": "OpenVocab is a community maintained vocabulary intended for use on the Semantic Web, ideal for properties and classes that don't warrant the effort of creating or maintaining a full schema. OpenVocab allows anyone to create and modify vocabulary terms using their web browser.", - "homepage": "http://open.vocab.org/terms", - "id": "lov.ov", - "name": "OpenVocab", - "prefix": "ov", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://open.vocab.org/terms/$1" - }, - "lov.owl": { - "authority": "lov", - "description": "This ontology partially describes the built-in classes and properties that together form the basis of the RDF/XML syntax of OWL 2.", - "homepage": "http://www.w3.org/2002/07/owl", - "id": "lov.owl", - "name": "The OWL 2 Schema vocabulary", - "prefix": "owl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2002/07/owl#$1" - }, - "lov.p-plan": { - "authority": "lov", - "description": "The Ontology for Provenance and Plans (P-Plan) is an extension of the PROV-O ontology [PROV-O] created to represent the plans that guided the execution of scientific processes. P-Plan describes how the plans are composed and their correspondence to provenance records that describe the execution itself.", - "homepage": "http://purl.org/net/p-plan#", - "id": "lov.p-plan", - "name": "The P-PLAN Ontology", - "prefix": "p-plan", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/p-plan#$1" - }, - "lov.parl": { - "authority": "lov", - "description": "An ontology of UK Parliament", - "homepage": "http://reference.data.gov.uk/def/parliament", - "id": "lov.parl", - "name": "Parliament Ontology", - "prefix": "parl", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences" - ], - "uri_format": "http://reference.data.gov.uk/def/parliament/$1" - }, - "lov.part": { - "authority": "lov", - "description": "The participation ontology is a simple model for describing the roles that people play within groups. It is intended that specific domains will create subclasses of roles within their own areas of expertise.", - "homepage": "http://purl.org/vocab/participation/schema", - "id": "lov.part", - "name": "Participation Schema", - "prefix": "part", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocab/participation/schema#$1" - }, - "lov.passim": { - "authority": "lov", - "description": "Description of the operation of a transport information service", - "homepage": "http://data.lirmm.fr/ontologies/passim", - "id": "lov.passim", - "name": "PASSIM ontology", - "prefix": "passim", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.lirmm.fr/ontologies/passim#$1" - }, - "lov.pat": { - "authority": "lov", - "description": "The Patch Request Ontology provides a schema to describe desired changes in Linked Data. By wrapping the Graph Update Ontology (guo) patch requests can be formulated to add, modify or delete particular triples (or subgraphs) within a dataset.", - "homepage": "http://purl.org/hpi/patchr#", - "id": "lov.pat", - "name": "Patch Request Ontology", - "prefix": "pat", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/hpi/patchr#$1" - }, - "lov.pattern": { - "authority": "lov", - "description": "An ontology defining formally patterns for segmenting a document into atomic components, in order to be manipulated independently and re-flowed in different contexts.", - "homepage": "http://www.essepuntato.it/2008/12/pattern", - "id": "lov.pattern", - "name": "The Pattern Ontology", - "prefix": "pattern", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.essepuntato.it/2008/12/pattern#$1" - }, - "lov.pav": { - "authority": "lov", - "description": "PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.", - "homepage": "http://purl.org/pav/", - "id": "lov.pav", - "name": "Provenance, Authoring and Versioning", - "prefix": "pav", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/pav/$1" - }, - "lov.pay": { - "authority": "lov", - "description": "Vocabulary for representing payments, such as government expenditures, using the data cube representation.", - "homepage": "http://reference.data.gov.uk/def/payment#", - "id": "lov.pay", - "name": "Payments ontology", - "prefix": "pay", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "http://reference.data.gov.uk/def/payment#$1" - }, - "lov.pbo": { - "authority": "lov", - "description": "The Play Back Ontology specification provides basic concepts and properties for describing concepts that are related to the play back domain.", - "homepage": "http://purl.org/ontology/pbo/core#", - "id": "lov.pbo", - "name": "Play Back Ontology", - "prefix": "pbo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/pbo/core#$1" - }, - "lov.pc": { - "authority": "lov", - "description": "Ontologie pro ve\u0159ejn\u00e9 zak\u00e1zky poskytuje vyjad\u0159ovac\u00ed prost\u0159edky pro popis zak\u00e1zek zad\u00e1van\u00fdch institucemi ve\u0159ejn\u00e9 spr\u00e1vy.", - "homepage": "http://purl.org/procurement/public-contracts", - "id": "lov.pc", - "name": "Public Contracts Ontology", - "prefix": "pc", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "http://purl.org/procurement/public-contracts#$1" - }, - "lov.pdo": { - "authority": "lov", - "description": "The Project Documents Ontology models the inherent structure and concepts of various documents in a project-specific setting, like meeting minutes, status reports etc.", - "homepage": "http://vocab.deri.ie/pdo", - "id": "lov.pdo", - "name": "Project Documents Ontology", - "prefix": "pdo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ontologies.smile.deri.ie/pdo#$1" - }, - "lov.peco": { - "authority": "lov", - "description": "This ontology defines a vocabulary for describing provenance traces of carbon emission calculations by capturing the quantifiable measurements of carbon emission sources used by some activities (e.g., electricity used by a machinery to produce a product, petrol used to make a car journey, etc.) and emission conversion factors used to estimate the carbon emissions produced by these. In addition, the ontology provides the ability to capture various data transformations that occurred before energy estimates may be used with relevant conversion factors. For example, sensors may provide raw readings about a water flow of an irrigation rig in an agri-food operation which is then used as a proxy to estimate the total volume of fertilisers used.", - "homepage": "https://w3id.org/peco", - "id": "lov.peco", - "name": "The Provenance of Emission Calculations Ontology", - "prefix": "peco", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/peco#$1" - }, - "lov.pep": { - "authority": "lov", - "description": "The process execution ontology is a proposal for a simple extension of both the [W3C Semantic Sensor Network](https://www.w3.org/TR/vocab-ssn/) and the [Semantic Actuator Network](https://www.irit.fr/recherches/MELODI/ontologies/SAN.owl) ontology cores.", - "homepage": "https://w3id.org/pep/", - "id": "lov.pep", - "name": "Process Execution ontology.", - "prefix": "pep", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/pep/$1" - }, - "lov.person": { - "authority": "lov", - "description": "The Person Core Vocabulary provides a minimum set of classes and properties for describing a natural person", - "homepage": "http://www.w3.org/ns/person", - "id": "lov.person", - "name": "ISA Programme Person Core Vocabulary", - "prefix": "person", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/person#$1" - }, - "lov.pext": { - "authority": "lov", - "description": "Upper-level ontology with extensions to handle Linked Open Data (LOD)", - "homepage": "http://www.ontotext.com/proton/protonext", - "id": "lov.pext", - "name": "PROTON Extent module", - "prefix": "pext", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontotext.com/proton/protonext#$1" - }, - "lov.phdd": { - "authority": "lov", - "description": "Physical data description (PHDD) of existing or published data (tables) in a rectangular format. The data could be either represented in records with character-separated values (CSV) or in records with fixed length.", - "homepage": "http://rdf-vocabulary.ddialliance.org/phdd", - "id": "lov.phdd", - "name": "Physical Data Description", - "prefix": "phdd", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdf-vocabulary.ddialliance.org/phdd#$1" - }, - "lov.pico": { - "authority": "lov", - "description": "The PICO ontology provides a machine accessible version of the PICO framework. It essentially provides a model for describing evidence in a consistent way. The model allows the specifying of complex populations, detailed interventions and their comparisons as well as the outcomes considered. The PICO ontology was originally designed to model the questions asked and answered in Cochrane's systematic reviews. As a leader in the field of evidence based healthcare Cochrane uses the PICO model when framing and publishing evidence based questions. The PICO model is widely adopted for describing healthcare evidence, furthermore is equally applicable in other evidence-based domains. It essentially provides a model for describing evidence in a consistent way.", - "homepage": "http://data.cochrane.org/ontologies/pico/", - "id": "lov.pico", - "name": "Cochrane PICO Ontology", - "prefix": "pico", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://data.cochrane.org/ontologies/pico/$1" - }, - "lov.pimsii": { - "authority": "lov", - "description": "The Physicalistic Interpretation of Modelling and Simulation - Interoperability Infrastructure (PIMS-II) is a mid-level ontology with a focus on documenting cognitive processes and epistemic metadata", - "homepage": "http://www.molmod.info/semantics/pims-ii.ttl", - "id": "lov.pimsii", - "name": "Physicalistic Interpretation of Modelling and Simulation - Interoperability Infrastructure (PIMS-II)", - "prefix": "pimsii", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.molmod.info/semantics/pims-ii.ttl#$1" - }, - "lov.place": { - "authority": "lov", - "description": "The Places Ontology is a simple lightweight ontology for describing places of geographic interest.", - "homepage": "http://purl.org/ontology/places", - "id": "lov.place", - "name": "The Places Ontology", - "prefix": "place", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://purl.org/ontology/places#$1" - }, - "lov.plink": { - "authority": "lov", - "description": "A Multilingual and Multicultural Ontology Representing Family Relationships.", - "homepage": "http://cedric.cnam.fr/isid/ontologies/PersonLink.owl", - "id": "lov.plink", - "name": "PersonLink Ontology", - "prefix": "plink", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://cedric.cnam.fr/isid/ontologies/PersonLink.owl#$1" - }, - "lov.plo": { - "authority": "lov", - "description": "An ontology for describing playlists, playlist entries and songs.", - "homepage": "http://purl.org/net/po#", - "id": "lov.plo", - "name": "Playlist Ontology", - "prefix": "plo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/po#$1" - }, - "lov.pmlp": { - "authority": "lov", - "description": "The provenance part of PML2 ontology. It is a fundamental component of PML2 ontology.", - "homepage": "http://inference-web.org/2.0/pml-provenance.owl", - "id": "lov.pmlp", - "name": "PML2 provenance ontology", - "prefix": "pmlp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://inference-web.org/2.0/pml-provenance.owl#$1" - }, - "lov.pmofn": { - "authority": "lov", - "description": "The FrameNet module of the PreMOn ontology extends the core module for representing concepts specific to FrameNet. The modeling is based on the [FrameNet II: Extended Theory and Practice](https://framenet2.icsi.berkeley.edu/docs/r1.5/book.pdf) book.", - "homepage": "http://premon.fbk.eu/ontology/fn", - "id": "lov.pmofn", - "name": "Predicate Model for Ontologies (PreMOn) - FrameNet ontology module", - "prefix": "pmofn", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://premon.fbk.eu/ontology/fn#$1" - }, - "lov.pmonb": { - "authority": "lov", - "description": "The NomBank module of the PreMOn ontology extends the core module for representing concepts specific to NomBank. The modelling is based on the NomBank Specifications.", - "homepage": "http://premon.fbk.eu/ontology/nb", - "id": "lov.pmonb", - "name": "Predicate Model for Ontologies (PreMOn) - NomBank ontology module", - "prefix": "pmonb", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://premon.fbk.eu/ontology/nb#$1" - }, - "lov.pmopb": { - "authority": "lov", - "description": "The PropBank module of the PreMOn ontology extends the core module for representing concepts specific to PropBank.", - "homepage": "http://premon.fbk.eu/ontology/pb", - "id": "lov.pmopb", - "name": "Predicate Model for Ontologies (PreMOn) - PropBank ontology module", - "prefix": "pmopb", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://premon.fbk.eu/ontology/pb#$1" - }, - "lov.pmovn": { - "authority": "lov", - "description": "The VerbNet module of the PreMOn ontology extends the core module with classes and properties specific to the VerbNet predicate model. The modelling is based on the VerbNet Annotation Guidelines.", - "homepage": "http://premon.fbk.eu/ontology/vn", - "id": "lov.pmovn", - "name": "Predicate Model for Ontologies (PreMOn) - VerbNet ontology module", - "prefix": "pmovn", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://premon.fbk.eu/ontology/vn#$1" - }, - "lov.pna": { - "authority": "lov", - "description": "Press.net Asset Ontology describes news assets (text, images, video, data, etc), the relationships between them and how assets can be classified and semantically annotated.", - "homepage": "http://data.press.net/ontology/asset/", - "id": "lov.pna", - "name": "Press.net Asset Ontology", - "prefix": "pna", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.press.net/ontology/asset/$1" - }, - "lov.pnc": { - "authority": "lov", - "description": "The Press.net Classification Ontology allows assets to be holistically classified using a controlled vocabulary or taxonomy.", - "homepage": "http://data.press.net/ontology/classification/", - "id": "lov.pnc", - "name": "Press.net Classification Ontology", - "prefix": "pnc", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://data.press.net/ontology/classification/$1" - }, - "lov.pne": { - "authority": "lov", - "description": "Press.net Event Ontology models news-worthy events and their relationship to news assets and stuff (simple entities) in the world.", - "homepage": "http://data.press.net/ontology/event/", - "id": "lov.pne", - "name": "Press.net Event Ontology", - "prefix": "pne", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.press.net/ontology/event/$1" - }, - "lov.pni": { - "authority": "lov", - "description": "The Identifier Ontology models non-RDF based Identifiers for resources. It is used to maintain a mapping between RDF resources identifiers and their equivalent IDs in an alternate, non-RDF based domain.", - "homepage": "http://data.press.net/ontology/identifier/", - "id": "lov.pni", - "name": "SNaP Identifier Ontology", - "prefix": "pni", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.press.net/ontology/identifier/$1" - }, - "lov.pns": { - "authority": "lov", - "description": "Press.net Stuff Ontology models real world entities. There are two kinds of stuff: tangibles and intangibles. Tangible stuff includes persons, locations and organizations. Intangibles are abstract concepts such as smoking, feminism or love.", - "homepage": "http://data.press.net/ontology/stuff/", - "id": "lov.pns", - "name": "Press.net Stuff Ontology", - "prefix": "pns", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.press.net/ontology/stuff/$1" - }, - "lov.pnt": { - "authority": "lov", - "description": "Press.net Tag Ontology defines relationships for semantically annotating taggable things (for example news assets) with domain entities (stuff) and events.", - "homepage": "http://data.press.net/ontology/tag/", - "id": "lov.pnt", - "name": "Press.net Tag Ontology", - "prefix": "pnt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.press.net/ontology/tag/$1" - }, - "lov.po": { - "authority": "lov", - "description": "This ontology aims at providing a simple vocabulary for describing programmes. It covers brands, series (seasons), episodes, broadcast events, broadcast services, etc.", - "homepage": "http://purl.org/ontology/po/", - "id": "lov.po", - "name": "Programmes ontology", - "prefix": "po", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/po/$1" - }, - "lov.poder": { - "authority": "lov", - "description": "A vocabulary to express information about people and their relations with Organizations, Companies, etc.", - "homepage": "http://dev.poderopedia.com/vocab/schema", - "id": "lov.poder", - "name": "Poder Vocabulary", - "prefix": "poder", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://dev.poderopedia.com/vocab/$1" - }, - "lov.poso": { - "authority": "lov", - "description": "This ontology provides the terminologies used for positioning systems.", - "homepage": "http://purl.org/poso/", - "id": "lov.poso", - "name": "Positioning System Ontology", - "prefix": "poso", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://purl.org/poso/$1" - }, - "lov.posocm": { - "authority": "lov", - "description": "This ontology provides the terminologies used for positioning systems.", - "homepage": "http://purl.org/poso/common/", - "id": "lov.posocm", - "name": "Positioning System Ontology Common Technologies, Algorithms and Systems", - "prefix": "posocm", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://purl.org/poso/common/$1" - }, - "lov.postcode": { - "authority": "lov", - "description": "An ontology describing the postcode geography in Great Britain.", - "homepage": "http://data.ordnancesurvey.co.uk/ontology/postcode/", - "id": "lov.postcode", - "name": "Postcode Ontology", - "prefix": "postcode", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://data.ordnancesurvey.co.uk/ontology/postcode/$1" - }, - "lov.poste": { - "authority": "lov", - "description": "Vocabulaire d\u00e9crivant la r\u00e9partition des points de contact du r\u00e9seau postal en France m\u00e9tropolitaine, Guadeloupe, Guyane, La R\u00e9union, Martinique, Mayotte, Monaco, Monte-Carlo et Saint-Pierre et Miquelon", - "homepage": "http://data.lirmm.fr/ontologies/poste", - "id": "lov.poste", - "name": "Ontologie de la Poste", - "prefix": "poste", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.lirmm.fr/ontologies/poste#$1" - }, - "lov.ppo": { - "authority": "lov", - "description": "An ontology to create privacy preferences for Linked Data", - "homepage": "http://vocab.deri.ie/ppo", - "id": "lov.ppo", - "name": "Privacy Preference Ontology", - "prefix": "ppo", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://vocab.deri.ie/ppo#$1" - }, - "lov.pproc": { - "authority": "lov", - "description": "The PPROC ontology defines the necessary concepts to describe public procurement process and the contracts of public sector (public e-procurement). The ontology has been designed with the main purpose of publishing data about public contracts.", - "homepage": "http://contsem.unizar.es/def/sector-publico/pproc", - "id": "lov.pproc", - "name": "PPROC ontology", - "prefix": "pproc", - "source": "lov.linkeddata.es", - "subjects": [ - "law" - ], - "uri_format": "http://contsem.unizar.es/def/sector-publico/pproc#$1" - }, - "lov.pr": { - "authority": "lov", - "description": "A vocabulary for describing the ontology design pattern of property reification.", - "homepage": "http://purl.org/ontology/prv/core#", - "id": "lov.pr", - "name": "Property Reification Vocabulary", - "prefix": "pr", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/prv/core#$1" - }, - "lov.premis": { - "authority": "lov", - "description": "This ontology identifies the classes and properties used to describe preservation metadata in RDF.", - "homepage": "http://www.loc.gov/premis/rdf/v1", - "id": "lov.premis", - "name": "PREMIS Ontology", - "prefix": "premis", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.loc.gov/premis/rdf/v1#$1" - }, - "lov.prissma": { - "authority": "lov", - "description": "PRISSMA (Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability) is a domain-independent vocabulary for displaying Web of Data resources in mobile environments.", - "homepage": "http://ns.inria.fr/prissma/v2#", - "id": "lov.prissma", - "name": "Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability", - "prefix": "prissma", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://ns.inria.fr/prissma/v2#$1" - }, - "lov.pro": { - "authority": "lov", - "description": "PRO, the Publishing Roles Ontology, is an ontology for describing the role(s) in the publication process of a particular agent over a defined period of time. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies.", - "homepage": "http://purl.org/spar/pro", - "id": "lov.pro", - "name": "The Publishing Roles Ontology", - "prefix": "pro", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/pro/$1" - }, - "lov.prof": { - "authority": "lov", - "description": "This vocabulary is for describing relationships between standards/specifications, profiles of them and supporting artifacts such as validating resources.\n\nThis model starts with [http://dublincore.org/2012/06/14/dcterms#Standard](dct:Standard) entities which can either be Base Specifications (a standard not profiling any other Standard) or Profiles (Standards which do profile others). Base Specifications or Profiles can have Resource Descriptors associated with them that defines implementing rules for the it. Resource Descriptors must indicate the role they play (to guide, to validate etc.) and the formalism they adhere to (dct:format) to allow for content negotiation. A vocabulary of Resource Roles are provided alongside this vocabulary but that list is extensible.", - "homepage": "http://www.w3.org/ns/dx/prof", - "id": "lov.prof", - "name": "Profiles Vocabulary", - "prefix": "prof", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/dx/prof/$1" - }, - "lov.prog": { - "authority": "lov", - "description": "This Vocabulary provides the means to create a document which describes a large event or other connected series of events. The primary purpose is to help humans comprehend the programme, not describe absolute truth. A single event (or even series) may have multiple programmes.", - "homepage": "http://purl.org/prog/", - "id": "lov.prog", - "name": "The Event Programme Vocabulary", - "prefix": "prog", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/prog/$1" - }, - "lov.prov": { - "authority": "lov", - "description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.", - "homepage": "http://www.w3.org/ns/prov#", - "id": "lov.prov", - "name": "W3C PROVenance Interchange", - "prefix": "prov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/prov#$1" - }, - "lov.provoc": { - "authority": "lov", - "description": "ProVoc (Product Vocabulary) is a vocabulary that can be used to represent information and manipulate them through the Web. This ontology reflects: 1) The basic hierarchy of a company: Group (Company), Divisions of a Group, Brand names attached to a Division or a Group, and 2) The production of a company: products, ranges of products (attached to a Brand), the composition of a product, packages of products...", - "homepage": "http://ns.inria.fr/provoc", - "id": "lov.provoc", - "name": "Product Vocabulary", - "prefix": "provoc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/provoc#$1" - }, - "lov.prv": { - "authority": "lov", - "description": "The Provenance Vocabulary Core Ontology provides the main classes and properties required to describe provenance of data on the Web.", - "homepage": "http://purl.org/net/provenance/ns#", - "id": "lov.prv", - "name": "Provenance Vocabulary Core Ontology", - "prefix": "prv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/provenance/ns#$1" - }, - "lov.prvt": { - "authority": "lov", - "description": "Extends the Provenance Vocabulary by defining subclasses of the types of provenance elements introduced in the core ontology.", - "homepage": "http://purl.org/net/provenance/types#", - "id": "lov.prvt", - "name": "Provenance Vocabulary types", - "prefix": "prvt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/provenance/types#$1" - }, - "lov.psh": { - "authority": "lov", - "description": "An OWL vocabulary to include and exploit probabilistic information in SHACL validation reports", - "homepage": "http://ns.inria.fr/probabilistic-shacl/", - "id": "lov.psh", - "name": "Probabilistic SHACL Validation", - "prefix": "psh", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.inria.fr/probabilistic-shacl/$1" - }, - "lov.pso": { - "authority": "lov", - "description": "an ontology for describing the status held by a bibliographic document or other publication entity at each of the various stages in the publishing process. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies", - "homepage": "http://purl.org/spar/pso", - "id": "lov.pso", - "name": "The Publishing Status Ontology", - "prefix": "pso", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/pso/$1" - }, - "lov.ptop": { - "authority": "lov", - "description": "The PROTON Top module represents the most general classes", - "homepage": "http://www.ontotext.com/proton/protontop", - "id": "lov.ptop", - "name": "PROTON (Proto Ontology), Top Module", - "prefix": "ptop", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontotext.com/proton/protontop#$1" - }, - "lov.pubsub": { - "authority": "lov", - "description": "The eccenca Publish-Subscribe Vocabulary defines concepts and relations to create statements about publishers, subscribers and their subscriptions in a Publish-Subscribe environment based on the PubSubHubbub Core 0.4 specification.", - "homepage": "https://vocab.eccenca.com/pubsub/", - "id": "lov.pubsub", - "name": "Eccenca Publish-Subscribe Vocabulary", - "prefix": "pubsub", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://vocab.eccenca.com/pubsub/$1" - }, - "lov.puv": { - "authority": "lov", - "description": "A simple ontology which implements the Parameter Usage Vocabulary semantic model, as described at https://github.com/nvs-vocabs/P01", - "homepage": "https://w3id.org/env/puv", - "id": "lov.puv", - "name": "Parameter Usage Vocabulary ontology", - "prefix": "puv", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/env/puv#$1" - }, - "lov.pwo": { - "authority": "lov", - "description": "An ontology for describing the workflow associated with the publication of a document.", - "homepage": "http://purl.org/spar/pwo", - "id": "lov.pwo", - "name": "The Publishing Workflow Ontology", - "prefix": "pwo", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/spar/pwo/$1" - }, - "lov.qb": { - "authority": "lov", - "description": "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF.", - "homepage": "http://purl.org/linked-data/cube", - "id": "lov.qb", - "name": "The data cube vocabulary", - "prefix": "qb", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/linked-data/cube#$1" - }, - "lov.qb4o": { - "authority": "lov", - "description": "This vocabulary allows to publish and operate with OLAP cubes in RDF", - "homepage": "http://purl.org/qb4olap/cubes", - "id": "lov.qb4o", - "name": "Vocabulary for publishing OLAP data cubes", - "prefix": "qb4o", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/qb4olap/cubes#$1" - }, - "lov.qu": { - "authority": "lov", - "description": "This ontology is partially based on the SysML QUDV (Quantities, Units, Dimensions and Values) proposed by a working group of the SysML 1.2 Revision Task Force (RTF), working in close coordination with the OMG MARTE specification group.\nIn order to generalize its potential usage and alignment with other standardization efforts concerning quantities and units, the QU ontology has been further developed as a complement to the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG).", - "homepage": "http://purl.oclc.org/NET/ssnx/qu/qu", - "id": "lov.qu", - "name": "Quantity Kinds and Units", - "prefix": "qu", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.oclc.org/NET/ssnx/qu/qu#$1" - }, - "lov.qudt": { - "authority": "lov", - "description": "The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems.", - "homepage": "http://qudt.org/schema/qudt", - "id": "lov.qudt", - "name": "Quantities, Units, Dimensions and Types", - "prefix": "qudt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://qudt.org/schema/qudt/$1" - }, - "lov.r-arco": { - "authority": "lov", - "description": "The ArCo module is the root of the network ArCo - Architecture of Knowledge. It imports all the other modules and models top-level distinctions from the cultural heritage domain.", - "homepage": "https://w3id.org/arco/ontology/arco", - "id": "lov.r-arco", - "name": "ArCo Ontology (ArCo network)", - "prefix": "r-arco", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "https://w3id.org/arco/ontology/arco/$1" - }, - "lov.r4r": { - "authority": "lov", - "description": "R4R is a light-weight ontology for representing general relationships of resource for publication and reusing. It asserts that a certain reusing context occurred and determined by its two basic relations, namely, isPackagedWith and isCitedBy. The isPackagedWith relation declares the resource is ready to be reused by incorporating License and Provenance information. The Cites relation is an exceptional to isCitedBy which occurs only two related objects cite each other at the same time. Five resource objects including article, data, code, provenance and license are major class concepts to represent in this ontology. \n\nThe namespace for all R4R terms is http://guava.iis.sinica.edu.tw/r4r/", - "homepage": "http://guava.iis.sinica.edu.tw/r4r", - "id": "lov.r4r", - "name": "Relations for Reusing (R4R) Ontology", - "prefix": "r4r", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://guava.iis.sinica.edu.tw/r4r/$1" - }, - "lov.radion": { - "authority": "lov", - "description": "RADion, and the higher level vocabularies that build upon it, are intended as a model that facilitates federation and co-operation. It is not the primary intention that repository owners redesign or convert their current systems and data to conform to RADion, but rather that it acts as a common layer among repositories that want to exchange data.", - "homepage": "http://www.w3.org/ns/radion#", - "id": "lov.radion", - "name": "Repository Asset Distribution", - "prefix": "radion", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/radion#$1" - }, - "lov.rains": { - "authority": "lov", - "description": "An ontology to model accountability of AI systems which use machine learning.", - "homepage": "https://w3id.org/rains", - "id": "lov.rains", - "name": "The RAInS Ontology", - "prefix": "rains", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/rains#$1" - }, - "lov.rami": { - "authority": "lov", - "description": "A vocabulary which represents the Reference Architecture Model for Industry 4.0 (RAMI), including the concept of the Administration Shell I4.0 Component.", - "homepage": "https://w3id.org/i40/rami/", - "id": "lov.rami", - "name": "rami - Reference Architecture Model", - "prefix": "rami", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://iais.fraunhofer.de/vocabs/rami#$1" - }, - "lov.raul": { - "authority": "lov", - "description": "A vocabulary to describe Web form widgets. Strongly aligned with the meta model of HTML Web forms. A RESTful service that can render HTML Web forms from RaUL models can be found at: http://w3c.org.au/raul", - "homepage": "http://vocab.deri.ie/raul", - "id": "lov.raul", - "name": "RAUL Vocabulary", - "prefix": "raul", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/NET/raul#$1" - }, - "lov.rb": { - "authority": "lov", - "description": "Ontology for describing datasets and profiles in the RiverBench benchmark suite.", - "homepage": "https://w3id.org/riverbench/schema/metadata", - "id": "lov.rb", - "name": "RiverBench metadata ontology", - "prefix": "rb", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "https://w3id.org/riverbench/schema/metadata#$1" - }, - "lov.rbdoc": { - "authority": "lov", - "description": "Ontology with metadata needed to generate documentation of datasets, distributions, profiles, etc. in RiverBench", - "homepage": "https://w3id.org/riverbench/schema/documentation", - "id": "lov.rbdoc", - "name": "RiverBench documentation ontology", - "prefix": "rbdoc", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "https://w3id.org/riverbench/schema/documentation#$1" - }, - "lov.rdaa": { - "authority": "lov", - "description": "The Agent properties element set consists of properties representing the attributes and relationships of the RDA Agent, Person, Family, and Corporate Body entities. Each property in the element set has a domain of the class representing one of these entities.", - "homepage": "http://rdaregistry.info/Elements/a", - "id": "lov.rdaa", - "name": "RDA Agent properties", - "prefix": "rdaa", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdaregistry.info/Elements/a/$1" - }, - "lov.rdac": { - "authority": "lov", - "description": "The Classes element set consists of classes representing the RDA entities, including Work, Expression, Manifestation, Item, Person, Family, Corporate Body, and Agent.", - "homepage": "http://rdaregistry.info/Elements/c", - "id": "lov.rdac", - "name": "RDA Classes", - "prefix": "rdac", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdaregistry.info/Elements/c/$1" - }, - "lov.rdae": { - "authority": "lov", - "description": "The Expression properties element set consists of properties representing the attributes and relationships of the RDA Expression entity. Each property in the element set has a domain of the class representing this entity.", - "homepage": "http://rdaregistry.info/Elements/e", - "id": "lov.rdae", - "name": "RDA Expression properties", - "prefix": "rdae", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdaregistry.info/Elements/e/$1" - }, - "lov.rdafrbr": { - "authority": "lov", - "description": "Defines the core RDA classes, including FRBR levels Work, Expression, Manifestation and Item.", - "homepage": "http://rdvocab.info/uri/schema/FRBRentitiesRDA", - "id": "lov.rdafrbr", - "name": "FRBR Entities for RDA", - "prefix": "rdafrbr", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdvocab.info/uri/schema/FRBRentitiesRDA/$1" - }, - "lov.rdag1": { - "authority": "lov", - "description": "This is the provisional registration of the RDA Group 1 Element Vocabulary, managed by the DCMI/RDA Task Group.", - "homepage": "http://rdvocab.info/Elements", - "id": "lov.rdag1", - "name": "RDA Group 1 Elements", - "prefix": "rdag1", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdvocab.info/Elements/$1" - }, - "lov.rdag2": { - "authority": "lov", - "description": "The second group of metadata elements defined by RDA", - "homepage": "http://rdvocab.info/ElementsGr2", - "id": "lov.rdag2", - "name": "RDA Group 2 Elements", - "prefix": "rdag2", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdvocab.info/ElementsGr2/$1" - }, - "lov.rdag3": { - "authority": "lov", - "description": "This group of RDA elements defines preferred and variant names for concepts, places and events", - "homepage": "http://rdvocab.info/ElementsGr3", - "id": "lov.rdag3", - "name": "RDA Group 3 Elements", - "prefix": "rdag3", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdvocab.info/ElementsGr3/$1" - }, - "lov.rdai": { - "authority": "lov", - "description": "The Item properties element set consists of properties representing the attributes and relationships of the RDA Item entity.", - "homepage": "http://rdaregistry.info/Elements/i", - "id": "lov.rdai", - "name": "RDA Item properties", - "prefix": "rdai", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdaregistry.info/Elements/i/$1" - }, - "lov.rdam": { - "authority": "lov", - "description": "The Manifestation properties element set consists of properties representing the attributes and relationships of the RDA Manifestation entity.", - "homepage": "http://rdaregistry.info/Elements/m", - "id": "lov.rdam", - "name": "RDA Manifestation properties", - "prefix": "rdam", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdaregistry.info/Elements/m/$1" - }, - "lov.rdarel": { - "authority": "lov", - "description": "A vocabulary defining a large variety of specific relationships between the various levels of the FRBR pile.", - "homepage": "http://rdvocab.info/RDARelationshipsWEMI", - "id": "lov.rdarel", - "name": "RDA Relationships for Works, Expressions, Manifestations, Items", - "prefix": "rdarel", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdvocab.info/RDARelationshipsWEMI/$1" - }, - "lov.rdarel2": { - "authority": "lov", - "description": "RDA Relationships for Persons, Corporate Bodies, Families", - "homepage": "http://metadataregistry.org/uri/schema/RDARelationshipsGR2", - "id": "lov.rdarel2", - "name": "RDA Relationships GR2", - "prefix": "rdarel2", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://metadataregistry.org/uri/schema/RDARelationshipsGR2/$1" - }, - "lov.rdarole": { - "authority": "lov", - "description": "Defines possible roles linking agents to FRBR objects (works, expressions, manifestations, items)", - "homepage": "http://rdvocab.info/roles", - "id": "lov.rdarole", - "name": "RDA Roles", - "prefix": "rdarole", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdvocab.info/roles/$1" - }, - "lov.rdau": { - "authority": "lov", - "description": "The Unconstrained properties element set consists of properties representing the attributes and relationships of the all RDA entities. Each property in the element set has semantics which are independent of the FRBR model and has no specified domain or range.", - "homepage": "http://rdaregistry.info/Elements/u", - "id": "lov.rdau", - "name": "RDA Unconstrained properties", - "prefix": "rdau", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdaregistry.info/Elements/u/$1" - }, - "lov.rdaw": { - "authority": "lov", - "description": "The Work properties element set consists of properties representing the attributes and relationships of the RDA Work entity.", - "homepage": "http://rdaregistry.info/Elements/w", - "id": "lov.rdaw", - "name": "RDA Work properties", - "prefix": "rdaw", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://rdaregistry.info/Elements/w/$1" - }, - "lov.rdf": { - "authority": "lov", - "description": "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts.", - "homepage": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "id": "lov.rdf", - "name": "The RDF Concepts Vocabulary", - "prefix": "rdf", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1" - }, - "lov.rdfa": { - "authority": "lov", - "description": "This document describes the RDFa Vocabulary for Term and Prefix Assignment. The Vocabulary is used to modify RDFa 1.1 processing behavior", - "homepage": "http://www.w3.org/ns/rdfa#", - "id": "lov.rdfa", - "name": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting", - "prefix": "rdfa", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/rdfa#$1" - }, - "lov.rdfg": { - "authority": "lov", - "description": "Properties allowing statement of intensional equivalence between RDF graphs", - "homepage": "http://www.w3.org/2004/03/trix/rdfg-1/", - "id": "lov.rdfg", - "name": "Graph", - "prefix": "rdfg", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2004/03/trix/rdfg-1/$1" - }, - "lov.rdfp": { - "authority": "lov", - "description": "## RDF Presentation and RDF Presentation Negotiation\n\nAn RDF graph can be presented in several ways, using different media types. Examples of RDF media types include `application/rdf+xml`, `text/turtle`, `application/json+ld`.\n\nToday, most of the content consumed/produced/published, on the Web is not presented in RDF. \n\nIn the Web of Things, HTTP servers and clients would rather exchange lightweight documents, potentially binary. \nCurrently, most existing RDF Presentations generically apply to any RDF graph, at the cost of being heavy text-based documents.\nYet, lightweight HTTP servers/clients could be better satisfied with consuming/producing/publishing lightweight documents, may its structure be application-specific.", - "homepage": "https://w3id.org/rdfp/", - "id": "lov.rdfp", - "name": "The RDF Presentation ontology", - "prefix": "rdfp", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/rdfp/$1" - }, - "lov.rdfs": { - "authority": "lov", - "description": "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.", - "homepage": "http://www.w3.org/2000/01/rdf-schema#", - "id": "lov.rdfs", - "name": "The RDF Schema vocabulary", - "prefix": "rdfs", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2000/01/rdf-schema#$1" - }, - "lov.rdft": { - "authority": "lov", - "description": "This is a vocabulary document and is used to define classes and properties used in\n RDF 1.1 Test Cases and associated test manifests.\n The URI of the vocabulary is http://www.w3.org/ns/rdftest# (abbreviated by rdft: in this document).\n Turtle and an JSON-LD versions of the vocabulary are also available.\n The vocabulary is published by W3C.", - "homepage": "http://www.w3.org/ns/rdftest", - "id": "lov.rdft", - "name": "The RDF 1.1 Test Vocabulary", - "prefix": "rdft", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/rdftest#$1" - }, - "lov.react": { - "authority": "lov", - "description": "The REACT ontology aims to represent all the necessary knowledge to support the achievement of island energy independence through renewable energy generation and storage, a demand response platform, and promoting user engagement in a local energy community.\n\nThe REACT ontology has been developed as part of the REACT project which has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement no. 824395.", - "homepage": "https://w3id.org/react", - "id": "lov.react", - "name": "The REACT Ontology", - "prefix": "react", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/react#$1" - }, - "lov.rec": { - "authority": "lov", - "description": "The Recommendation Ontology specification provides basic concepts and properties for describing recommendations on/ for the Semantic Web.", - "homepage": "http://purl.org/ontology/rec/core#", - "id": "lov.rec", - "name": "Recommendation Ontology", - "prefix": "rec", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/rec/core#$1" - }, - "lov.rec54": { - "authority": "lov", - "description": "This is (the start of) an event-based model of the W3C process; e.g. RECdd is the class of Recommendation Director's Decisions; \ti.e. messages to w3c-ac-members announcing a new W3C Recommendation.", - "homepage": "http://www.w3.org/2001/02pd/rec54#", - "id": "lov.rec54", - "name": "Model of the W3C Process", - "prefix": "rec54", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2001/02pd/rec54#$1" - }, - "lov.reco": { - "authority": "lov", - "description": "The RECO ontology defines the vocabulary for representing preferences-as-constraints and preferences-as-ratings as RDF graphs. This lightweight vocabulary provides domain-independent means to describe user profiles in a coherent and context-aware way. RECO has been designed as an extension of both Friend-Of-A-Friend (FOAF) and Who Am I! (WAI) ontologies.", - "homepage": "http://purl.org/reco#", - "id": "lov.reco", - "name": "RECommendations Ontology", - "prefix": "reco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/reco#$1" - }, - "lov.reegle": { - "authority": "lov", - "description": "Vocabulary used to describe clean energy actors, projects and technologies", - "homepage": "http://reegle.info/schema", - "id": "lov.reegle", - "name": "Renewable Energy and Energy Efficiency", - "prefix": "reegle", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://reegle.info/schema#$1" - }, - "lov.rel": { - "authority": "lov", - "description": "A vocabulary for describing relationships between people", - "homepage": "http://purl.org/vocab/relationship/", - "id": "lov.rel", - "name": "Relationship", - "prefix": "rel", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocab/relationship/$1" - }, - "lov.remetca": { - "authority": "lov", - "description": "Ontology for poetry description", - "homepage": "http://www.purl.org/net/remetca#", - "id": "lov.remetca", - "name": "ReMetCa Ontology", - "prefix": "remetca", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://www.purl.org/net/remetca#$1" - }, - "lov.rev": { - "authority": "lov", - "description": "Vocabulary for expressing reviews and ratings", - "homepage": "http://purl.org/stuff/rev#", - "id": "lov.rev", - "name": "Review Vocabulary", - "prefix": "rev", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/stuff/rev#$1" - }, - "lov.rico": { - "authority": "lov", - "description": "RiC-O (Records in Contexts-Ontology) is an OWL ontology for describing\n archival record resources. As the second part of Records in Contexts standard,\n it is a formal representation of Records in Contexts Conceptual Model (RiC-CM). \t\t\n The current official version is v0.2; it is\n compliant with RiC-CM v0.2 full draft, that will be published in February or\n March 2021, and that is slightly different from RiC-CM\n v0.2 preview, that was published in December 2019.\n RiC-O provides a generic vocabulary and formal rules for creating RDF\n datasets (or generating them from existing archival metadata) that describe in a\n consistent way any kind of archival record resource. It can support publishing\n RDF datasets as Linked Data, querying them using SPARQL, and making inferences\n using the logic of the ontology.", - "homepage": "https://www.ica.org/standards/RiC/ontology", - "id": "lov.rico", - "name": "International Council on Archives Records in Contexts Ontology (ICA RiC-O)", - "prefix": "rico", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "https://www.ica.org/standards/RiC/ontology#$1" - }, - "lov.rlog": { - "authority": "lov", - "description": "This is a helper ontology for NIF 2.0 to be able to log errors and warning messages.", - "homepage": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#", - "id": "lov.rlog", - "name": "RDF Logging Ontology", - "prefix": "rlog", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#$1" - }, - "lov.ro": { - "authority": "lov", - "description": "This ontology shows how AO and ORE ontologies can be used together to define a ResearchObject. This ontology is further customized by the wf4ever ontology.", - "homepage": "http://purl.org/wf4ever/ro", - "id": "lov.ro", - "name": "The Research Object Ontology", - "prefix": "ro", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/wf4ever/ro#$1" - }, - "lov.roh": { - "authority": "lov", - "description": "An ontology to address the Research Management of the CRUE's Spanish University System (Sistema Universitario Espa\u00f1ol) by applying an encompassing model not only capable of addressing the universities of the CRUE but also more belonging to the European Union.", - "homepage": "http://w3id.org/roh", - "id": "lov.roh", - "name": "The ASIO ontology", - "prefix": "roh", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://w3id.org/roh#$1" - }, - "lov.rooms": { - "authority": "lov", - "description": "A simple vocabulary for describing the rooms in a building.", - "homepage": "http://vocab.deri.ie/rooms", - "id": "lov.rooms", - "name": "Buildings and Rooms Vocabulary", - "prefix": "rooms", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://vocab.deri.ie/rooms#$1" - }, - "lov.rov": { - "authority": "lov", - "description": "Le vocabulaire des organisations enregistr\u00e9es est un profil de l'ontologie des organisations pour d\u00e9crire les organisations ayant acquis un statut l\u00e9gal au travers d'un processus d'inscription formel, typiquement dans un registre national ou r\u00e9gional.", - "homepage": "http://www.w3.org/ns/regorg", - "id": "lov.rov", - "name": "Registered Organization Vocabulary", - "prefix": "rov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/regorg#$1" - }, - "lov.rr": { - "authority": "lov", - "description": "A vocabulary which can be used to specify a mapping of relational data to RDF.", - "homepage": "http://www.w3.org/ns/r2rml#", - "id": "lov.rr", - "name": "RDB to RDF Mapping Language Schema", - "prefix": "rr", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/r2rml#$1" - }, - "lov.rsctx": { - "authority": "lov", - "description": "This ontology represent context which may be interesting in providing recommendations to users.", - "homepage": "http://softeng.polito.it/rsctx", - "id": "lov.rsctx", - "name": "Recommender System Context", - "prefix": "rsctx", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://softeng.polito.it/rsctx#$1" - }, - "lov.rss": { - "authority": "lov", - "description": "RDF Schema declaration for Rich Site Summary (RSS) 1.0", - "homepage": "http://purl.org/rss/1.0", - "id": "lov.rss", - "name": "Vocabulary for Rich Site Summary (RSS) 1.0", - "prefix": "rss", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/rss/1.0/$1" - }, - "lov.rto": { - "authority": "lov", - "description": "The Rail Topology Ontology models foundational rail topology concepts..", - "homepage": "https://w3id.org/rail/topo#", - "id": "lov.rto", - "name": "Rail Topology Ontology", - "prefix": "rto", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/rail/topo#$1" - }, - "lov.ru": { - "authority": "lov", - "description": "Draft for a recommendation for metadata on Representational Units (RU) which appear in ontologies. It is so far harmonized for implementation through owl annotation properties.", - "homepage": "http://purl.org/imbi/ru-meta.owl", - "id": "lov.ru", - "name": "Representational Units Metadata Ontology", - "prefix": "ru", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/imbi/ru-meta.owl#$1" - }, - "lov.ruto": { - "authority": "lov", - "description": "The Databugger ontology describes concepts used in Databugger, a test driven data-debugging framework that can run automatically generated (based on a schema) and manually generated test cases against an endpoint.", - "homepage": "http://rdfunit.aksw.org/ns/core#", - "id": "lov.ruto", - "name": "Test-Driven Data Debugging Ontology", - "prefix": "ruto", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdfunit.aksw.org/ns/core#$1" - }, - "lov.s4ac": { - "authority": "lov", - "description": "A lightweight vocabulary to create fine-grained access control policies for Linked Data.", - "homepage": "http://ns.inria.fr/s4ac/v2", - "id": "lov.s4ac", - "name": "Social Semantic SPARQL Security For Access Control Ontology", - "prefix": "s4ac", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://ns.inria.fr/s4ac/v2#$1" - }, - "lov.s4agri": { - "authority": "lov", - "description": "This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain.", - "homepage": "https://saref.etsi.org/saref4agri/", - "id": "lov.s4agri", - "name": "SAREF extension for Agriculture", - "prefix": "s4agri", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries", - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4agri/$1" - }, - "lov.s4bldg": { - "authority": "lov", - "description": "This ontology extends the SAREF ontology for the building domain by defining building devices and how they are located in a building. This extension is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for data sharing in the construction and facility management industries. The descriptions of the classes and properties extracted from IFC have been taken from the IFC documentation.", - "homepage": "https://saref.etsi.org/saref4bldg/", - "id": "lov.s4bldg", - "name": "SAREF extension for building devices", - "prefix": "s4bldg", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4bldg/$1" - }, - "lov.s4city": { - "authority": "lov", - "description": "This ontology extends the SAREF ontology for the Smart City domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Smart City domain.", - "homepage": "https://saref.etsi.org/saref4city/", - "id": "lov.s4city", - "name": "SAREF extension for Smart City", - "prefix": "s4city", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences", - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4city/$1" - }, - "lov.s4ehaw": { - "authority": "lov", - "description": "The objective of SAREF4EHAW is to extend SAREF ontology for the eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document shortly introduces a high level view of the envisioned SAREF4EHAW semantic model and modular ontology, with the retained concepts (i.e. classes) and their relations. \nSAREF4EHAW extension has been specified and formalised by investigating EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential stakeholders, standardization initiatives, alliances/associations, European projects, EC directives, existing ontologies, and data repositories. Therefore, SAREF4EHAW modular ontology shall both:\n - Allow the implementation of a limited set of typical EHAW related use cases already identified in ETSI TR 103 509, i.e.\n - Use case 1 ?elderly at home monitoring and support?,\n - Use case 2 ?monitoring and support of healthy lifestyles for citizens?,\n - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?.\n - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509, mainly the ontological ones that were mostly taken as input for the ontology specification.\n\nSAREF4EHAW mainly reuses the following existing ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension and W3C SSN System module. The following figure presents the high level view of SAREF4EHAW ontology.\n![SAREF4SYST overview](diagrams/SAREF4EHAW_Model.jpg)\nFor semantic interoperability handling purposes, an ontology based solution, combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW. Therefore, an upper level ontology, at service level, shall also behas been fully modelled (Service class and sub-classes depicted in the previous figure).\nFor embedded semantic analytics purposes, SAREF4EHAW shall behas been designed using the modularity principle (see ETSI TR 103 509) and can thus be mainly described by the following self-contained knowledge sub-ontologies (or modules): HealthActor, Ban, HealthDevice, Function (measured data related concepts included) and Service.", - "homepage": "https://saref.etsi.org/saref4ehaw/", - "id": "lov.s4ehaw", - "name": "SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain", - "prefix": "s4ehaw", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4ehaw/$1" - }, - "lov.s4ener": { - "authority": "lov", - "description": "This is the extension of SAREF for the EEBus and Energy@Home project. The documentation of SAREF4EE is available at http://ontology.tno.nl/SAREF4EE_Documentation_v0.1.pdf. SAREF4EE represents 1) The configuration information exchanged in the use case 'Remote Network Management' according to the EEBus Technical Report, Protocol Specification- Remote Network Management, version 1.0.0.2, 2015-09-19; 2) The scheduling information about power sequences exchanged in the use cases Appliance scheduling through CEM and remote start' and 'Automatic cycle rescheduling', according to the message structures described in General Message Structures, version 0.1.1, 2015-10-07; 3) The monitor and control information exchanged in the use case 'Communicate appliance status and info on manually planned cycles', according to the monitoring and control part of the Energy@Home Data Model, version 1.0; and 4) the event-based data exchanged in the use case 'Demand Response', according to General Message Structures, version 0.1.1, 2015-10-07.", - "homepage": "https://saref.etsi.org/saref4ener/", - "id": "lov.s4ener", - "name": "SAREF4EE: the EEbus/Energy@home extension of SAREF", - "prefix": "s4ener", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://saref.etsi.org/saref4ener/$1" - }, - "lov.s4envi": { - "authority": "lov", - "description": "This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc.", - "homepage": "https://saref.etsi.org/saref4envi/", - "id": "lov.s4envi", - "name": "SAREF extension for environment", - "prefix": "s4envi", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4envi/$1" - }, - "lov.s4inma": { - "authority": "lov", - "description": "SAREF4INMA is an extension of SAREF for the industry and manufacturing domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing domain to solve the lack of interoperability between various types of production equipment that produce items in a factory and, once outside the factory, between different organizations in the value chain to uniquely track back the produced items to the corresponding production equipment, batches, material and precise time in which they were manufactured. SAREF4INMA is specified and published by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was created to be aligned with related initiatives in the smart industry and manufacturing domain in terms of modelling and standardization, such as the Reference Architecture Model for Industry 4.0 (RAMI), which combines several standards used by the various national initiatives in Europe that support digitalization in manufacturing. The full list of use cases, standards and requirements that guided the creation of SAREF4INMA are described in the associated ETSI TR 103 507.", - "homepage": "https://saref.etsi.org/saref4inma/", - "id": "lov.s4inma", - "name": "SAREF4INMA: an extension of SAREF for the industry and manufacturing domain", - "prefix": "s4inma", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4inma/$1" - }, - "lov.s4syst": { - "authority": "lov", - "description": "The present document is the technical specification of SAREF4SYST, a generic extension of [ETSI TS 103 264 SAREF](https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/02.01.01_60/ts_103264v020101p.pdf) that defines an ontology pattern which can be instantiated for different domains. SAREF4SYST defines Systems, Connections between systems, and Connection Points at which systems may be connected. These core concepts can be used generically to define the topology of features of interest, and can be specialized for multiple domains. The topology of features of interest is highly important in many use cases. If a room holds a lighting device, and if it is adjacent with an open window to a room whose luminosity is low, then by turning on the lighting device in the former room one may expect that the luminosity in the latter room will rise.\n\nThe SAREF4SYST ontology pattern can be instantiated for different domains. For example to describe zones inside a building (systems), that share a frontier (connections). Properties of systems are typically state variables (e.g. agent population, temperature), whereas properties of connections are typically flows (e.g. heat flow).\n\nSAREF4SYST has two main aims: on the one hand, to extend SAREF with the capability or representing general topology of systems and how they are connected or interact and, on the other hand, to exemplify how ontology patterns may help to ensure an homogeneous structure of the overall SAREF ontology and speed up the development of extensions.\n\nSAREF4SYST consists both of a core ontology, and guidelines to create ontologies following the SAREF4SYST ontology pattern. The core ontology is a lightweight OWL-DL ontology that defines 3 classes and 9 object properties.\n\nUse cases for ontology patterns are described extensively in [ETSI TR 103 549 Clauses 4.2 and 4.3](https://www.etsi.org/deliver/etsi_tr/103500_103599/103549/01.01.01_60/tr_103549v010101p.pdf).\n\nFor the Smart Energy domain:\n\n- Electric power systems can exchange electricity with other electric power systems. The electric energy can flow both ways in some cases (from the Public Grid to a Prosumer), or in only one way (from the Public Grid to a Load). Electric power systems can be made up of different sub-systems. Generic sub-types of electric power systems include producers, consumers, storage systems, transmission systems. \n- Electric power systems may be connected one to another through electrical connection points. An Electric power system may have multiple connection points (Multiple Winding Transformer generally have one single primary winding with two or more secondary windings). Generic sub-types of electrical connection points include plugs, sockets, direct-current, single-phase, three-phase, connection points. \n- An Electrical connection may exist between two Electric power systems at two of their respective connection points. Generic sub-types of electrical connections include Single-phase Buses, Three-phase Buses. A single-phase electric power system can be connected using different configurations at a three-phase bus (RN, SN, TN types).\n\nFor the Smart Building domain:\n\n- Buildings, Storeys, Spaces, are different sub-types of Zones. Zones can contain sub-zones. Zones can be adjacent or intersect with other zones. \n- Two zones may share one or more connections. For example some fresh air may be created inside a storey if it has two controllable openings to the exterior at different cardinal points. \n\nA graphical overview of the SAREF4SYST ontology is provided in Figure 1. In such figure:\n\n- Rectangles are used to denote Classes. The label of the rectangle is the identifier of the Class.\n- Plain arrows are used to represent Object Properties between Classes. The label of the arrow is the identifier of the Object Property. The origin of the arrow is the domain Class of the property, and the target of the arrow is the range Class of the property.\n- Dashed arrows with identifiers between stereotype signs (i.e. \"`<< >>`\") refer to OWL axioms that are applied to some property. Four pairs of properties are inverse one of the other; the property `s4syst:connectedTo` is symmetric, and properties `s4syst:hasSubSystem` and `s4syst:hasSubSystem` are transitive.\n- A symbol =1 near the target of an arrow denotes that the associated property is functional. A symbol ? denotes a local existential restriction.\n\n\n![SAREF4SYST overview](diagrams/overview.png)", - "homepage": "https://saref.etsi.org/saref4syst/", - "id": "lov.s4syst", - "name": "SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections", - "prefix": "s4syst", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4syst/$1" - }, - "lov.s4watr": { - "authority": "lov", - "description": "This ontology extends the SAREF ontology for the water domain. This work has been developed in the context of the STF 566, which was established with the goal to create three SAREF extensions, one of them for the water domain.", - "homepage": "https://saref.etsi.org/saref4watr/", - "id": "lov.s4watr", - "name": "SAREF extension for water", - "prefix": "s4watr", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4watr/$1" - }, - "lov.s4wear": { - "authority": "lov", - "description": "SAREF4WEAR is an extension of SAREF for Wearables", - "homepage": "https://saref.etsi.org/saref4wear/", - "id": "lov.s4wear", - "name": "SAREF4WEAR: an extension of SAREF for Wearables", - "prefix": "s4wear", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/saref4wear/$1" - }, - "lov.sam": { - "authority": "lov", - "description": "An OWL representation of the Sampling Features Schema described in clauses 8-10 of ISO 19156:2011 Geographic Information - Observations and Measurements.", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/sampling", - "id": "lov.sam", - "name": "The Sampling Features Schema Vocabulary", - "prefix": "sam", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19156/2011/sampling#$1" - }, - "lov.samfl": { - "authority": "lov", - "description": "A simple OWL representation of the Sampling Features Schema described in clauses 9-11 of ISO 19156:2011 Geographic Information - Observations and Measurements", - "homepage": "http://def.seegrid.csiro.au/ontology/om/sam-lite", - "id": "lov.samfl", - "name": "OWL for Sampling Features", - "prefix": "samfl", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://def.seegrid.csiro.au/ontology/om/sam-lite#$1" - }, - "lov.san": { - "authority": "lov", - "description": "This ontology is intended to describe Semantic Actuator Networks, as a counterpoint to SSN definition of Semantic Sensor Networks. An actuator is a physical device having an effect on the world (see Actuator for more information).\n\nIt is worth noticing that some concepts are imported from SSN, but not SSN as a whole. This is a design choice intended to separate as much as possible the definition on actuator from the definition of sensor, which are completely different concept that can be used independantly from each other.\n\nThis ontology is used as a ontological module in IoT-O ontology.", - "homepage": "http://www.irit.fr/recherches/MELODI/ontologies/SAN", - "id": "lov.san", - "name": "SAN (Semantic Actuator Network)", - "prefix": "SAN", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.irit.fr/recherches/MELODI/ontologies/SAN#$1" - }, - "lov.san-lod": { - "authority": "lov", - "description": "SAN Ontology", - "homepage": "http://dati.san.beniculturali.it/SAN/", - "id": "lov.san-lod", - "name": "SAN Ontologia", - "prefix": "san-lod", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://dati.san.beniculturali.it/SAN/$1" - }, - "lov.sao": { - "authority": "lov", - "description": "The SALT Annotation Ontology represents the connection layer between the rhetorical and argumentation and the document structure and content", - "homepage": "http://salt.semanticauthoring.org/ontologies/sao", - "id": "lov.sao", - "name": "SALT Annotation Ontology", - "prefix": "sao", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://salt.semanticauthoring.org/ontologies/sao#$1" - }, - "lov.saont": { - "authority": "lov", - "description": "An ontology to model accountability of generic systems.", - "homepage": "https://w3id.org/sao", - "id": "lov.saont", - "name": "The System Accountability Ontology", - "prefix": "saont", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/sao#$1" - }, - "lov.saref": { - "authority": "lov", - "description": "The Smart Appliances REFerence (SAREF) ontology is a shared model of consensus that facilitates the matching of existing assets (standards/protocols/datamodels/etc.) in the smart appliances domain. The SAREF ontology provides building blocks that allow separation and recombination of different parts of the ontology depending on specific needs.", - "homepage": "https://saref.etsi.org/core/", - "id": "lov.saref", - "name": "SAREF: the Smart Appliances REFerence ontology", - "prefix": "saref", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://saref.etsi.org/core/$1" - }, - "lov.saws": { - "authority": "lov", - "description": "Ontology for the Sharing Ancient Wisdoms (SAWS) project, to represent the information and knowledge available in medieval gnomologia (collections of wise sayings). SAWS concentrates mainly on Ancient Greek and Arabic manuscripts containing wisdom literature. All class descriptions are provided by domain experts and the ontology has been developed through collaboration between these experts and ontology developers.", - "homepage": "http://purl.org/saws/ontology", - "id": "lov.saws", - "name": "Sharing Ancient Wisdoms Ontology", - "prefix": "saws", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://purl.org/saws/ontology#$1" - }, - "lov.sbeo": { - "authority": "lov", - "description": "Smart Building Evacuation Ontology (SBEO) is an ontology that couples the information about any building with its occupants such that it can be used in many useful ways. For example, indoor localization of people, detection of any hazard, a recommendation of normal routes such as shopping or stadium seating routes, or safe and feasible emergency evacuation routes or both of them all together. \n\nThe core SBEO covers the concepts related to the geometry of building, devices and components of the building, route graphs correspondent to the building topology, users' characteristics and preferences, situational awareness of both building (hazard detection, status of routes in terms of availability and occupancy) and users (tracking, management of groups, status in terms of fitness), and emergency evacuation.", - "homepage": "https://w3id.org/sbeo", - "id": "lov.sbeo", - "name": "SBEO: Smart Building Evacuation Ontology", - "prefix": "sbeo", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://w3id.org/sbeo#$1" - }, - "lov.schema": { - "authority": "lov", - "description": "Search engines including Bing, Google, Yahoo! and Yandex rely on schema.org markup to improve the display of search results, making it easier for people to find the right web pages.", - "homepage": "http://schema.org/", - "id": "lov.schema", - "name": "Schema.org vocabulary", - "prefix": "schema", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://schema.org/$1" - }, - "lov.scip": { - "authority": "lov", - "description": "A vocabulary for description of scientific people, focused on bio sciences", - "homepage": "http://lod.taxonconcept.org/ontology/sci_people.owl", - "id": "lov.scip", - "name": "Scientific People Ontology", - "prefix": "scip", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://lod.taxonconcept.org/ontology/sci_people.owl#$1" - }, - "lov.scoro": { - "authority": "lov", - "description": "SCoRO, the Scholarly Contributions and Roles Ontology, is an ontology for use by authors and publishers for describing the contributions that may be made and the roles that may be held by a person with respect to a journal article or other publication, and by research administrators and others for describing contributions and roles with respect to other aspects of scholarly research.", - "homepage": "http://purl.org/spar/scoro/", - "id": "lov.scoro", - "name": "Scholarly Contributions and Roles Ontology", - "prefix": "scoro", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://purl.org/spar/scoro/$1" - }, - "lov.scot": { - "authority": "lov", - "description": "SCOT is an ontology for describing the structure and the semantics for tagging data across heterogenous users, sources, and applications.", - "homepage": "http://rdfs.org/scot/ns#", - "id": "lov.scot", - "name": "Social Semantic Cloud of Tags", - "prefix": "scot", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdfs.org/scot/ns#$1" - }, - "lov.scovo": { - "authority": "lov", - "description": "A vocabulary for representing statistical data on the Web. Note :The SCOVO vocabulary is deprecated. We strongly advise to use the Data Cube Vocabulary instead.", - "homepage": "http://vocab.deri.ie/scovo", - "id": "lov.scovo", - "name": "The Statistical Core Vocabulary", - "prefix": "scovo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/NET/scovo#$1" - }, - "lov.scsv": { - "authority": "lov", - "description": "Mapping vocabulary for CSV files that use Schema.org terms in the header.", - "homepage": "http://vocab.deri.ie/scsv", - "id": "lov.scsv", - "name": "Schema.org CSV", - "prefix": "scsv", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/NET/schema-org-csv#$1" - }, - "lov.sd": { - "authority": "lov", - "description": "Un vocabulaire pour d\u00e9crire des services SPARQL publi\u00e9s via le protocole SPARQL 1.1 pour RDF. Ces descriptions fournissent un m\u00e9canisme par lequel un client ou un utilisateur final peuvent obtenir des informations sur le service SPARQL, telles que les extensions de fonctions support\u00e9es ou les d\u00e9tails \u00e0 propos des jeux de donn\u00e9es disponibles.", - "homepage": "http://www.w3.org/ns/sparql-service-description", - "id": "lov.sd", - "name": "SPARQL 1.1 Service Description", - "prefix": "sd", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/sparql-service-description#$1" - }, - "lov.sdm": { - "authority": "lov", - "description": "A small vocabulary for representing SPARQL endpoint metadata on the web", - "homepage": "https://w3id.org/vocab/sdm", - "id": "lov.sdm", - "name": "SPARQL endpoint metadata", - "prefix": "sdm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/vocab/sdm#$1" - }, - "lov.sdmx": { - "authority": "lov", - "description": "This vocabulary extends the data cube vocabulary to support publication of statistical data in RDF, using an information model based on SDMX", - "homepage": "http://purl.org/linked-data/sdmx", - "id": "lov.sdmx", - "name": "SDMX-RDF vocabulary", - "prefix": "sdmx", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/linked-data/sdmx#$1" - }, - "lov.sdmx-code": { - "authority": "lov", - "description": "Defines subclasses and instances of codes used in SDMX, such as currencies, decimals, frequencies ...", - "homepage": "http://purl.org/linked-data/sdmx/2009/code", - "id": "lov.sdmx-code", - "name": "SDMX Code", - "prefix": "sdmx-code", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/linked-data/sdmx/2009/code#$1" - }, - "lov.sdmx-dimension": { - "authority": "lov", - "description": "Defines dimensions for the statistical \"cubes\" defined by SDMX", - "homepage": "http://purl.org/linked-data/sdmx/2009/dimension", - "id": "lov.sdmx-dimension", - "name": "SDMX Dimension", - "prefix": "sdmx-dimension", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/linked-data/sdmx/2009/dimension#$1" - }, - "lov.sdo": { - "authority": "lov", - "description": "The SALT Document Ontology captures the linear structure of the publication, in addition to the identification and revisioning information of the publication's content.", - "homepage": "http://salt.semanticauthoring.org/ontologies/sdo", - "id": "lov.sdo", - "name": "SALT Document Ontology", - "prefix": "sdo", - "source": "lov.linkeddata.es", - "subjects": [ - "other humanities" - ], - "uri_format": "http://salt.semanticauthoring.org/ontologies/sdo#$1" - }, - "lov.sealit": { - "authority": "lov", - "description": "The SeaLiT Ontology is a formal ontology intended to facilitate the integration, mediation and interchange of heterogeneous information related to maritime history. It aims at providing the semantic definitions needed to transform disparate, localised information sources of maritime history into a coherent global resource. It also serves as a common language for domain experts and IT developers to formulate requirements and to agree on system functionalities with respect to the correct handling of historical information. The ontology uses and extends the CIDOC Conceptual Reference Model (ISO 21127:2014), in particular version 7.1.1, as a general ontology of human activity, things and events happening in space and time.", - "homepage": "http://www.sealitproject.eu/ontology/", - "id": "lov.sealit", - "name": "SeaLiT Ontology", - "prefix": "sealit", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.sealitproject.eu/ontology/$1" - }, - "lov.search": { - "authority": "lov", - "description": "A vocabulary for ranked search results, for use in the Sindice API.", - "homepage": "http://vocab.deri.ie/search", - "id": "lov.search", - "name": "Sindice Search Vocabulary", - "prefix": "search", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://sindice.com/vocab/search#$1" - }, - "lov.seas": { - "authority": "lov", - "description": "This vocabulary is version v0.1 of the ITEA2 Smart Energy Aware Systems project vocabulary. It enables the description of electricity measurements of a site using the Data Cube W3C vocabulary.", - "homepage": "https://w3id.org/seas/", - "id": "lov.seas", - "name": "SEAS ontology", - "prefix": "seas", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seas-eval": { - "authority": "lov", - "description": "The Evaluation ontology describes evaluation of [`seas:Property`ies](https://w3id.org/seas/Property). There may be:\n\n- direct evaluations, or\n- qualified evaluations.", - "homepage": "https://w3id.org/seas/EvaluationOntology", - "id": "lov.seas-eval", - "name": "The SEAS Evaluation ontology", - "prefix": "seas-eval", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seas-op": { - "authority": "lov", - "description": "The SEAS Operating Ontology defines evaluations of operating features of interest.", - "homepage": "https://w3id.org/seas/OperatingOntology", - "id": "lov.seas-op", - "name": "The SEAS Failable System ontology", - "prefix": "seas-op", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seas-qudt": { - "authority": "lov", - "description": "This ontology defines proposed alignemnts with the QUDT ontology.", - "homepage": "https://w3id.org/seas/QUDTAlignment", - "id": "lov.seas-qudt", - "name": "QUDT Alignment.", - "prefix": "seas-qudt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seas-stats": { - "authority": "lov", - "description": "This ontology defines common evaluation interpretation concepts for statistics.", - "homepage": "https://w3id.org/seas/StatisticsOntology", - "id": "lov.seas-stats", - "name": "The SEAS Statistics ontology.", - "prefix": "seas-stats", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seas-sys": { - "authority": "lov", - "description": "The System Ontology defines Systems, Connections between systems, and Connection Points at which systems may be connected. This ontology is then specialized for multiple domains. For example:\n\n- In electric energy: \n - power systems consume, produce, store, and exchange electricity;\n - power connections are where electricity flows between systems;\n - power connection points are plugs, sockets, or power busses.\n- In the electricity market:\n - players and markets are systems;\n - connections are contracts or transactions between two players, or between a player and a market;\n - connection points include offers and bids.", - "homepage": "https://w3id.org/seas/SystemOntology", - "id": "lov.seas-sys", - "name": "The SEAS System ontology", - "prefix": "seas-sys", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seasb": { - "authority": "lov", - "description": "This ontology defines batteries and their state of charge ratio property.", - "homepage": "https://w3id.org/seas/BatteryOntology", - "id": "lov.seasb", - "name": "The SEAS Battery ontology.", - "prefix": "seasb", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seasbo": { - "authority": "lov", - "description": "The SEAS Building ontology describes a taxonomy of buildings, building spaces, and rooms.\n\nSome categorizations are based on the energy efficiency related to their insulation etc., although the actual values for classes depend the country specific regulations and geographical locations.\n\nOther categorizations are based on occupancy and activities. There is no single accepted categorization available. This taxonomy uses some types selected from:\n\n- International building occupancy based categories (USA)\n- The Classification of Types of Constructions (EU)\n- Finnish building categorization VTJ2000 (Finland)\n- Wikipedia category page for Rooms: https://en.wikipedia.org/wiki/Category:Rooms", - "homepage": "https://w3id.org/seas/BuildingOntology", - "id": "lov.seasbo", - "name": "The SEAS Building Ontology", - "prefix": "seasbo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seasd": { - "authority": "lov", - "description": "The SEAS Device ontology defines `seas:Device` as physical system that are designed to execute one or more procedures that involve the physical world.", - "homepage": "https://w3id.org/seas/DeviceOntology", - "id": "lov.seasd", - "name": "The SEAS Device ontology", - "prefix": "seasd", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seasfo": { - "authority": "lov", - "description": "The SEAS Forecasting ontology extends the [Procedure Execution ontology (PEP)](https://w3id.org/pep/)", - "homepage": "https://w3id.org/seas/ForecastingOntology", - "id": "lov.seasfo", - "name": "The SEAS Forecasting ontology", - "prefix": "seasfo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seast": { - "authority": "lov", - "description": "This ontology defines:\n- a set of subclasses of `seas:Evaluation` to better interpret evaluations of quantifiable properties.\n- a set of sub properties of `seas:hasProperty` to qualify time-related properties.", - "homepage": "https://w3id.org/seas/TimeOntology", - "id": "lov.seast", - "name": "The SEAS Time Ontology.", - "prefix": "seast", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.seasto": { - "authority": "lov", - "description": "The Seas Trading Ontology defines concepts and relations to describe ownership, trading, bilateral contracts and market licenses:\n\n- players own systems and trade commodities, which have a price;\n- bilateral electricity contracts are connections between electricity traders at which they exchange\nelectricity;\n- electricity markets are connections between electricity traders at which they exchange electricity,\nusing a market license;\n- electricity markets can be cleared, and balanced;\n- evaluations can have a traded volume validity context", - "homepage": "https://w3id.org/seas/TradingOntology", - "id": "lov.seasto", - "name": "The SEAS Trading ontology", - "prefix": "seasto", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "https://w3id.org/seas/$1" - }, - "lov.security": { - "authority": "lov", - "description": "A security ontology to annotate resources with security-related information", - "homepage": "http://securitytoolbox.appspot.com/securityMain", - "id": "lov.security", - "name": "Security Ontology", - "prefix": "security", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://securitytoolbox.appspot.com/securityMain#$1" - }, - "lov.sem": { - "authority": "lov", - "description": "The SEM Ontology defines entities that make up the context of an event: Events, Actors, Places, Times.", - "homepage": "http://semanticweb.cs.vu.nl/2009/11/sem/", - "id": "lov.sem", - "name": "The SEM Ontology", - "prefix": "sem", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semanticweb.cs.vu.nl/2009/11/sem/$1" - }, - "lov.semio": { - "authority": "lov", - "description": "A vocabulary to describe signs in a semiotic approach", - "homepage": "http://www.lingvoj.org/semio.rdf", - "id": "lov.semio", - "name": "Semio, an ontology of signs", - "prefix": "semio", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.lingvoj.org/semio#$1" - }, - "lov.semiotics": { - "authority": "lov", - "description": "A content ontology pattern that encodes a basic semiotic theory, by reusing the situation pattern. The basic classes are: Expression, Meaning, Reference (the semiotic triangle), LinguisticAct (for the pragmatics), and Agent.\nA linguistic act is said to be context for expressions, with their meanings and references, and agents involved.\nBased on this pattern, several specific linguistic acts, such as 'tagging', 'translating', 'defining', 'formalizing', etc. can be defined, so constituting a formal vocabulary for a pragmatic web.", - "homepage": "http://www.ontologydesignpatterns.org/cp/owl/semiotics.owl", - "id": "lov.semiotics", - "name": "A content ontology pattern that encodes a basic semiotic theory, by reusing the situation pattern.", - "prefix": "semiotics", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.ontologydesignpatterns.org/cp/owl/semiotics.owl#$1" - }, - "lov.semsur": { - "authority": "lov", - "description": "SemSur, the Semantic Survey Ontology, is a core ontology for describing individual research problems, approaches, implementations and evaluations in a structured, comparable way.", - "homepage": "http://purl.org/SemSur/", - "id": "lov.semsur", - "name": "The Semantic Survey Ontology (semsur)", - "prefix": "semsur", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/SemSur/$1" - }, - "lov.seo": { - "authority": "lov", - "description": "The vocabulary allows for the description of data about scientific events such as conferences, symposiums and workshops.", - "homepage": "https://w3id.org/seo", - "id": "lov.seo", - "name": "The Scientific Events Ontology", - "prefix": "seo", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "https://w3id.org/seo#$1" - }, - "lov.seq": { - "authority": "lov", - "description": "Intended to represent sequence schemas. It defines the notion of transitive and intransitive precedence and their inverses. It can then be used between tasks, processes, time intervals, spatially locate objects, situations, etc.", - "homepage": "http://www.ontologydesignpatterns.org/cp/owl/sequence.owl", - "id": "lov.seq", - "name": "Sequence Pattern", - "prefix": "seq", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/cp/owl/sequence.owl#$1" - }, - "lov.service": { - "authority": "lov", - "description": "A micro-ontology that defines the general concept of a service.", - "homepage": "http://purl.org/ontology/service", - "id": "lov.service", - "name": "The Service Ontology", - "prefix": "service", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/service#$1" - }, - "lov.sf": { - "authority": "lov", - "description": "A specification of GeoSPARQL for simple features geometries (points, lines, polygons ...)", - "homepage": "http://www.opengis.net/ont/sf", - "id": "lov.sf", - "name": "Simplified Features Geometry", - "prefix": "sf", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://www.opengis.net/ont/sf#$1" - }, - "lov.sh": { - "authority": "lov", - "description": "This vocabulary defines terms used in SHACL, the W3C Shapes Constraint Language.", - "homepage": "http://www.w3.org/ns/shacl#", - "id": "lov.sh", - "name": "W3C Shapes Constraint Language (SHACL) Vocabulary", - "prefix": "sh", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/shacl#$1" - }, - "lov.shoah": { - "authority": "lov", - "description": "The ontology describing the Shoah domain, proposed here in beta version, aims to formally describe concepts and relationships that characterize the process of persecution and deportation of Jews in Italy between 1943 and 1945.", - "homepage": "http://dati.cdec.it/lod/shoah/", - "id": "lov.shoah", - "name": "Shoah Vocabulary Specification", - "prefix": "shoah", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://dati.cdec.it/lod/shoah/$1" - }, - "lov.shw": { - "authority": "lov", - "description": "An ontology defining weather-related concepts and properties being relevant to smart home systems that provide predictive control.", - "homepage": "http://paul.staroch.name/thesis/SmartHomeWeather.owl#", - "id": "lov.shw", - "name": "Smart Home Weather", - "prefix": "shw", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "http://paul.staroch.name/thesis/SmartHomeWeather.owl#$1" - }, - "lov.sim": { - "authority": "lov", - "description": "An ontology to describe associations between things. Although this ontology was designed with music similarity in mind, it can readily be applied to other domains.", - "homepage": "http://purl.org/ontology/similarity/", - "id": "lov.sim", - "name": "The Similarity Ontology", - "prefix": "sim", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/similarity/$1" - }, - "lov.simu": { - "authority": "lov", - "description": "This ontology was designed to conceptualize symbolic meanings following Baudrillard's Simulacra and Simulation theory. Symbols, their meaning, the context in which the symbolic meaning (or simulation) exists and the source of the simulation are linked to a N-ary Simulation Class.", - "homepage": "https://www.w3id.org/simulation/ontology/", - "id": "lov.simu", - "name": "Simulation Ontology", - "prefix": "simu", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "https://www.w3id.org/simulation/ontology/$1" - }, - "lov.sio": { - "authority": "lov", - "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.", - "homepage": "http://semanticscience.org/ontology/sio.owl", - "id": "lov.sio", - "name": "Semanticscience Integrated Ontology", - "prefix": "sio", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://semanticscience.org/resource/$1" - }, - "lov.sioc": { - "authority": "lov", - "description": "SIOC is an ontology for describing the information in online communities.", - "homepage": "http://rdfs.org/sioc/ns#", - "id": "lov.sioc", - "name": "Semantically-Interlinked Online Communities", - "prefix": "sioc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdfs.org/sioc/ns#$1" - }, - "lov.situ": { - "authority": "lov", - "description": "A pattern to represent contexts or situations, and the things that are contextualized.", - "homepage": "http://www.ontologydesignpatterns.org/cp/owl/situation.owl", - "id": "lov.situ", - "name": "Situation Pattern", - "prefix": "situ", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/cp/owl/situation.owl#$1" - }, - "lov.skos": { - "authority": "lov", - "description": "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web.", - "homepage": "http://www.w3.org/2004/02/skos/core", - "id": "lov.skos", - "name": "Simple Knowledge Organization System", - "prefix": "skos", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2004/02/skos/core#$1" - }, - "lov.skosxl": { - "authority": "lov", - "description": "SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.", - "homepage": "http://www.w3.org/2008/05/skos-xl", - "id": "lov.skosxl", - "name": "SKOS eXtension for Labels", - "prefix": "skosxl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2008/05/skos-xl#$1" - }, - "lov.smg": { - "authority": "lov", - "description": "A Profile of the IEC Common Information Model for Smart Grids, developed by the Cerise-SG project.", - "homepage": "http://ns.cerise-project.nl/energy/def/cim-smartgrid", - "id": "lov.smg", - "name": "CERISE CIM Profile for Smart Grids", - "prefix": "smg", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://ns.cerise-project.nl/energy/def/cim-smartgrid#$1" - }, - "lov.snarm": { - "authority": "lov", - "description": "This ontology is designed for representing access rights within a simple network of associated users/groups", - "homepage": "http://rdf.myexperiment.org/ontologies/snarm/", - "id": "lov.snarm", - "name": "Simple Network Access Rights Management Ontology", - "prefix": "snarm", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://rdf.myexperiment.org/ontologies/snarm/$1" - }, - "lov.solid": { - "authority": "lov", - "description": "Solid terms", - "homepage": "http://www.w3.org/ns/solid/terms", - "id": "lov.solid", - "name": "Solid terms", - "prefix": "solid", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://www.w3.org/ns/solid/terms#$1" - }, - "lov.sor": { - "authority": "lov", - "description": "The Social Relationships ONtology (SORON) attempts to describe the different types of social relationships in society (both objective and subjective). Current version focuses on inter-personal 1:1 relationships (except family relationships). Other types of relationships may be covered in later versions. It complements FOAF and RELATIONSHIP ontologies.", - "homepage": "http://purl.org/net/soron", - "id": "lov.sor", - "name": "SORON: Social Relationships ONtology", - "prefix": "sor", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/soron/$1" - }, - "lov.sosa": { - "authority": "lov", - "description": "This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.", - "homepage": "http://www.w3.org/ns/sosa/", - "id": "lov.sosa", - "name": "Sensor, Observation, Sample, and Actuator (SOSA) Ontology", - "prefix": "sosa", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/ns/sosa/$1" - }, - "lov.sp": { - "authority": "lov", - "description": "An RDF Schema to syntactically represent SPARQL queries (including SPARQL UPDATE) as RDF triples.", - "homepage": "http://spinrdf.org/sp", - "id": "lov.sp", - "name": "SPIN SPARQL Syntax", - "prefix": "sp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://spinrdf.org/sp#$1" - }, - "lov.spatial": { - "authority": "lov", - "description": "A vocabulary for describing topological relations between features", - "homepage": "http://geovocab.org/spatial", - "id": "lov.spatial", - "name": "NeoGeo Spatial Ontology", - "prefix": "spatial", - "source": "lov.linkeddata.es", - "subjects": [ - "mathematics" - ], - "uri_format": "http://geovocab.org/spatial#$1" - }, - "lov.spcm": { - "authority": "lov", - "description": "La planificaci\u00f3n y monitorizaci\u00f3n de la ejecuci\u00f3n de proyectos software puede llevarse a cabo con diferentes herramientas, desde sistemas basados en gesti\u00f3n de tareas, hasta herramientas especializadas en diagramas de Gantt o incluso mediante simples hojas de c\u00e1lculo. Este vocabulario contempla los elementos t\u00edpicos a la hora de controlar los proyectos de desarrollo o mantenimiento de software.", - "homepage": "http://spi-fm.uca.es/spdef/models/deployment/spcm/1.0", - "id": "lov.spcm", - "name": "Software Process Control Model", - "prefix": "spcm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://spi-fm.uca.es/spdef/models/deployment/spcm/1.0#$1" - }, - "lov.spfood": { - "authority": "lov", - "description": "Defines concepts and properties specific for the SmartProducts Philips use case (cooking domain).", - "homepage": "http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl", - "id": "lov.spfood", - "name": "SmartProducts Food Domain Model", - "prefix": "spfood", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl#$1" - }, - "lov.spin": { - "authority": "lov", - "description": "An RDF Schema that can be used to attach constraints and rules to RDFS classes, and to encapsulate reusable SPARQL queries into functions and templates.", - "homepage": "http://spinrdf.org/spin", - "id": "lov.spin", - "name": "SPIN Inferencing Vocabulary", - "prefix": "spin", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://spinrdf.org/spin#$1" - }, - "lov.sport": { - "authority": "lov", - "description": "A simple ontology for representing competitive sports events.", - "homepage": "http://www.bbc.co.uk/ontologies/sport", - "id": "lov.sport", - "name": "BBC Sport Ontology", - "prefix": "sport", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.bbc.co.uk/ontologies/sport/$1" - }, - "lov.spt": { - "authority": "lov", - "description": "TheSPITFIRE Ontology (spt) is based on the alignment among Dolce+DnS Ultralite(dul), the W3C Semantic Sensor Network ontology (ssn) and the Event Model-F ontology (event).", - "homepage": "http://spitfire-project.eu/ontology/ns", - "id": "lov.spt", - "name": "SPITFIRE Ontology", - "prefix": "spt", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://spitfire-project.eu/ontology/ns/$1" - }, - "lov.spvqa": { - "authority": "lov", - "description": "The ontology is aimed at the support of research groups in the field of Business Modeling and Knowledge Engineering (BMaKE) in their collaborative work for qualitatively analyzing scholarly papers as well as sharing the results of that analyses and judgements.", - "homepage": "https://bmake.th-brandenburg.de/spv", - "id": "lov.spvqa", - "name": "Scholarly Papers Vocabulary with Focus on Qualtitative Analysis", - "prefix": "spvqa", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://bmake.th-brandenburg.de/spv#$1" - }, - "lov.sql": { - "authority": "lov", - "description": "The SQL AST Vocabulary allows SQL code abstract syntax trees to be published in RDF.", - "homepage": "http://ns.inria.fr/ast/sql#", - "id": "lov.sql", - "name": "SQL Abstract Syntax Trees Vocabulary", - "prefix": "sql", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://ns.inria.fr/ast/sql#$1" - }, - "lov.ssn": { - "authority": "lov", - "description": "This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.", - "homepage": "http://www.w3.org/ns/ssn/", - "id": "lov.ssn", - "name": "Semantic Sensor Network Ontology", - "prefix": "ssn", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/ns/ssn/$1" - }, - "lov.ssno": { - "authority": "lov", - "description": "This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.", - "homepage": "http://www.w3.org/ns/ssn/", - "id": "lov.ssno", - "name": "Semantic Sensor Network Ontology", - "prefix": "ssno", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/ns/ssn/$1" - }, - "lov.ssso": { - "authority": "lov", - "description": "An event-based RDF ontology for typical status in fulfillment of a service", - "homepage": "http://purl.org/ontology/ssso", - "id": "lov.ssso", - "name": "Simple Service Status Ontology", - "prefix": "ssso", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/ssso#$1" - }, - "lov.st": { - "authority": "lov", - "description": "This ontology provides the predicates necessary to describe an arrival of a transit vehicle and its departure at a certain Stop.", - "homepage": "http://semweb.mmlab.be/ns/stoptimes#Ontology", - "id": "lov.st", - "name": "The Stop Times ontology", - "prefix": "st", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://semweb.mmlab.be/ns/stoptimes#$1" - }, - "lov.stac": { - "authority": "lov", - "description": "A vocabulary to describe main security and cryptographic concepts: attacks, security mechanisms, OSI model, security protocols, security tools in numerous technologies: Web applications, network management, Sensor networks, Cellular (2G, 3G, 4G) and Wireless (Wifi), etc.", - "homepage": "http://securitytoolbox.appspot.com/stac", - "id": "lov.stac", - "name": "Security Toolbox : Attacks and Countermeasures", - "prefix": "stac", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://securitytoolbox.appspot.com/stac#$1" - }, - "lov.step": { - "authority": "lov", - "description": "A lightweight ontology for representing semantic trajectories and contextual elements in terms of features of interests and episodes.", - "homepage": "http://purl.org/net/step", - "id": "lov.step", - "name": "Semantic Trajectory Episodes", - "prefix": "step", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://purl.org/net/step#$1" - }, - "lov.sto": { - "authority": "lov", - "description": "A vocabulary to describe the relation between standards in use on the Industry 4.0, and related concepts", - "homepage": "https://w3id.org/i40/sto#", - "id": "lov.sto", - "name": "i40 Standards Lanscape Vocabulary", - "prefix": "sto", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/i40/sto#$1" - }, - "lov.stories": { - "authority": "lov", - "description": "The Stories ontology was developed in collaboration with the BBC, with an aim to creating an ontology for narrative representation that could be applied across a diverse set of cases. These included accounts of events in Northern Ireland, the storylines of Doctor Who episodes, and key events of the Battle of Britain.", - "homepage": "http://purl.org/ontology/stories/", - "id": "lov.stories", - "name": "Stories Ontology", - "prefix": "stories", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/stories/$1" - }, - "lov.summa": { - "authority": "lov", - "description": "The SUMMA Vocabulary enables to request and represent summarized RDf resources. It should be used in context to the SUMMA API definition.", - "homepage": "http://purl.org/voc/summa/", - "id": "lov.summa", - "name": "SUMMA Vocabulary", - "prefix": "summa", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/voc/summa/$1" - }, - "lov.sur": { - "authority": "lov", - "description": "Ontology for surveys based on the Coney data model.", - "homepage": "https://www.w3id.org/survey-ontology", - "id": "lov.sur", - "name": "The Survey Ontology", - "prefix": "sur", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/survey-ontology#$1" - }, - "lov.sw-quality": { - "authority": "lov", - "description": "Quality, architecture, and process are considered the keystones of software engineering. ISO defines them in three separate standards. However, their interaction has been poorly studied, so far. The SQuAP model (Software Quality, Architecture, Process) describes twenty-eight main factors that impact on software quality in banking systems, and each factor is described as a relation among some characteristics from the three ISO standards. Hence, SQuAP makes such relations emerge rigorously, although informally. SQaAP-Ont is an OWL ontology that formalises those relations in order to represent and reason via Linked Data about software engineering in a three-dimensional model consisting of quality, architecture, and process characteristics.", - "homepage": "https://w3id.org/squap/", - "id": "lov.sw-quality", - "name": "SQuAP Ontology", - "prefix": "sw-quality", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/squap/SoftwareQuality/$1" - }, - "lov.swc": { - "authority": "lov", - "description": "The Semantic Web Conference ontology (SWC) is an ontology for describing academic conferences", - "homepage": "http://data.semanticweb.org/ns/swc/ontology", - "id": "lov.swc", - "name": "Semantic Web Conference Ontology", - "prefix": "swc", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://data.semanticweb.org/ns/swc/ontology#$1" - }, - "lov.swemls": { - "authority": "lov", - "description": "An ontology to describe a Semantic-Web Machine Learning System (SWeMLS)", - "homepage": "https://w3id.org/semsys/ns/swemls", - "id": "lov.swemls", - "name": "Semantic-Web Machine Learning System (SWeMLS) Ontology", - "prefix": "swemls", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/semsys/ns/swemls#$1" - }, - "lov.swp": { - "authority": "lov", - "description": "This vocabulary allows to attach an authority to a named graph", - "homepage": "http://www.w3.org/2004/03/trix/swp-1", - "id": "lov.swp", - "name": "Graph Authority", - "prefix": "swp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2004/03/trix/swp-1/$1" - }, - "lov.swpm": { - "authority": "lov", - "description": "During the modeling of software processes, work products are traditionally treated as atomic units, with names but no structure, and they are generated or changed during the course of the projects. In fact, the language SPEM does not offer mechanisms to detail the structure of work products, allowing only identify whether it is an artifact, a deliverable or an outcome of the project. The typical work products in the software processes are often documents or source code and they are managed from specialized or generic tools. For example, software modeling tools such as Rational Rose, or version control systems such as Git are examples of specialized tools that provide support to the management of certain types of work products. However, other generic tools such as content management systems, document management systems and collaborative editing systems or wikis can also be used to manage evidences of the processes. The design of models for certain types of work products has been an approach used in model-driven web methodologies. However, it is common the need for adapting and customizing well-known methodologies for their application in concrete situations and in specific organizations, a.k.a. process tailoring. Therefore, a vocabulary to define flexible work products in terms of structure and type of its artifacts is proposed here.", - "homepage": "http://spi-fm.uca.es/spdef/models/deployment/swpm/1.0", - "id": "lov.swpm", - "name": "Software Work Product Model", - "prefix": "swpm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://spi-fm.uca.es/spdef/models/deployment/swpm/1.0#$1" - }, - "lov.swpo": { - "authority": "lov", - "description": "The aim of the Semantic Web Portal Ontology is to serve as the conceptual backbone for community portals driven by Semantic Web technologies.", - "homepage": "http://sw-portal.deri.org/ontologies/swportal", - "id": "lov.swpo", - "name": "Semantic Web Portal Ontology", - "prefix": "swpo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://sw-portal.deri.org/ontologies/swportal#$1" - }, - "lov.swrc": { - "authority": "lov", - "description": "An ontology for modeling entities of research communities such as persons, organisations, publications (bibliographic metadata) and their relationship", - "homepage": "http://swrc.ontoware.org/ontology-07", - "id": "lov.swrc", - "name": "Semantic Web for Research Communities", - "prefix": "swrc", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://swrc.ontoware.org/ontology#$1" - }, - "lov.swrl": { - "authority": "lov", - "description": "OWL definition of the RDF Concrete Syntax for the Semantic Web Rule Language", - "homepage": "http://www.w3.org/2003/11/swrl", - "id": "lov.swrl", - "name": "Semantic Web Rule Language", - "prefix": "swrl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2003/11/swrl#$1" - }, - "lov.synsem": { - "authority": "lov", - "description": "A model for the representation of lexical information relative to ontologies. Syntax and semantics module.", - "homepage": "http://www.w3.org/ns/lemon/synsem", - "id": "lov.synsem", - "name": "Lexicon Model for Ontologies - Synsem", - "prefix": "synsem", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/lemon/synsem#$1" - }, - "lov.tac": { - "authority": "lov", - "description": "The TripleAccessControl Ontology is an extension to WebAccessControl Ontology to describe access control rules for RDF triples.", - "homepage": "http://ns.bergnet.org/tac/0.1/triple-access-control", - "id": "lov.tac", - "name": "TripleAccessControl Ontology", - "prefix": "tac", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://ns.bergnet.org/tac/0.1/triple-access-control#$1" - }, - "lov.tag": { - "authority": "lov", - "description": "An ontology that let users define relationships between Tag objects and URIs of Semantic Web resources", - "homepage": "http://www.holygoat.co.uk/owl/redwood/0.1/tags/", - "id": "lov.tag", - "name": "Tag ontology", - "prefix": "tag", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.holygoat.co.uk/owl/redwood/0.1/tags/$1" - }, - "lov.tao": { - "authority": "lov", - "description": "TAO is a light-weight vocabulary to describe asserted user\u2019s subjective trust values.", - "homepage": "http://vocab.deri.ie/tao", - "id": "lov.tao", - "name": "Trust Assertion Ontology", - "prefix": "tao", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.deri.ie/tao#$1" - }, - "lov.tax": { - "authority": "lov", - "description": "EUdaphobase Taxonomy Ontology for the European Soil-Biology Data Warehouse for Soil Protection", - "homepage": "https://w3id.org/EUTaxO", - "id": "lov.tax", - "name": "EUTaxO - EUdaphobase Taxonomy Ontology", - "prefix": "tax", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "https://w3id.org/EUTaxO#$1" - }, - "lov.taxon": { - "authority": "lov", - "description": "This is the initial vocabulary for mapping the various taxon classes on the Linked Open Data Cloud", - "homepage": "http://purl.org/biodiversity/taxon/", - "id": "lov.taxon", - "name": "TaxonMap Ontology", - "prefix": "taxon", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://purl.org/biodiversity/taxon/$1" - }, - "lov.taxref-ld": { - "authority": "lov", - "description": "Representation of the TAXREF taxonomic register as linked data. This resource is at the same time an ontology of classes depicting the taxa and a thesaurus (SKOS concept scheme) of the scientific names attached to the taxa.", - "homepage": "http://taxref.mnhn.fr/lod/taxref-ld", - "id": "lov.taxref-ld", - "name": "TAXREF-LD Ontology", - "prefix": "taxref-ld", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences", - "earth and related environmental sciences" - ], - "uri_format": "http://taxref.mnhn.fr/lod/$1" - }, - "lov.tb": { - "authority": "lov", - "description": "An ontology to describe people and requests for timebanks. This includes the poeple's skills, limitations, and environment.", - "homepage": "https://w3id.org/timebank", - "id": "lov.tb", - "name": "Timebank Ontology", - "prefix": "tb", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/timebank#$1" - }, - "lov.td": { - "authority": "lov", - "description": "This ontology aims to model the Web of Things domain according to the W3C Interest Group (http://w3c.github.io/wot/)", - "homepage": "https://www.w3.org/2019/wot/td", - "id": "lov.td", - "name": "Thing Description Ontology", - "prefix": "td", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://www.w3.org/2019/wot/td#$1" - }, - "lov.tddfa": { - "authority": "lov", - "description": "Module for Action (and Frame) modelling inside domain.", - "homepage": "https://w3id.org/todo/tododfa", - "id": "lov.tddfa", - "name": "TODODFA: Frame-Action Module for Task-Oriented Dialogue management Ontology (TODO)", - "prefix": "tddfa", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/todo/tododfa#$1" - }, - "lov.tddial": { - "authority": "lov", - "description": "Module for dialogue process and system output management.", - "homepage": "https://w3id.org/todo/tododial", - "id": "lov.tddial", - "name": "TODODial: Dialogue Module for Task-Oriented Dialogue management Ontology (TODO)", - "prefix": "tddial", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/todo/tododial#$1" - }, - "lov.tddm": { - "authority": "lov", - "description": "Module for dialogue process and system output management.", - "homepage": "https://w3id.org/todo/tododm", - "id": "lov.tddm", - "name": "TODODM: Dialogue Management Module for Task-Oriented Dialogue management Ontology (TODO)", - "prefix": "tddm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/todo/tododm#$1" - }, - "lov.tddom": { - "authority": "lov", - "description": "Module for domain modelling.", - "homepage": "https://w3id.org/todo/tododom", - "id": "lov.tddom", - "name": "TODODom: Domain Module for Task-Oriented Dialogue management Ontology (TODO)", - "prefix": "tddom", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/todo/tododom#$1" - }, - "lov.tddt": { - "authority": "lov", - "description": "Module for dialogue tracing.", - "homepage": "https://w3id.org/todo/tododt", - "id": "lov.tddt", - "name": "TODODT: Dialogue Tracing Module for Task-Oriented Dialogue management Ontology (TODO)", - "prefix": "tddt", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/todo/tododt#$1" - }, - "lov.tddw": { - "authority": "lov", - "description": "Module for scenario modelling (world elements) of domain.", - "homepage": "https://w3id.org/todo/tododw", - "id": "lov.tddw", - "name": "TODODW: World Module for Task-Oriented Dialogue management Ontology (TODO)", - "prefix": "tddw", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/todo/tododw#$1" - }, - "lov.te": { - "authority": "lov", - "description": "An entry sub-ontology of time (OWL-Time).", - "homepage": "http://www.w3.org/2006/time-entry", - "id": "lov.te", - "name": "Time Entry", - "prefix": "te", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2006/time-entry#$1" - }, - "lov.teach": { - "authority": "lov", - "description": "TEACH, the Teaching Core Vocabulary, is a lightweight vocabulary providing terms to enable teachers to relate things in their courses together. The Teaching Core Vocabulary is based on practical requirements set by providing seminar and course descriptions as Linked Data.", - "homepage": "http://linkedscience.org/teach/ns#", - "id": "lov.teach", - "name": "Teaching Core Vocabulary Specification", - "prefix": "teach", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://linkedscience.org/teach/ns#$1" - }, - "lov.tempo": { - "authority": "lov", - "description": "In a typical (uni)temporal data model every resource's appearance (and disappearance) is being tracked.\nNumerous systems accomplish unitemporal tracking, either externally by e.g. using git to record the insertion or deletion of a resource, or internally by e.g. using prov:generatedAtTime and prov:invalidatedAtTime.\nThis axis of time is known as *system time*, and none of TempO's concern because for one there is readily available support, and moreover because unitemporal tracking is used for principally true statements, i.e. those that have always been (considered) true or will always be (considered) true.\n\nTempO addresses bitemporal and tritemporal setups: Resources which are (known or believed to be) valid and efficacious for some time.\nA second time axis orthogonal to system time is introduced, that is a resource can be valid even though it is currently not in the system, or, conversely, can be already or still invalid by the time it enters the system.\n\nEfficacy, sometimes called decision time, is yet another concept orthogonal to validity, i.e. a resource that is no longer or not yet valid can be efficacious.\nThe converse, a valid but inefficacious resource in the system, is *usually* not encountered but TempO does not impose restrictions on the shape of the time area.\n\nIn general the necessity for tracking both validity and efficacy arises in areas where concepts are assigned a code or label that is subject to reuse following invalidation.\nTracking efficacy and validity concurrently then allows for fine-grained control over how much future knowledge or how much past knowledge we tolerate in a datset.\n\nExample:\n--------\nCzechoslovakia was founded in 1918 but became part of Germany, Hungary and Poland in 1938.\nIt was reestablished in 1945 but split into two sovereign states in 1993.\nThe ISO 3166 country code for Czechoslovakia used to be 'CS', assigned in 1974, published in February 1978, and invalidated with the country's split.\nIn 2003 ISO 3166 reassigned the country code 'CS' to Serbia and Montenegro.\nThe facts were assembled in 2018 and written down as follows:\n\n cc:CSHH\n a cc:ISO3166-CountryCode ;\n rdfs:label \"CS\" ;\n cc:refersTo \"Czechoslovakia\" ;\n prov:generatedAtTime \"2018-02-29T04:00:00Z\"^^xsd:dateTime .\n tempo:validFrom \"1978-02\"^^xsd:gYearMonth ;\n tempo:validTill \"1993-01-01\"^^xsd:date ;\n tempo:efficaciousFrom \"1918\"^^xsd:gYear , \"1945\"^^xsd:gYear ;\n tempo:efficaciousTill \"1938\"^^xsd:gYear , \"2003\"^^xsd:gYear .\n\nThe use of the country code 'CS' in a statement from 1988 can be resolved to cc:CSHH, as of today, free from ambiguity; it was valid back then after all and we know that today.\nThe same query in 2017 (point-in-time query) would have yielded no results because the information hadn't been in the system back then.\nPoint-in-time queries, however, are not TempO's major concern so only as-of-today queries are assumed from now on.\n\nFollowing the country's split it is highly likely that news reports from, say, 1994 highlighting the then-recent past would still have used 'CS' to refer to cc:CSHH.\nAccording to the resource this is possible, a query for 'CS' in 1994 would bring up cc:CSHH as it is efficacious but marked as invalidated.\n\nOn the other end of history, the use of the code 'CS' in, say, 1976 is plausible. The code was decided on but not yet formally published.\nA query for 'CS' as used in 1976 would bring up cc:CSHH, marked as anachronistic.\nGoing back further, a statement from, say 1942, using the code 'CS' must clearly refer to something else.\nA query for 'CS' as used in 1976 would yield not yield any results.\n\n--\n\nThe ontology IRI http://purl.org/tempo/ always resolve to the latest version of TempO. Particular versionIRIs such as http://purl.org/tempo/0.1/ can be used by clients to force the import of a particular version.\n\nThe goal of TempO is to allow for temporal constraints with control over how much future or past is permissible directly on the published resource, and as such, TempO does not restrict domain/ranges.", - "homepage": "http://purl.org/tempo", - "id": "lov.tempo", - "name": "TempO - Temporal Ontology", - "prefix": "tempo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/tempo/$1" - }, - "lov.test": { - "authority": "lov", - "description": "This ontology aims at defining the Quality Assurance Framework by collecting the test development experience of W3C Working Groups and summarizing the work done about tests and metadata.", - "homepage": "http://www.w3.org/2006/03/test-description", - "id": "lov.test", - "name": "Test Metadata", - "prefix": "test", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2006/03/test-description#$1" - }, - "lov.tfo": { - "authority": "lov", - "description": "This document describes functions which transform HTTP representations, i.e., the actual literal payloads of HTTP messages.", - "homepage": "https://privatealpha.com/ontology/transformation/1#", - "id": "lov.tfo", - "name": "Transformation Functions Ontology", - "prefix": "tfo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://privatealpha.com/ontology/transformation/1#$1" - }, - "lov.theatre": { - "authority": "lov", - "description": "An ontology for organising theatrical data.", - "homepage": "http://purl.org/theatre#", - "id": "lov.theatre", - "name": "Theatre Ontology", - "prefix": "theatre", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/theatre#$1" - }, - "lov.thors": { - "authority": "lov", - "description": "An OWL representation of the model for Temporal Ordinal Reference Systems defined in GeoSciML v3.", - "homepage": "http://resource.geosciml.org/ontology/timescale/thors", - "id": "lov.thors", - "name": "The Temporal Ordinal Reference Systems", - "prefix": "thors", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://resource.geosciml.org/ontology/timescale/thors#$1" - }, - "lov.ti": { - "authority": "lov", - "description": "This pattern is extracted from DOLCE-UltraLite by partial clone of elements and expansion. Two datatype properties have been added which allow to express the boundaries of the time interval.", - "homepage": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl", - "id": "lov.ti", - "name": "The Time Interval Pattern", - "prefix": "ti", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#$1" - }, - "lov.time": { - "authority": "lov", - "description": "This vocabulary defines temporal entities such as time intervals, their properties and relationships.", - "homepage": "http://www.w3.org/2006/time", - "id": "lov.time", - "name": "Time Ontology", - "prefix": "time", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2006/time#$1" - }, - "lov.tio": { - "authority": "lov", - "description": "A vocabulary for describing tickets for events, transportation, or points of interest for e-commerce.", - "homepage": "http://purl.org/tio/ns#", - "id": "lov.tio", - "name": "The Tickets Ontology", - "prefix": "tio", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/tio/ns#$1" - }, - "lov.tis": { - "authority": "lov", - "description": "A generic pattern usable for all situations that require a temporal indexing.", - "homepage": "http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl", - "id": "lov.tis", - "name": "Time Indexed Situation", - "prefix": "tis", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl$1" - }, - "lov.tisc": { - "authority": "lov", - "description": "TISC, the Open Time and Space Core Vocabulary, is a lightweight spatiotemporal vocabulary aiming to provide spatial and temporal terms such as \"happensAt\", \"locatedAt\", \"rightOf\" to enable practitioners to relate their data to time and space.", - "homepage": "http://www.observedchange.com/tisc/ns#", - "id": "lov.tisc", - "name": "Open Time and Space Core Vocabulary", - "prefix": "tisc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://observedchange.com/tisc/ns#$1" - }, - "lov.tl": { - "authority": "lov", - "description": "Extends owl-time ontology with support for several timelines, acting as a backbone to adress time interval/instants. Mainly designed with a multimedia use-case in mind.", - "homepage": "http://purl.org/NET/c4dm/timeline.owl", - "id": "lov.tl", - "name": "The Timeline Ontology", - "prefix": "tl", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/NET/c4dm/timeline.owl#$1" - }, - "lov.tm": { - "authority": "lov", - "description": "An OWL representation of part of the model for Temporal objects and reference systems from ISO 19108:2002 Geographic Information - Temporal Schema", - "homepage": "http://def.seegrid.csiro.au/isotc211/iso19108/2002/temporal", - "id": "lov.tm", - "name": "A vocabulary for temporal objects in Geographic Information", - "prefix": "tm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://def.seegrid.csiro.au/isotc211/iso19108/2002/temporal#$1" - }, - "lov.tmo": { - "authority": "lov", - "description": "The Translational Medicine Ontology (TMO) is a high-level, patient-centric ontology that extends existing domain ontologies to integrate data across aspects of drug discovery and clinical practice. The ontology has been developed by participants in the World Wide Web Consortium's Semantic Web for Health Care and Life Sciences Interest Group", - "homepage": "http://www.w3.org/2001/sw/hcls/ns/transmed/", - "id": "lov.tmo", - "name": "Translational Medicine Ontology", - "prefix": "tmo", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "http://www.w3.org/2001/sw/hcls/ns/transmed/$1" - }, - "lov.toco": { - "authority": "lov", - "description": "A ontology developed for telecommunciation network systems with hybrid technologies, e.g., WiFi, LiFi, LTE, 2G/3G, optical, etc.", - "homepage": "http://purl.org/toco/", - "id": "lov.toco", - "name": "Toucan Ontology", - "prefix": "toco", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/toco/$1" - }, - "lov.todo": { - "authority": "lov", - "description": "With the aim of enhancing natural communication between workers in industrial environments and the systems to be used by them, TODO (Task-Oriented Dialogue management Ontology) has been developed to be the core of task-oriented dialogue systems. TODO is a core ontology that provides task-oriented dialogue systems with the necessary means to be capable of naturally interacting with workers (both at understanding and at ommunication levels) and that can be easily adapted to different industrial scenarios, reducing adaptation time and costs. Moreover, it allows to store and reproduce the dialogue process to be able to learn from new interactions.", - "homepage": "https://w3id.org/todo", - "id": "lov.todo", - "name": "TODO: Task-Oriented Dialogue management Ontology", - "prefix": "todo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/todo#$1" - }, - "lov.topo": { - "authority": "lov", - "description": "Ontologie d\u00e9crivant les \u00e9l\u00e9ments du territoire et ses infrastructures. Elle repend l'essentiel du vocabulaire de la BDTOPO(IGN) et vise \u00e0 couvrir l'ensemble des entit\u00e9s topographiques et administratives du territoire national. Les th\u00e8mes couverts sont: le r\u00e9seau routier, le r\u00e9seau ferroviaire, le r\u00e9seau de transport d'\u00e9nergie, le r\u00e9seau hydrographique, les b\u00e2timents, la v\u00e9g\u00e9tation arbor\u00e9e, l'orographie, les communes, les points d'activit\u00e9 ou d'int\u00e9r\u00eat.", - "homepage": "http://data.ign.fr/def/topo", - "id": "lov.topo", - "name": "Ontologie des \u00e9l\u00e9ments du territoire et de ses infrastructures de l'IGN", - "prefix": "topo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://data.ign.fr/def/topo#$1" - }, - "lov.tp": { - "authority": "lov", - "description": "A vocabulary to describe touristic places: accommodations, points of interest, restaurants and attractions.", - "homepage": "http://tour-pedia.org/download/tp.owl", - "id": "lov.tp", - "name": "Tourpedia Ontology", - "prefix": "tp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://tour-pedia.org/download/tp.owl#$1" - }, - "lov.traffic": { - "authority": "lov", - "description": "An ontology that describes the management of the traffic in a straight road with two lanes, both in the same direction.", - "homepage": "http://www.sensormeasurement.appspot.com/ont/transport/traffic", - "id": "lov.traffic", - "name": "Road Traffic Management", - "prefix": "traffic", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.sensormeasurement.appspot.com/ont/transport/traffic#$1" - }, - "lov.trait": { - "authority": "lov", - "description": "OntoMedia (Ontology for Media) has been designed to describe the traits of entities.", - "homepage": "http://contextus.net/ontology/ontomedia/ext/common/trait#", - "id": "lov.trait", - "name": "OntoMedia Trait Representation", - "prefix": "trait", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://contextus.net/ontology/ontomedia/ext/common/trait#$1" - }, - "lov.transit": { - "authority": "lov", - "description": "A vocabulary for describing transit systems and routes", - "homepage": "http://vocab.org/transit/terms/", - "id": "lov.transit", - "name": "TRANSIT", - "prefix": "transit", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://vocab.org/transit/terms/$1" - }, - "lov.trao": { - "authority": "lov", - "description": "Transport Administration Ontology (TAO) for describing data from Swedish Transport Administration Web site.", - "homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/tao#", - "id": "lov.trao", - "name": "Transport Administration Ontology", - "prefix": "trao", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://linkeddata.finki.ukim.mk/lod/ontology/tao#$1" - }, - "lov.tree": { - "authority": "lov", - "description": "A hypermedia specification for fragmenting collections.", - "homepage": "https://w3id.org/tree", - "id": "lov.tree", - "name": "TREE", - "prefix": "tree", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/tree#$1" - }, - "lov.tresiot": { - "authority": "lov", - "description": "This ontology models trust recommendation concepts in SIoT to bridge the gap between abstract trust concepts and real-world device concepts.", - "homepage": "https://liidr.org/trust-recommendation-in-social-internet-of-things/", - "id": "lov.tresiot", - "name": "Ontology for Trust Recommendation in Social Internet of Things", - "prefix": "tresiot", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://liidr.org/trust-recommendation-in-social-internet-of-things/$1" - }, - "lov.tsioc": { - "authority": "lov", - "description": "Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms.", - "homepage": "http://rdfs.org/sioc/types#", - "id": "lov.tsioc", - "name": "SIOC Types Ontology Module", - "prefix": "tsioc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdfs.org/sioc/types#$1" - }, - "lov.tsn": { - "authority": "lov", - "description": "This RDF ontology allows describing any Territorial Statistical Nomenclature (TSN) (i.e., partition of the territory) used as a support to socio-economic data (statistical data that describe territory in terms of population, unemployement rate, transport access, etc.).", - "homepage": "http://purl.org/net/tsn#", - "id": "lov.tsn", - "name": "Territorial Statistical Nomenclature Ontology", - "prefix": "tsn", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences", - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://purl.org/net/tsn#$1" - }, - "lov.tsnc": { - "authority": "lov", - "description": "The TSN-Change ontology aims at describing changes that occured from one version of a Territorial Statistical Nomenclature (TSN) (i.e., partition of the territory) and its subsequent (e.g., change in territorial units boundaries to reflect an administrative reorganisation).", - "homepage": "http://purl.org/net/tsnchange#", - "id": "lov.tsnc", - "name": "Territorial Statistical Nomenclature Change Ontology", - "prefix": "tsnc", - "source": "lov.linkeddata.es", - "subjects": [ - "political sciences", - "earth and related environmental sciences", - "mathematics" - ], - "uri_format": "http://purl.org/net/tsnchange#$1" - }, - "lov.turismo": { - "authority": "lov", - "description": "Esta ontolog\u00eda se ha construido dentro del proyecto financiado por el Ayuntamiento de Zaragoza: \"Un visitante, una ruta\", una aplicaci\u00f3n inform\u00e1tica para el c\u00e1lculo de rutas tur\u00edsticas en la ciudad de Zaragoza en base al perfil y contexto del usuario.", - "homepage": "http://idi.fundacionctic.org/cruzar/turismo", - "id": "lov.turismo", - "name": "Ontolog\u00eda de Turismo para el Ayuntamiento de Zaragoza", - "prefix": "turismo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://idi.fundacionctic.org/cruzar/turismo#$1" - }, - "lov.tvc": { - "authority": "lov", - "description": "A pattern for the description of scenarios that involve entities having some value during a particular time and within a particular context.", - "homepage": "http://www.essepuntato.it/2012/04/tvc", - "id": "lov.tvc", - "name": "The Time-indexed Value in Context", - "prefix": "tvc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.essepuntato.it/2012/04/tvc/$1" - }, - "lov.txn": { - "authority": "lov", - "description": "This ontology and the related TaxonConcept data set mints identifiers that are tied to a specific species concept which can have several names and classifications.", - "homepage": "http://lod.taxonconcept.org/ontology/txn.owl", - "id": "lov.txn", - "name": "TaxonConcept Ontology", - "prefix": "txn", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://lod.taxonconcept.org/ontology/txn.owl#$1" - }, - "lov.tzont": { - "authority": "lov", - "description": "A vocabulary to describe time zones and their geographical coverage.", - "homepage": "http://www.w3.org/2006/timezone", - "id": "lov.tzont", - "name": "Time Zone Ontology", - "prefix": "tzont", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2006/timezone#$1" - }, - "lov.uby": { - "authority": "lov", - "description": "OLiA Annotation Model for Uby Parts of Speech (Gurevych et al, 2012)\nextracted from the Uby DTD (http://purl.org/olia/ubyCat.owl, version of Nov 21th, 2012).\n\nReferences\nIryna Gurevych, Judith Eckle-Kohler, Silvana Hartmann, Michael Matuschek, Christian M. Meyer and Christian Wirth, 2012, Uby - A Large-Scale Unified Lexical-Semantic Resource, Proceedings of the 13th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2012), Avignon, France.\n\nThe DTD is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0) license which is available at http://creativecommons.org/licenses/by-sa/3.0/\nYou are free to share (copy, distribute and transmit) the work, to develop your own extensions (adapt, remix) of the work, and to make commercial use of the work.", - "homepage": "http://purl.org/olia/ubyCat.owl", - "id": "lov.uby", - "name": "ubyCat.owl", - "prefix": "uby", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/olia/ubyCat.owl#$1" - }, - "lov.uco": { - "authority": "lov", - "description": "Vocabulaire Web pour d\u00e9crire les caract\u00e9ristiques des voitures d'occasion pour le commerce \u00e9lectronique.", - "homepage": "http://purl.org/uco/ns#", - "id": "lov.uco", - "name": "Used Cars Ontology", - "prefix": "uco", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/uco/ns#$1" - }, - "lov.ucum": { - "authority": "lov", - "description": "The instances of this ontology have been automatically\n generated from the UCUM (The Unified Code for Units of Measure).\n See http://aurora.rg.iupui.edu/UCUM/ for more details\n on UCUM. The members of the MyMobileWeb consortium\n explicitly acknowledge the copyright of the data from\n the UCUM ontology.", - "homepage": "http://purl.oclc.org/NET/muo/ucum/", - "id": "lov.ucum", - "name": "Units of measurement ontology", - "prefix": "ucum", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://purl.oclc.org/NET/muo/ucum/$1" - }, - "lov.ui": { - "authority": "lov", - "description": "An ontology suitable for describing forms, sequences in widgets", - "homepage": "http://www.w3.org/ns/ui", - "id": "lov.ui", - "name": "A user interface ontology", - "prefix": "ui", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/ui#$1" - }, - "lov.uiot": { - "authority": "lov", - "description": "Core module of the suite of ontologies for urban IoT devices.", - "homepage": "http://www.w3id.org/urban-iot/core", - "id": "lov.uiot", - "name": "Urban IoT Ontologies - Core Module", - "prefix": "uiot", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3id.org/urban-iot/core#$1" - }, - "lov.uiote": { - "authority": "lov", - "description": "Electric Mobility module of the suite of ontologies for urban IoT devices.", - "homepage": "http://www.w3id.org/urban-iot/electric", - "id": "lov.uiote", - "name": "Ontologie per gli Apparati IoT Urbani - Modulo Electric Mobility", - "prefix": "uiote", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3id.org/urban-iot/electric#$1" - }, - "lov.uiots": { - "authority": "lov", - "description": "Modulo Sharing Mobility delle ontologie per gli apparati IoT urbani.", - "homepage": "http://www.w3id.org/urban-iot/sharing", - "id": "lov.uiots", - "name": "Ontologie per gli Apparati IoT Urbani - Modulo Sharing Mobility", - "prefix": "uiots", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3id.org/urban-iot/sharing#$1" - }, - "lov.umbel": { - "authority": "lov", - "description": "UMBEL provides a general vocabulary of classes and predicates for describing domain ontologies, with the specific aim of promoting interoperability with external datasets and domains.", - "homepage": "http://umbel.org/umbel", - "id": "lov.umbel", - "name": "Upper Mapping and Binding Exchange Layer", - "prefix": "umbel", - "source": "lov.linkeddata.es", - "subjects": [ - "generic" - ], - "uri_format": "http://umbel.org/umbel#$1" - }, - "lov.uneskos": { - "authority": "lov", - "description": "An RDF vocabulary for extending some SKOS and ISO-THES functions in order to improve the linked data consumption of SKOS datasets", - "homepage": "http://purl.org/umu/uneskos", - "id": "lov.uneskos", - "name": "UNESKOS Vocabulary", - "prefix": "uneskos", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/umu/uneskos#$1" - }, - "lov.uniprot": { - "authority": "lov", - "description": "Properties and classes used for protein annotation", - "homepage": "http://purl.uniprot.org/core/", - "id": "lov.uniprot", - "name": "Uniprot Core Ontology", - "prefix": "uniprot", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://purl.uniprot.org/core/$1" - }, - "lov.uri4uri": { - "authority": "lov", - "description": "This vocabulary describes the entities which may be derived from a URI and the relationships between them, such as Internet Domains, prototcols, file suffixes etc. It was initially issued as part of an April 1st gag, but has utility beyond the initial joke.", - "homepage": "http://uri4uri.net/vocab", - "id": "lov.uri4uri", - "name": "URI Vocabulary", - "prefix": "uri4uri", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://uri4uri.net/vocab#$1" - }, - "lov.usability": { - "authority": "lov", - "description": "Ontology 'Usability' created to describe and store information about interactions of user with a software user interface", - "homepage": "https://w3id.org/usability", - "id": "lov.usability", - "name": "Usability", - "prefix": "usability", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/usability#$1" - }, - "lov.va": { - "authority": "lov", - "description": "This vocabulary allows the semantic description of visual analytics applications. It is based on the RDF Data Cube Vocabulary and the Semanticscience Integrated Ontology.", - "homepage": "http://code-research.eu/ontology/visual-analytics", - "id": "lov.va", - "name": "The Visual Analytics Vocabulary", - "prefix": "va", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://code-research.eu/ontology/visual-analytics#$1" - }, - "lov.vaem": { - "authority": "lov", - "description": "The purpose of VAEM is to provide, by import, a foundation for commonly needed resources when building an ontology.", - "homepage": "http://www.linkedmodel.org/schema/vaem", - "id": "lov.vaem", - "name": "Vocabulary for Attaching Essential Metadata", - "prefix": "vaem", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.linkedmodel.org/schema/vaem#$1" - }, - "lov.vag": { - "authority": "lov", - "description": "The Vagueness Ontology (VO) allows one to specify vagueness characterisations of the TBox entities of an ontology.", - "homepage": "http://www.essepuntato.it/2013/10/vagueness", - "id": "lov.vag", - "name": "The Vagueness Ontology", - "prefix": "vag", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.essepuntato.it/2013/10/vagueness/$1" - }, - "lov.vann": { - "authority": "lov", - "description": "A vocabulary for annotating descriptions of vocabularies with examples and usage notes.", - "homepage": "http://purl.org/vocab/vann/", - "id": "lov.vann", - "name": "VANN: A vocabulary for annotating vocabulary descriptions", - "prefix": "vann", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocab/vann/$1" - }, - "lov.vartrans": { - "authority": "lov", - "description": "A model for the representation of lexical information relative to ontologies. Variation and translation module.", - "homepage": "http://www.w3.org/ns/lemon/vartrans", - "id": "lov.vartrans", - "name": "Lexicon Model for Ontologies - Vartrans", - "prefix": "vartrans", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/ns/lemon/vartrans#$1" - }, - "lov.vcard": { - "authority": "lov", - "description": "This ontology models and represents vCards in RDF using current best practices", - "homepage": "http://www.w3.org/2006/vcard/ns", - "id": "lov.vcard", - "name": "An Ontology for vCards", - "prefix": "vcard", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2006/vcard/ns#$1" - }, - "lov.vdpp": { - "authority": "lov", - "description": "The Vocabulary of Dataset Publication Projects (VDPP) allows to represent the status of a dataset publication project. It is mainly based on the Provenance Vocabulary (PRV), the Dataset Provenance Vocabulary (VOIDP), the Vocabulary of Interlinked Datasets (VoID), and the Description of a Project (DOAP) vocabulary.", - "homepage": "http://data.lirmm.fr/ontologies/vdpp", - "id": "lov.vdpp", - "name": "Vocabulary for Dataset Publication Projects", - "prefix": "vdpp", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://data.lirmm.fr/ontologies/vdpp#$1" - }, - "lov.veo": { - "authority": "lov", - "description": "An ontology for describing vehicles and their emissions.", - "homepage": "http://linkeddata.finki.ukim.mk/lod/ontology/veo#", - "id": "lov.veo", - "name": "Vehicle Emissions Ontology", - "prefix": "veo", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://linkeddata.finki.ukim.mk/lod/ontology/veo#$1" - }, - "lov.vgo": { - "authority": "lov", - "description": "The Video Game Ontology is an ontology designed for describing video games and all the resources related to their game plays.", - "homepage": "http://purl.org/net/VideoGameOntology", - "id": "lov.vgo", - "name": "The Video Game Ontology", - "prefix": "vgo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/VideoGameOntology#$1" - }, - "lov.vin": { - "authority": "lov", - "description": "This ontology was used as example in the first OWL Recommendation (February 2004)", - "homepage": "http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine", - "id": "lov.vin", - "name": "Wine Ontology", - "prefix": "vin", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#$1" - }, - "lov.vir": { - "authority": "lov", - "description": "This ontology, called VIR, is an extension of CIDOC-CRM created to sustain propositions on the nature of visual elements and permit these descriptions to be published on the Web.\nWith the term visual element, we refer to those signs identified in the visual space as distinct and documentable units, and subject to an analytical interpretation.\nThe scope of this ontology is to s to provide a framework to support the identification, annotation and interconnections between diverse visual elements and presents and assist their documentation and retrieval. Specifically, the model aims to clarify the identity and the relation of these visual signs, providing the necessary classes to characterise their constituent elements, reference, symbolic content and source of interpretation.\nVIR expands on key entities and properties from CIDOC-CRM, introducing new classes and relationships responding to the visual and art historical community, specifically building up on the iconographical tradition. The result is a model which differentiates between interpretation and element identified, providing a clear distinction between denotation and signification of an element. As a consequence of such distinction, the ontology allows for the definition of diverse denotative criteria for the same representation, which could change based on traditions and perspective. Visual objects can be, in fact, polysemic and ambiguous, and it is not so easy to pin down a denotative or connotative meaning because they are very much context-dependent.", - "homepage": "http://w3id.org/vir#", - "id": "lov.vir", - "name": "VIR - Visual Representation ontology", - "prefix": "vir", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://w3id.org/vir#$1" - }, - "lov.vivo": { - "authority": "lov", - "description": "An ontology of academic and research domain, developed in the framework of the VIVO project", - "homepage": "http://vivoweb.org/ontology/core", - "id": "lov.vivo", - "name": "VIVO Core Ontology", - "prefix": "vivo", - "source": "lov.linkeddata.es", - "subjects": [ - "educational sciences" - ], - "uri_format": "http://vivoweb.org/ontology/core#$1" - }, - "lov.vmm": { - "authority": "lov", - "description": "In Software Engineering, as well as in other disciplines, it is common to use model-editing tools using a visual language. In particular, the editing tools allow you to design UML software models, so that let you manage much of the work products of a project. From the study of several UML tools, such as Enterprise Architect, Visual Paradigm for UML or Rational Rose, this vocabulary has been defined. This vocabulary represents the basic structure of these UML tools, but does not exclude others that allow you to use other visual languages for modeling software systems or other entities.", - "homepage": "http://spi-fm.uca.es/spdef/models/genericTools/vmm/1.0", - "id": "lov.vmm", - "name": "Visual Modeling tool Model", - "prefix": "vmm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://spi-fm.uca.es/spdef/models/genericTools/vmm/1.0#$1" - }, - "lov.voaf": { - "authority": "lov", - "description": "A vocabulary to describe linked data vocabularies and their relations", - "homepage": "http://purl.org/vocommons/voaf", - "id": "lov.voaf", - "name": "Vocabulary of a Friend", - "prefix": "voaf", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vocommons/voaf#$1" - }, - "lov.voag": { - "authority": "lov", - "description": "VOAG is intended to specify licensing, attribution, provenance and governance of an ontology.", - "homepage": "http://voag.linkedmodel.org/schema/voag", - "id": "lov.voag", - "name": "Vocabulary Of Attribution and Governance", - "prefix": "voag", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://voag.linkedmodel.org/voag#$1" - }, - "lov.vocals": { - "authority": "lov", - "description": "This ontology aims to model RDF streams, their metadata, and access endpoints for publishing and consuming these streams", - "homepage": "http://w3id.org/rsp/vocals#", - "id": "lov.vocals", - "name": "VoCaLS: A Vocabulary and Catalog for Linked Streams", - "prefix": "vocals", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://w3id.org/rsp/vocals#$1" - }, - "lov.void": { - "authority": "lov", - "description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets.", - "homepage": "http://vocab.deri.ie/void", - "id": "lov.void", - "name": "Vocabulary of Interlinked Datasets", - "prefix": "void", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdfs.org/ns/void#$1" - }, - "lov.voidext": { - "authority": "lov", - "description": "The Extension of the Vocabulary of Interlinked Datasets (VoID) RDF Schema that includes the concept of virtual links. This extension enhances interoperability among heterogeneous and distributed RDF data sets by bridging them through explicitly defined virtual links.", - "homepage": "http://purl.org/query/voidext", - "id": "lov.voidext", - "name": "Extended Vocabulary of Interlinked Datasets (VoIDext)", - "prefix": "voidext", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/query/voidext#$1" - }, - "lov.voidwh": { - "authority": "lov", - "description": "An extension of W3C VoID that is able to represent these metrics for expressing the Connectivity Metrics of a Semantic Warehouse.", - "homepage": "http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl", - "id": "lov.voidwh", - "name": "Void Warehouse Ontology", - "prefix": "voidwh", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl$1" - }, - "lov.vra": { - "authority": "lov", - "description": "Le VRA Core est un ensemble de propri\u00e9t\u00e9s de m\u00e9tadonn\u00e9es pour d\u00e9crire les oeuvres d'art visuelles et les images qui les documentent.", - "homepage": "http://simile.mit.edu/2003/10/ontologies/vraCore3#", - "id": "lov.vra", - "name": "RDFS Ontology for VRA", - "prefix": "vra", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://simile.mit.edu/2003/10/ontologies/vraCore3#$1" - }, - "lov.vrank": { - "authority": "lov", - "description": "The Vocabulary for Ranking (vRank) is an RDF Schema vocabulary for materializing ranking computations.", - "homepage": "http://vocab.sti2.at/vrank", - "id": "lov.vrank", - "name": "Vocabulary for Ranking", - "prefix": "vrank", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/voc/vrank#$1" - }, - "lov.vs": { - "authority": "lov", - "description": "An RDF vocabulary for relating SW vocabulary terms to their status.", - "homepage": "http://www.w3.org/2003/06/sw-vocab-status/ns", - "id": "lov.vs", - "name": "SemWeb Vocab Status ontology", - "prefix": "vs", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2003/06/sw-vocab-status/ns#$1" - }, - "lov.vsearch": { - "authority": "lov", - "description": "The vSearch vocabulary facilitates the querying and retrieval of vocabulary terms from a vocabularies directory. It can be used to map keywords with mapped result terms accompanied with a ranking value.", - "homepage": "http://purl.org/vsearch/", - "id": "lov.vsearch", - "name": "vSearch Vocabulary", - "prefix": "vsearch", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vsearch/$1" - }, - "lov.vso": { - "authority": "lov", - "description": "The Vehicle Sales Ontology for Semantic Web-based E-Commerce", - "homepage": "http://purl.org/vso/ns", - "id": "lov.vso", - "name": "Vehicle Sales Ontology", - "prefix": "vso", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vso/ns#$1" - }, - "lov.vvo": { - "authority": "lov", - "description": "A vocabulary for describing Volkswagen-specific features of automobiles and their components", - "homepage": "http://purl.org/vvo/ns#", - "id": "lov.vvo", - "name": "Volkswagen Vehicles Ontology", - "prefix": "vvo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/vvo/ns#$1" - }, - "lov.w3c-ssn": { - "authority": "lov", - "description": "This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. as these are intended to be included from other ontologies via OWL imports.", - "homepage": "https://www.w3.org/ns/ssn", - "id": "lov.w3c-ssn", - "name": "Semantic Sensor Network Ontology", - "prefix": "w3c-ssn", - "source": "lov.linkeddata.es", - "subjects": [ - "earth and related environmental sciences", - "computer and information sciences" - ], - "uri_format": "https://www.w3.org/ns/ssn/$1" - }, - "lov.wai": { - "authority": "lov", - "description": "WAI vocabulary aims to extend the FOAF specification through introducing the concepts of roles and profiles. In society, people are more than just persons, they can be musicians, presidents of government, firemen, football players or car drivers in a traffic jam.", - "homepage": "http://purl.org/wai#", - "id": "lov.wai", - "name": "Roles and Profiles Ontology", - "prefix": "wai", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/wai#$1" - }, - "lov.wdrs": { - "authority": "lov", - "description": "The Protocol for Web Description Resources (POWDER) allows metadata to be associated with groups of resources such as those found on a Web site.", - "homepage": "http://www.w3.org/2007/05/powder-s", - "id": "lov.wdrs", - "name": "Protocol for Web Description Resources", - "prefix": "wdrs", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/2007/05/powder-s#$1" - }, - "lov.wf-invoc": { - "authority": "lov", - "description": "Wf-invoc is a simple profile of the P-plan ontology to describe how workflow steps are invoked within a workflow execution.", - "homepage": "http://purl.org/net/wf-invocation", - "id": "lov.wf-invoc", - "name": "Workflow Invocation Ontology", - "prefix": "wf-invoc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/wf-invocation#$1" - }, - "lov.wfdesc": { - "authority": "lov", - "description": "This ontology (\"wfdesc\") describes an abstract workflow description structure, allowing the description of a scientific workflow as a direct acyclic graph, or a dataflow. This ontology is meant as an upper ontology for more specific workflow definitions, and as a way to express abstract workflows. The wfprov ontology shows how to link these descriptions to a provenance trace of a workflow execution.", - "homepage": "http://purl.org/wf4ever/wfdesc", - "id": "lov.wfdesc", - "name": "The Wfdesc ontology", - "prefix": "wfdesc", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/wf4ever/wfdesc#$1" - }, - "lov.wfm": { - "authority": "lov", - "description": "Ontology for describing Workflow Motifs. Workflow Motifs outline the kinds of data-intensive activities that are observed in workflows (data-operation motifs) and the different manners in which activities are implemented within workflows (workflow-oriented motifs).", - "homepage": "http://purl.org/net/wf-motifs", - "id": "lov.wfm", - "name": "The Workflow Motif Ontology", - "prefix": "wfm", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/net/wf-motifs#$1" - }, - "lov.wfprov": { - "authority": "lov", - "description": "The wfprov ontology shows how to express minimal provenance information about the execution of a workflow described using the wfdesc ontology.", - "homepage": "http://purl.org/wf4ever/wfprov", - "id": "lov.wfprov", - "name": "The Wfprov Ontology", - "prefix": "wfprov", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/wf4ever/wfprov#$1" - }, - "lov.whisky": { - "authority": "lov", - "description": "A small vocabulary for describing whisky varieties", - "homepage": "http://vocab.org/whisky/terms", - "id": "lov.whisky", - "name": "Whisky Ontology", - "prefix": "whisky", - "source": "lov.linkeddata.es", - "subjects": [ - "agriculture, forestry, and fisheries" - ], - "uri_format": "http://vocab.org/whisky/terms/$1" - }, - "lov.whois": { - "authority": "lov", - "description": "A vocabulary to describe a person's profile and history", - "homepage": "http://www.kanzaki.com/ns/whois", - "id": "lov.whois", - "name": "Who's who description vocabulary", - "prefix": "whois", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.kanzaki.com/ns/whois#$1" - }, - "lov.wi": { - "authority": "lov", - "description": "The Weighted Interests Vocabulary specification provides basic concepts and properties for describing describing preferences (interests) within contexts, their temporal dynamics and their origin on/ for the Semantic Web.", - "homepage": "http://purl.org/ontology/wi/core#", - "id": "lov.wi", - "name": "The Weighted Interests Vocabulary", - "prefix": "wi", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/wi/core#$1" - }, - "lov.wikibase": { - "authority": "lov", - "description": "The system ontology of Wikibase", - "homepage": "http://wikiba.se/ontology", - "id": "lov.wikibase", - "name": "Wikibase system ontology", - "prefix": "wikibase", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://wikiba.se/ontology#$1" - }, - "lov.wikim": { - "authority": "lov", - "description": "A partir del an\u00e1lisis de diversos sistemas, como MediaWiki, Confluence o DokuWiki, se ha dise\u00f1ado este vocabulario. T\u00e9ngase en cuenta que este modelo no describe completamente el modelo conceptual de todos los tipos de sistemas wiki, sino s\u00f3lo de los elementos principales.", - "homepage": "http://spi-fm.uca.es/spdef/models/genericTools/wikim/1.0", - "id": "lov.wikim", - "name": "WIKI tool Model", - "prefix": "wikim", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://spi-fm.uca.es/spdef/models/genericTools/wikim/1.0#$1" - }, - "lov.wl": { - "authority": "lov", - "description": "WSMO-Lite is a lightweight approach to the semantic annotation of Web service descriptions, defined by the STI2 working group Conceptual Models for Services", - "homepage": "http://www.wsmo.org/ns/wsmo-lite#", - "id": "lov.wl", - "name": "WSMO-Lite Ontology", - "prefix": "wl", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.wsmo.org/ns/wsmo-lite#$1" - }, - "lov.wlo": { - "authority": "lov", - "description": "A simple vocabulary for describing biological species and related taxa.", - "homepage": "http://purl.org/ontology/wo/", - "id": "lov.wlo", - "name": "BBC Wildlife Ontology", - "prefix": "wlo", - "source": "lov.linkeddata.es", - "subjects": [ - "biological sciences" - ], - "uri_format": "http://purl.org/ontology/wo/$1" - }, - "lov.wo": { - "authority": "lov", - "description": "The Weighting Ontology specification provides a vocabulary for describing weightings and their referenced scales, on/ for the Semantic Web.", - "homepage": "http://purl.org/ontology/wo/core#", - "id": "lov.wo", - "name": "Weighting Ontology", - "prefix": "wo", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://purl.org/ontology/wo/core#$1" - }, - "lov.wot": { - "authority": "lov", - "description": "Web Of Trust (wot) RDF vocabulary, described using W3C RDF Schema and the Web Ontology Language.", - "homepage": "http://xmlns.com/wot/0.1/", - "id": "lov.wot", - "name": "Web Of Trust", - "prefix": "wot", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://xmlns.com/wot/0.1/$1" - }, - "lov.wotsec": { - "authority": "lov", - "description": "Security mechanisms for the the Web of Thing", - "homepage": "https://www.w3.org/2019/wot/security#", - "id": "lov.wotsec", - "name": "Security mechanisms for the Web of Things", - "prefix": "wotsec", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "https://www.w3.org/2019/wot/security#$1" - }, - "lov.xapi": { - "authority": "lov", - "description": "This ontology contains a list of the classes and properties that can be used when for creating and publishing a controlled vocabulary dataset for xAPI communities of practice.", - "homepage": "http://purl.org/xapi/ontology#", - "id": "lov.xapi", - "name": "xAPI Controlled Vocabulary Ontology", - "prefix": "xapi", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://purl.org/xapi/ontology#$1" - }, - "lov.xbrll": { - "authority": "lov", - "description": "An attempt to publish XBRL standard following best practices on the Web. Not an official version from XBRL International and under development", - "homepage": "https://w3id.org/vocab/xbrll", - "id": "lov.xbrll", - "name": "A lightweight XBRL vocabulary", - "prefix": "xbrll", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "https://w3id.org/vocab/xbrll#$1" - }, - "lov.xhv": { - "authority": "lov", - "description": "This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax.", - "homepage": "http://www.w3.org/1999/xhtml/vocab", - "id": "lov.xhv", - "name": "XHTML Vocabulary", - "prefix": "xhv", - "source": "lov.linkeddata.es", - "subjects": [ - "computer and information sciences" - ], - "uri_format": "http://www.w3.org/1999/xhtml/vocab#$1" - }, - "lov.xkos": { - "authority": "lov", - "description": "Extension de SKOS pour la repr\u00e9sentation des nomenclatures", - "homepage": "http://rdf-vocabulary.ddialliance.org/xkos", - "id": "lov.xkos", - "name": "XKOS", - "prefix": "xkos", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://rdf-vocabulary.ddialliance.org/xkos#$1" - }, - "lov.xsd": { - "authority": "lov", - "description": "The XML Schema representation", - "homepage": "http://www.w3.org/2001/XMLSchema", - "id": "lov.xsd", - "name": "XML Schema", - "prefix": "xsd", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://www.w3.org/2001/XMLSchema#$1" - }, - "lov.yoga": { - "authority": "lov", - "description": "Yoga Ontology is the list of vocabularies that define the yogic practice. Where Yoga is the union of the mind and body.", - "homepage": "https://yogaontology.org/ontology/", - "id": "lov.yoga", - "name": "Yoga Ontology", - "prefix": "yoga", - "source": "lov.linkeddata.es", - "subjects": [ - "health sciences" - ], - "uri_format": "https://yogaontology.org/ontology/$1" - }, - "lov.zbwext": { - "authority": "lov", - "description": "Extensions to SKOS and other standard vocabularies used by the German National Library of Economics (ZBW)", - "homepage": "http://zbw.eu/namespaces/zbw-extensions", - "id": "lov.zbwext", - "name": "ZBW Extensions", - "prefix": "zbwext", - "source": "lov.linkeddata.es", - "subjects": [], - "uri_format": "http://zbw.eu/namespaces/zbw-extensions/$1" - } -} diff --git a/fuji_server/data/linked_vocabs/lov_ontologies.yaml b/fuji_server/data/linked_vocabs/lov_ontologies.yaml new file mode 100644 index 00000000..06f6c332 --- /dev/null +++ b/fuji_server/data/linked_vocabs/lov_ontologies.yaml @@ -0,0 +1,9332 @@ +lov.a-loc: + authority: lov + description: >- + The module Location models information related to the localization and + georeferencing of a cultural property. + + In this module are used as template the following Ontology Design Patterns: + + - http://www.ontologydesignpatterns.org/cp/owl/collectionentity.owl + + - http://www.ontologydesignpatterns.org/cp/owl/classification.owl + + - http://www.ontologydesignpatterns.org/cp/owl/place.owl + + - http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl + + - http://www.ontologydesignpatterns.org/cp/owl/situation.owl + homepage: https://w3id.org/arco/ontology/location + id: lov.a-loc + name: Location Ontology (ArCo network) + prefix: a-loc + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://w3id.org/arco/ontology/location/$1 +lov.ac: + authority: lov + description: This term list includes all currently valid terms that have been defined in the core Audubon Core namespace ac:. + homepage: http://rs.tdwg.org/ac/terms/ + id: lov.ac + name: Core terms defined by Audubon Core + prefix: ac + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://rs.tdwg.org/ac/terms/$1 +lov.acco: + authority: lov + description: A vocabulary for the description of hotels, vacation homes, camping sites, and other accommodation offers for e-commerce + homepage: http://purl.org/acco/ns + id: lov.acco + name: Accomodation Ontology + prefix: acco + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/acco/ns#$1 +lov.acl: + authority: lov + description: Defines the element of Authorization and its essential properties, and also some classes of access such as read and write. + homepage: http://www.w3.org/ns/auth/acl + id: lov.acl + name: Basic Access Control ontology + prefix: acl + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3.org/ns/auth/acl#$1 +lov.acm: + authority: lov + description: This ontology is a representation of The ACM Computing Classification System [1998] + homepage: http://www.rkbexplorer.com/ontologies/acm + id: lov.acm + name: ACM Classification Ontology + prefix: acm + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://acm.rkbexplorer.com/ontologies/acm#$1 +lov.acrt: + authority: lov + description: This document specifies a vocabulary for asserting the existence of official endorsements or certifications of agents, such as people and organizations. + homepage: http://privatealpha.com/ontology/certification/1# + id: lov.acrt + name: Agent Certification Ontology + prefix: acrt + source: lov.linkeddata.es + subjects: [] + uri_format: http://privatealpha.com/ontology/certification/1#$1 +lov.adms: + authority: lov + description: ADMS is a profile of DCAT, used to describe semantic assets (or just 'Assets'), defined as highly reusable metadata (e.g. xml schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies) that are used for eGovernment system development. + homepage: http://www.w3.org/ns/adms + id: lov.adms + name: Asset Description Metadata Schema + prefix: adms + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/adms#$1 +lov.af: + authority: lov + description: This vocabulary expresses some common concepts to represent some features of audio signals. + homepage: http://purl.org/ontology/af/ + id: lov.af + name: Audio Features Ontology + prefix: af + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/af/$1 +lov.agls: + authority: lov + description: The AGLS Metadata Terms Namespace provides URIs for the AGLS Metadata Terms Vocabulary in the context of AGLS Metadata Standard, a set of metadata properties and associated usage guidelines to improve the visibility, manageability and interoperability of online information and services. Vocabulary terms are declared using RDF Schema language to support RDF applications. It will be updated according to AGLS Working Group decisions. + homepage: http://www.agls.gov.au/agls/terms + id: lov.agls + name: AGLS Metadata Terms + prefix: agls + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.agls.gov.au/agls/terms/$1 +lov.agr: + authority: lov + description: This Agreements Ontology is designed to model 'agreements' which are social contracts that include licenses, laws, contracts, Memoranda of Understanding, standards and definitional metadata. Its purpose is to support data sharing by making explicit the relationships between agreements and data and agreements and Agents (people and organisations). Eventually it will also help with the interplay between different classes of agreements. + homepage: http://promsns.org/def/agr + id: lov.agr + name: Agreements ontology + prefix: agr + source: lov.linkeddata.es + subjects: + - political sciences + - law + uri_format: http://promsns.org/def/agr#$1 +lov.agrelon: + authority: lov + description: The ontology of agent relationships, AgRelOn, defines relations of persons to other persons and to organisations + homepage: http://d-nb.info/standards/elementset/agrelon + id: lov.agrelon + name: Agent Relationship Ontology + prefix: agrelon + source: lov.linkeddata.es + subjects: [] + uri_format: http://d-nb.info/standards/elementset/agrelon#$1 +lov.aiiso: + authority: lov + description: The Academic Institution Internal Structure Ontology (AIISO) provides classes and properties to describe the internal organizational structure of an academic institution. AIISO is designed to work in partnership with Participation (http://purl.org/vocab/participation/schema), FOAF (http://xmlns.com/foaf/0.1/) and aiiso-roles (http://purl.org/vocab/aiiso-roles/schema) to describe the roles that people play within an institution. + homepage: http://purl.org/vocab/aiiso/schema + id: lov.aiiso + name: Academic Institution Internal Structure Ontology + prefix: aiiso + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://purl.org/vocab/aiiso/schema#$1 +lov.airo: + authority: lov + description: AIRO represents AI risk concepts and relations based on the AI Act draft and ISO 31000 standard series. + homepage: https://w3id.org/AIRO + id: lov.airo + name: AI Risk Ontology + prefix: airo + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/AIRO#$1 +lov.airs: + authority: lov + description: 'The AIRS Linked Open Vocabulary is a way to describe human services information and referral (I&R) concepts. AIRS is the Alliance of Information and Referral Services (airs.org), which possesses over 1,000 member agencies primarily in the United States and Canada. The AIRS LOV is based on the AIRS XML Schema, available at: https://airs-xml.googlecode.com/hg/tags/3.1/airs.xsd' + homepage: https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl# + id: lov.airs + name: Alliance of Information and Referral Services (AIRS) Vocabulary + prefix: airs + source: lov.linkeddata.es + subjects: [] + uri_format: https://raw.githubusercontent.com/airs-linked-data/lov/latest/src/airs_vocabulary.ttl#$1 +lov.akt: + authority: lov + description: The AKT Reference Ontology has been designed to support the AKT-2 demonstrator ("AKTive Portal"), and subsequent activities. The ontology, designed by the AKT-2 group and codified by Enrico Motta, extends Version 1. + homepage: http://www.aktors.org/ontology/portal + id: lov.akt + name: AKT Reference Ontology + prefix: akt + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.aktors.org/ontology/portal#$1 +lov.akts: + authority: lov + description: The AKT Reference Ontology has been designed to support the AKT-2 demonstrator ("AKTive Portal"), and subsequent activities + homepage: http://www.aktors.org/ontology/support + id: lov.akts + name: AKT Support Ontology + prefix: akts + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.aktors.org/ontology/support#$1 +lov.algo: + authority: lov + description: An ontology describing cryptographic algorithms + homepage: http://securitytoolbox.appspot.com/securityAlgorithms# + id: lov.algo + name: Algorithms Ontology + prefix: algo + source: lov.linkeddata.es + subjects: [] + uri_format: http://securitytoolbox.appspot.com/securityAlgorithms#$1 +lov.am: + authority: lov + description: This specification builds on the Open Services for Lifecycle Collaboration (OSLC) Core v2.0 Specification to define the resources, properties and operations supported by an OSLC Asset Management (OSLC-Asset) provider. Asset Management resources include Assets, Artifacts and supporting resources defined in the OSLC Core specification. + homepage: http://open-services.net/ns/asset# + id: lov.am + name: OSLC Asset Management Vocabulary + prefix: am + source: lov.linkeddata.es + subjects: [] + uri_format: http://open-services.net/ns/asset#$1 +lov.aml: + authority: lov + description: A vocabulary to represent the AutomationML Standard - IEC 62714 + homepage: https://w3id.org/i40/aml + id: lov.aml + name: AutomationML Ontology + prefix: aml + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/i40/aml#$1 +lov.amlo-core: + authority: lov + description: The AMLO-core is the main module of the AMLO projects that extends the Financial Industry Business Ontology (FIBO) with some concepts to describe the Anti Money Laundering (AML) knowledge and facts. + homepage: http://w3id.org/amlo/core + id: lov.amlo-core + name: AMLO-core vocabulary + prefix: amlo-core + source: lov.linkeddata.es + subjects: [] + uri_format: http://w3id.org/amlo/core#$1 +lov.amv: + authority: lov + description: Metadata vocabularies are used in various domains of study. It provides an in-depth description of the resources. In this work, we develop Algorithm Metadata Vocabulary (AMV), a vocabulary for capturing and storing the metadata about the algorithms (a procedure or a set of rules that is followed step-by-step to solve a problem, especially by a computer). The snag faced by the researchers in the current time is the failure of getting relevant results when searching for algorithms in any search engine. AMV is represented as a semantic model and produced OWL file, which can be directly used by anyone interested to create and publish algorithm metadata as a knowledge graph, or to provide metadata service through SPARQL endpoint. To design the vocabulary, we propose a well-defined methodology, which considers real issues faced by the algorithm users and the practitioners. The evaluation shows a promising result. + homepage: https://w3id.org/amv + id: lov.amv + name: AMV:Algorithm Metadata Vocabulary + prefix: amv + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/amv#$1 +lov.ao: + authority: lov + description: Provides basic concepts and properties for describing specific association statements to something, e.g. an occasion, a genre or a mood ... + homepage: http://purl.org/ontology/ao/core# + id: lov.ao + name: Association Ontology + prefix: ao + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/ao/core#$1 +lov.aos: + authority: lov + description: Appearances is an ontology that grew out of the need to record personal appearance details about individuals while taking into account errors of perception and translation between various diffferent standards. Originally it was meant to record physical caracteristics of Great War soldiers from their medical files, but it became evident that the resource was also useful for other purposes. + homepage: http://rdf.muninn-project.org/ontologies/appearances + id: lov.aos + name: Appearances Ontology Specification + prefix: aos + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdf.muninn-project.org/ontologies/appearances#$1 +lov.apco: + authority: lov + description: APCO est une ontologie ayant pour but la description des termes des marchés publics + homepage: https://purl.org/cm/onto/apco + id: lov.apco + name: African Public Contract Ontology + prefix: apco + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: https://purl.org/cm/onto/apco#$1 +lov.api: + authority: lov + description: Configuration vocabulary for the Linked Data API + homepage: http://purl.org/linked-data/api/vocab# + id: lov.api + name: Linked Data API Vocabulary + prefix: api + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/linked-data/api/vocab#$1 +lov.apps4x: + authority: lov + description: apps4X is an RDF vocabulary defined to facilitate the description of Open-Data-based Co-creation events + homepage: http://semweb.mmlab.be/ns/apps4X + id: lov.apps4x + name: The vocabulary for Co-creation Events based on Open Data + prefix: apps4X + source: lov.linkeddata.es + subjects: [] + uri_format: http://semweb.mmlab.be/ns/apps4X#$1 +lov.arch: + authority: lov + description: An RDF vocabulary for describing archival collections and the names associated with them + homepage: http://purl.org/archival/vocab/arch + id: lov.arch + name: Archival collections ontology + prefix: arch + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/archival/vocab/arch#$1 +lov.arco: + authority: lov + description: The Core module represents general-purpose concepts orthogonal to the whole network, which are imported by all other ontology modules (e.g. part-whole relation, classification). + homepage: https://w3id.org/arco/ontology/core + id: lov.arco + name: Core Ontology (ArCo network) + prefix: arco + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/arco/ontology/core/$1 +lov.arp: + authority: lov + description: >- + Arpenteur ontology is dedicated to photogrammetry, archeology and oceanology + communities in order to perform tasks such as image processing, photogrammetry and modelling. + homepage: http://www.arpenteur.org/ontology/Arpenteur.owl + id: lov.arp + name: Arpenteur Ontology + prefix: arp + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - mathematics + uri_format: http://www.arpenteur.org/ontology/Arpenteur.owl#$1 +lov.atd: + authority: lov + description: Defines concepts related to airport status, including weather, forecasts, and airport operations + homepage: https://data.nasa.gov/ontologies/atmonto/data# + id: lov.atd + name: Air Traffic Data + prefix: atd + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://data.nasa.gov/ontologies/atmonto/data#$1 +lov.atm: + authority: lov + description: Defines specific air traffic management concepts used in aircraft navigation through the US National Airspace System + homepage: https://data.nasa.gov/ontologies/atmonto/ATM# + id: lov.atm + name: Air Traffic Management (ATM) Vocabulary + prefix: atm + source: lov.linkeddata.es + subjects: [] + uri_format: https://data.nasa.gov/ontologies/atmonto/ATM#$1 +lov.atts: + authority: lov + description: Defines temporal / spatial concepts and general-purpose datastructures + homepage: https://data.nasa.gov/ontologies/atmonto/general# + id: lov.atts + name: Air Traffic Temporal and Spacial Vocabulary + prefix: atts + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - mathematics + - computer and information sciences + uri_format: https://data.nasa.gov/ontologies/atmonto/general#$1 +lov.awol: + authority: lov + description: The AtomOWL ontology is inspired from the work done by the atom working group. This ontology is working off the rfc 4287 published among othe places at http://www.atompub.org/rfc4287.html . The AtomOWL ontology uses as much as possible the same terms as the format there to make the relation easy to understand. The AtomOWL name space is slightly different from the atom namespace [see post http://www.imc.org/atom-syntax/mail-archive/msg16476.html]. But this is a good thing as it helps distinguish the ontology from the rfc 4287 serialisation. + homepage: http://bblfish.net/work/atom-owl/2006-06-06/ + id: lov.awol + name: Atom Syndication Ontology + prefix: awol + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://bblfish.net/work/atom-owl/2006-06-06/#$1 +lov.aws: + authority: lov + description: This ontology is part of the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG). It is published here in order to generalize the potential usage and the alignment with other standardization efforts of the SSN ontology. + homepage: http://purl.oclc.org/NET/ssnx/meteo/aws + id: lov.aws + name: Ontology for Meteorological sensors + prefix: aws + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: http://purl.oclc.org/NET/ssnx/meteo/aws#$1 +lov.bag: + authority: lov + description: Basisregistraties Adressen en Gebouwen (BAG) vocabulaire + homepage: http://bag.basisregistraties.overheid.nl/def/bag + id: lov.bag + name: Vocabulary for the Dutch base registration of buildings and addresses (BAG) + prefix: bag + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://bag.basisregistraties.overheid.nl/def/bag#$1 +lov.basic: + authority: lov + description: An OWL representation of (some of) the basic types described in ISO 19103:2005, required as primitives in other ontologies based on ISO 19100 series standards + homepage: http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic + id: lov.basic + name: OWL representation of ISO 19103 (Basic types package) + prefix: basic + source: lov.linkeddata.es + subjects: [] + uri_format: http://def.seegrid.csiro.au/isotc211/iso19103/2005/basic#$1 +lov.bbc: + authority: lov + description: The BBC ontology is used to describe BBC concepts in the store. For example, the BBC divisions (products) publishing linked data and interfacing with the triplestore, the platforms for which we produce content and the web documents that publish or are relevant to the BBC's content. + homepage: http://www.bbc.co.uk/ontologies/bbc + id: lov.bbc + name: BBC Ontology + prefix: bbc + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.bbc.co.uk/ontologies/bbc/$1 +lov.bbccms: + authority: lov + description: An ontology to represent the content management systems and their interaction with the triplestore. + homepage: http://www.bbc.co.uk/ontologies/cms + id: lov.bbccms + name: BBC CMS Ontology + prefix: bbccms + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.bbc.co.uk/ontologies/cms/$1 +lov.bbccore: + authority: lov + description: The generic BBC ontology for people, places,events, organisations, themes which represent things that make sense across the BBC. This model is meant to be generic enough, and allow clients (domain experts) link their own concepts + homepage: http://www.bbc.co.uk/ontologies/coreconcepts + id: lov.bbccore + name: BBC Core Concepts + prefix: bbccore + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.bbc.co.uk/ontologies/coreconcepts/$1 +lov.bbcprov: + authority: lov + description: The provenance ontology supports data management and auditing tasks. It is used to define the different types of named graphs we used in the store (quad store) and enables their association with metadata that allow us to manage, validate and expose data to BBC services + homepage: http://www.bbc.co.uk/ontologies/provenance + id: lov.bbcprov + name: BBC Provenance Ontology + prefix: bbcprov + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.bbc.co.uk/ontologies/provenance/$1 +lov.bci: + authority: lov + description: The BCI ontology specifies a foundational metadata model set for real-world multimodal Brain Computing Interface (BCI) data capture activities. The ontology defines a minimalist and simple abstract metadata foundational model for real-world BCI applications that monitors human activity in any scenario. BCI multimodal domain applications are encouraged to extend and use this ontology in their implementations. + homepage: https://w3id.org/BCI-ontology + id: lov.bci + name: Brain Computing Interface (BCI) Ontology + prefix: bci + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/BCI-ontology#$1 +lov.bcom: + authority: lov + description: 'The Building Concrete Monitoring Ontology (BCOM) is defined for capturing information of concrete work, concrete curing and testing of concrete properties. Further Information on the development and usage of the Ontology can be found in the following publication: Liu et al. (2021): An ontology integrating as-built information for infrastructure asset management using BIM and semantic web. In: Proceedings of 2021 European Conference on Computing in Construction, Online eConference, URL: https://ec-3.org/publications/conferences/2021/paper/?id=167' + homepage: https://w3id.org/bcom + id: lov.bcom + name: Building Concrete Monitoring Ontology (BCOM) + prefix: bcom + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/bcom#$1 +lov.being: + authority: lov + description: A vocabulary to describe the interactions between persons and groups occurring in multimedia. + homepage: http://contextus.net/ontology/ontomedia/ext/common/being# + id: lov.being + name: OntoMedia Being Representation + prefix: being + source: lov.linkeddata.es + subjects: [] + uri_format: http://contextus.net/ontology/ontomedia/ext/common/being#$1 +lov.bevon: + authority: lov + description: Beverage Ontology is a Web vocabulary for describing beverages, mainly alcoholic. + homepage: http://rdfs.co/bevon/ + id: lov.bevon + name: 'BEVON: Beverage Ontology' + prefix: bevon + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://rdfs.co/bevon/$1 +lov.bibo: + authority: lov + description: The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web. + homepage: http://purl.org/ontology/bibo/ + id: lov.bibo + name: The Bibliographic Ontology + prefix: bibo + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/ontology/bibo/$1 +lov.bibtex: + authority: lov + description: Transformation of bibTeX into an OWL ontology + homepage: http://purl.org/net/nknouf/ns/bibtex + id: lov.bibtex + name: BibTeX ontology + prefix: bibtex + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/net/nknouf/ns/bibtex#$1 +lov.bimerr-op: + authority: lov + description: The Occupancy Profile ontology has been developed to represent people’s behavior inside building spaces. + homepage: http://bimerr.iot.linkeddata.es/def/occupancy-profile# + id: lov.bimerr-op + name: Occupancy Profile ontology + prefix: bimerr-op + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://bimerr.iot.linkeddata.es/def/occupancy-profile#$1 +lov.bio: + authority: lov + description: A vocabulary for describing biographical information about people, both living and dead. + homepage: http://purl.org/vocab/bio/0.1/ + id: lov.bio + name: 'BIO: A vocabulary for biographical information' + prefix: bio + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocab/bio/0.1/$1 +lov.biol: + authority: lov + description: An RDF vocabulary for the taxonomy of all forms of life + homepage: http://purl.org/NET/biol/ns# + id: lov.biol + name: Biological Taxonomy Vocabulary 0.2 (Core) + prefix: biol + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://purl.org/NET/biol/ns#$1 +lov.biopax: + authority: lov + description: The goal of the BioPAX group is to develop a common exchange format for biological pathway data. More information is available at http://www.biopax.org. This ontology is freely available under the LGPL license + homepage: http://www.biopax.org/release/biopax-level3.owl + id: lov.biopax + name: BioPAX Level 3 ontology + prefix: biopax + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://www.biopax.org/release/biopax-level3.owl#$1 +lov.biotop: + authority: lov + description: Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network + homepage: http://purl.org/biotop/biotop.owl + id: lov.biotop + name: BioTop + prefix: biotop + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://purl.org/biotop/biotop.owl#$1 +lov.biro: + authority: lov + description: BiRO, the Bibliographic Reference Ontology, is an ontology structured according to the FRBR model to define bibliographic records (as subclasses of frbr:Work) and bibliographic references (as subclasses of frbr:Expression), and their compilations into bibliographic collections such as library catalogues, and into bibliographic lists such as reference lists in journal articles, respectively. + homepage: http://purl.org/spar/biro + id: lov.biro + name: The Bibliographic Reference Ontology + prefix: biro + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/biro/$1 +lov.blt: + authority: lov + description: 'Some useful terms for describing bibliographic resources that other models did not include. Version 1.4: brings the description for this schema in line with "Metadata recommendations for Linked Open Vocabulairies", version 1.1.; dct:license replaced by cc:license and the value changed from http://www.opendatacommons.org/licenses/pddl/1.0/ to http://creativecommons.org/publicdomain/mark/1.0/; various typos corrected. Version 1.4.1: added links to previous schema versions' + homepage: http://www.bl.uk/schemas/bibliographic/blterms + id: lov.blt + name: British Library Terms RDF schema + prefix: blt + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.bl.uk/schemas/bibliographic/blterms#$1 +lov.bot: + authority: lov + description: A vocabulary to describe data sources in a way they can be easily reused and accessed by chatbots. + homepage: http://swa.cefriel.it/ontologies/botdcat-ap + id: lov.bot + name: BotDCAT-AP - Data Catalogue vocabulary Application Profile for chatbots + prefix: bot + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://swa.cefriel.it/ontologies/botdcat-ap#$1 +lov.botany: + authority: lov + description: This is a specialist botanical variant of the Biological Taxonomy Vocabulary. + homepage: http://purl.org/NET/biol/botany# + id: lov.botany + name: Biological Taxonomy Vocabulary 0.2 (Botany) + prefix: botany + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://purl.org/NET/biol/botany#$1 +lov.bperson: + authority: lov + description: Person ontology in Dutch + homepage: http://data.vlaanderen.be/ns/persoon + id: lov.bperson + name: Person + prefix: bperson + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.vlaanderen.be/ns/persoon#$1 +lov.br: + authority: lov + description: A lightweight ontology to structure e- brainstorming sessions + homepage: http://vocab.deri.ie/br + id: lov.br + name: Brainstorm Ontology + prefix: br + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.deri.ie/br#$1 +lov.brk: + authority: lov + description: Basisregistratie Kadaster (BRK) vocabulaire + homepage: http://brk.basisregistraties.overheid.nl/def/brk + id: lov.brk + name: Key Register Cadastre (BRK) vocabulary + prefix: brk + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://brk.basisregistraties.overheid.nl/def/brk#$1 +lov.brt: + authority: lov + description: Basisregistratie Topografie (BRT) vocabulaire + homepage: http://brt.basisregistraties.overheid.nl/def/top10nl + id: lov.brt + name: Key Register Topography (BRT) vocabulary + prefix: brt + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://brt.basisregistraties.overheid.nl/def/top10nl#$1 +lov.bto: + authority: lov + description: >- + The Building Topology Ontology (BOT) is a simple ontology defining the core + concepts of a building. + + + It is a simple, easy to extend ontology for the construction industry to document and exchange building data on the web. + + + Changes since version 0.2.0 of the ontology are documented in: + + https://w3id.org/bot/bot.html#changes + + + The version 0.2.0 of the ontology is documented in: + + Mads Holten Rasmussen, Pieter Pauwels, Maxime Lefrançois, Georg Ferdinand Schneider, Christian Anker Hviid and Jan Karlshøj (2017) Recent changes in the Building Topology Ontology, 5th Linked Data in Architecture and Construction Workshop (LDAC2017), November 13-15, 2017, Dijon, France, https://www.researchgate.net/publication/320631574_Recent_changes_in_the_Building_Topology_Ontology + + + The initial version 0.1.0 of the ontology was documented in: + + Mads Holten Rasmussen, Pieter Pauwels, Christian Anker Hviid and Jan Karlshøj (2017) Proposing a Central AEC Ontology That Allows for Domain Specific Extensions, Lean and Computing in Construction Congress (LC3): Volume I – Proceedings of the Joint Conference on Computing in Construction (JC3), July 4-7, 2017, Heraklion, Greece, pp. 237-244 https://doi.org/10.24928/JC3-2017/0153 + homepage: https://w3id.org/bot + id: lov.bto + name: 'BOT: Building Topology Ontology' + prefix: bto + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/bot#$1 +lov.c4n: + authority: lov + description: A vocabulary to describe calls, such as call for tenders, call for proposals, call for papers, etc. + homepage: http://vocab.deri.ie/c4n + id: lov.c4n + name: Call for Anything vocabulary + prefix: c4n + source: lov.linkeddata.es + subjects: + - law + uri_format: http://vocab.deri.ie/c4n#$1 +lov.c4o: + authority: lov + description: C4O allows the characterization of bibliographic citations in terms of their number and their context. + homepage: http://purl.org/spar/c4o + id: lov.c4o + name: C4O, the Citation Counting and Context Characterization Ontology + prefix: c4o + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/c4o/$1 +lov.cal: + authority: lov + description: A vocabulary for description of events and calendars + homepage: http://www.w3.org/2002/12/cal/ical + id: lov.cal + name: Internet Calendaring and Scheduling Core Object Specification + prefix: cal + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2002/12/cal/ical#$1 +lov.caresses: + authority: lov + description: The CARESSES Ontology encodes guidelines defined by experts in Transcultural Nursing, with the aim of offering a specific tool for endowing social assistive robots (assisting older adults) with cultural competence. + homepage: http://caressesrobot.org/ontology + id: lov.caresses + name: CARESSES Ontology + prefix: caresses + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://caressesrobot.org/ontology#$1 +lov.cart: + authority: lov + description: Ontology for representation of cartesian co-ordinates + homepage: http://purl.org/net/cartCoord# + id: lov.cart + name: cartCoordOnt + prefix: cart + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - mathematics + uri_format: http://purl.org/net/cartCoord#$1 +lov.caso: + authority: lov + description: CASO (Context Aware System Observation) is an ontology for context aware system and observation services. Its goal is to describe all the processing of the context. + homepage: http://www.w3id.org/def/caso# + id: lov.caso + name: Context Aware System Observation Ontology + prefix: caso + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3id.org/def/caso#$1 +lov.cbcm: + authority: lov + description: This ontology describes terms concerning companies, their cross-border movements within the European Union (EU), and associated EU company legislation. + homepage: http://w3id.org/um/cbcm/eu-cm-ontology + id: lov.cbcm + name: The European Union Company Mobility Ontology (EUCM ontology) + prefix: cbcm + source: lov.linkeddata.es + subjects: [] + uri_format: http://w3id.org/um/cbcm/eu-cm-ontology#$1 +lov.cbo: + authority: lov + description: A metadata vocabulary for describing comic books and comic book collections. + homepage: http://comicmeta.org/cbo/ + id: lov.cbo + name: Comic Book Ontology + prefix: cbo + source: lov.linkeddata.es + subjects: [] + uri_format: http://comicmeta.org/cbo/$1 +lov.cbs: + authority: lov + description: Ontologie voor datasets van het CBS + homepage: http://betalinkeddata.cbs.nl/def/cbs + id: lov.cbs + name: De Centraal Bureau voor de Statistiek (CBS) ontologie + prefix: cbs + source: lov.linkeddata.es + subjects: + - political sciences + - earth and related environmental sciences + uri_format: http://betalinkeddata.cbs.nl/def/cbs#$1 +lov.cc: + authority: lov + description: The Creative Commons Rights Expression Language (CC REL) lets you describe copyright licenses in RDF + homepage: http://creativecommons.org/ns + id: lov.cc + name: Creative Commons Rights Expression Language + prefix: cc + source: lov.linkeddata.es + subjects: [] + uri_format: http://creativecommons.org/ns#$1 +lov.cci: + authority: lov + description: Ontology for Cloud Computing Instances. Instance are classes of VM that comprise varying combinations of CPU, memory, storage, and networking capacity. This ontology allows to define the instantiation model of MVs used in large cloud computing providers such as Amazon, Azure, etc. + homepage: http://cookingbigdata.com/linkeddata/ccinstances + id: lov.cci + name: Ontology for Cloud Computing instances + prefix: cci + source: lov.linkeddata.es + subjects: [] + uri_format: http://cookingbigdata.com/linkeddata/ccinstances#$1 +lov.cco: + authority: lov + description: The Cognitive Characteristics Ontology specification provides a vocabulary for describing cognitive pattern within contexts, their temporal dynamics and their origins, on/ for the Semantic Web. + homepage: http://purl.org/ontology/cco/core# + id: lov.cco + name: Cognitive Characteristics Ontology + prefix: cco + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/cco/core#$1 +lov.ccp: + authority: lov + description: Simple and direct pricing ontology for Cloud Computing Services. This ontology allows to define model of prices used in large cloud computing providers such as Amazon, Azure, etc., including options for regions, type of instances, prices specification, etc. + homepage: http://cookingbigdata.com/linkeddata/ccpricing + id: lov.ccp + name: Vocabulary for prices options in Cloud Computing Services + prefix: ccp + source: lov.linkeddata.es + subjects: [] + uri_format: http://cookingbigdata.com/linkeddata/ccpricing#$1 +lov.ccr: + authority: lov + description: Ontology for the definition of regions and zones of availability on CloudComputing platforms and services. This ontology allows to define model of regions used in large cloud computing providers such as Amazon, Azure, etc. + homepage: http://cookingbigdata.com/linkeddata/ccregions + id: lov.ccr + name: Vocabulary for Regions and Zones on Cloud Computing + prefix: ccr + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://cookingbigdata.com/linkeddata/ccregions#$1 +lov.ccsla: + authority: lov + description: Service Level Agreement for Cloud Computing Services. This ontology allows to define model of SLA/SLO used in large cloud computing providers such as Amazon, Azure, etc., including terms, claims, credit, compensations, etc + homepage: http://cookingbigdata.com/linkeddata/ccsla + id: lov.ccsla + name: Service Level Agreement for Cloud Computing + prefix: ccsla + source: lov.linkeddata.es + subjects: [] + uri_format: http://cookingbigdata.com/linkeddata/ccsla#$1 +lov.cdc: + authority: lov + description: The Construction Dataset Context (CDC) ontology is an extension of DCAT v2.0, a W3C Recommendation ontology for describing (RDF and non-RDF) datasets published on the Web. Using this extension, it becomes possible to describe a context for construction-related datasets that are being distributed using Web technology as well as datasets that are not shared outside an organization such as local copies, work in progress and other datasets that remain internal. This dataset metadata encompasses the temporal context (period or snapshot), the type of content of the dataset (as-built, design, etc.) and relations between contextualized datasets (previous as-built, requirements related to a design, etc.). In addition, this DCAT extension also provides terminology for managing dataset distributions that are scoped to a certain (named or default) graph of an RDF file or quadstore. + homepage: https://w3id.org/cdc + id: lov.cdc + name: 'CDC: Construction Dataset Context ontology' + prefix: cdc + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/cdc#$1 +lov.cdesc: + authority: lov + description: 'The Context Description module includes models for the context of a cultural property, in a broad sense: agents (e.g.: author, collector, copyright holder), objects (e.g.: inventories, bibliography, protective measures, other cultural properties, collections etc.), activities (e.g.: surveys, conservation interventions), situations (e.g.: commission, coin issuance, estimate, legal situation) related, involved or involving the cultural property. Thus it represents attributes that do not result from a measurement of features in a cultural property, but are associated with it.' + homepage: https://w3id.org/arco/ontology/context-description + id: lov.cdesc + name: Context Description Ontology (ArCo network) + prefix: cdesc + source: lov.linkeddata.es + subjects: + - generic + uri_format: https://w3id.org/arco/ontology/context-description/$1 +lov.cdm: + authority: lov + description: An attempt to represent how universal/accepted/popular a URI is + homepage: http://purl.org/twc/ontology/cdm.owl# + id: lov.cdm + name: Conceptual Depth and Momentum + prefix: cdm + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/twc/ontology/cdm.owl#$1 +lov.cdtype: + authority: lov + description: Types defined by the Dublin Core Collections Application Profile + homepage: http://purl.org/cld/cdtype/ + id: lov.cdtype + name: The Collection Description Type Namespace + prefix: cdtype + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/cld/cdtype/$1 +lov.cem: + authority: lov + description: 'The Crime Event Model is an ontology for the representation of crime events extracted from local newspapers. It could be employed for Crime Analysis purposes: extracting crime information from newspapers and enriching them with proper machine-readable semantics is a critical task to help law enforcement agencies at preventing crime, supporting criminal investigations and evaluating the action of law enforcement agencies themselves. The model is based on the fundamental 5W1H journalistic questions, that are Who?, What?, When?, Where?, Why? and How?. Another important requirement was the attempt to exploit existing knowledge graphs and ontologies such as the Simple Event Model (SEM) Ontology and the Schema.org data model for interoperability and interconnection.' + homepage: https://w3id.org/CEMontology + id: lov.cem + name: Crime Event Model (CEM) + prefix: cem + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/CEMontology/$1 +lov.ceo: + authority: lov + description: An Ontology for Consumer Electronics Products and Services + homepage: http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1 + id: lov.ceo + name: Consumer Electronics Ontology + prefix: ceo + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ebusiness-unibw.org/ontologies/consumerelectronics/v1#$1 +lov.cerif: + authority: lov + description: The Common European Research Information Format (CERIF) Ontology Specification provides basic concepts and properties for describing research information as semantic data. + homepage: http://www.eurocris.org/ontologies/cerif/1.3 + id: lov.cerif + name: CERIF Ontology 1.3 + prefix: cerif + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.eurocris.org/ontologies/cerif/1.3#$1 +lov.cert: + authority: lov + description: Ontology for Certificates and crypto stuff. + homepage: http://www.w3.org/ns/auth/cert# + id: lov.cert + name: The Cert Ontology + prefix: cert + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/auth/cert#$1 +lov.cevent: + authority: lov + description: The Cultural Event module models cultural events, i.e. events involving cultural properties. + homepage: https://w3id.org/arco/ontology/cultural-event + id: lov.cevent + name: Cultural Event Ontology (ArCo network) + prefix: cevent + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/arco/ontology/cultural-event/$1 +lov.cff: + authority: lov + description: This is an ontology representation of the generic features defined by Climate and Forecast (CF) standard names vocabulary (http://cf-pcmdi.llnl.gov/documents/cf-standard-names/), maintained by the Program for Climate Model Diagnosis and Intercomparison (http://cf-pcmdi.llnl.gov/ ) which is intended for use with climate and forecast data, in the atmosphere, surface and ocean domains. + homepage: http://purl.oclc.org/NET/ssnx/cf/cf-feature + id: lov.cff + name: Climate and Forecast (CF) features + prefix: cff + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://purl.oclc.org/NET/ssnx/cf/cf-feature#$1 +lov.cfp: + authority: lov + description: This is an ontology representation of the climatic data variables defined by Climate and Forecast (CF) standard names vocabulary (http://cf-pcmdi.llnl.gov/documents/cf-standard-names/), maintained by the Program for Climate Model Diagnosis and Intercomparison (http://cf-pcmdi.llnl.gov/ ) which is intended for use with climate and forecast data, in the atmosphere, surface and ocean domains. + homepage: http://purl.oclc.org/NET/ssnx/cf/cf-property + id: lov.cfp + name: Climate and Forecast (CF) standard names parameter vocabulary + prefix: cfp + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: http://purl.oclc.org/NET/ssnx/cf/cf-property#$1 +lov.cfrl: + authority: lov + description: The Corporate Financial Reports and Loans Ontology (CFRL). + homepage: http://linkeddata.finki.ukim.mk/lod/ontology/cfrl# + id: lov.cfrl + name: Corporate Financial Reports and Loans Ontology + prefix: cfrl + source: lov.linkeddata.es + subjects: [] + uri_format: http://linkeddata.finki.ukim.mk/lod/ontology/cfrl#$1 +lov.cgov: + authority: lov + description: An ontology of UK central government + homepage: http://reference.data.gov.uk/def/central-government + id: lov.cgov + name: Central Government Ontology + prefix: cgov + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://reference.data.gov.uk/def/central-government/$1 +lov.chord: + authority: lov + description: This document describes the first draft of a chord ontology based on work from the Centre for Digital Music, Queen Mary, University of London. It has been created as part of the OMRAS2 project and is intended to provide a common, versatile vocabulary for describing chords and chord sequences in RDF. + homepage: http://purl.org/ontology/chord/ + id: lov.chord + name: The OMRAS2 Chord Ontology + prefix: chord + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/chord/$1 +lov.ci: + authority: lov + description: This vocabulary defines a number of concepts peculiar to content strategy which are not accounted for by other vocabularies. + homepage: https://privatealpha.com/ontology/content-inventory/1# + id: lov.ci + name: A Content Inventory Vocabulary + prefix: ci + source: lov.linkeddata.es + subjects: [] + uri_format: https://privatealpha.com/ontology/content-inventory/1#$1 +lov.cis: + authority: lov + description: The ontology aims at modelling the data on cultural institutes or sites such as data regarding the agents that play a specific role on cultural institutes or sites, the sites themselves, the contact points, all multimedia files which describe the cultural institute or site and any other information useful to the public in order to access the institute or site. Moreover, the ontology represents events that can take place in specific cultural institutes or sites. + homepage: http://dati.beniculturali.it/cultural-ON/cultural-ON.owl + id: lov.cis + name: 'Cultural-ON (Cultural ONtology): Cultural Institute/Site and Cultural Event Ontology' + prefix: cis + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://dati.beniculturali.it/cis/$1 +lov.cito: + authority: lov + description: The Citation Typing Ontology enables characterization of the nature or type of citations + homepage: http://purl.org/spar/cito + id: lov.cito + name: CiTO, the Citation Typing Ontology + prefix: cito + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/cito/$1 +lov.citof: + authority: lov + description: CiTOFunctions is an ontology that provides a classification for citations. In particular, it classifies CiTO properties (each defining a particular citational act) + homepage: http://www.essepuntato.it/2013/03/cito-functions + id: lov.citof + name: Functions of Citations + prefix: citof + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.essepuntato.it/2013/03/cito-functions/$1 +lov.cl: + authority: lov + description: >- + Le projet Advene a pour objectif de fournir un modèle et plusieurs formats + de données pour partager des annotations sur des vidéos numériques (films, + cours, conférences...), ainsi que des outils pour éditer et visualiser les + hypérvidéos générées à partir de ces vidéos et des annotations. Les + enseignants, les amateurs de cinéma, etc., peuvent les utiliser pour + échanger leurs commentaires et analyse de documents audiovisuels. + + + Le modèle Cinelab permet non seulement de représenter les annotations vidéos, mais aussi d'expliciter leur structure (à travers les notions de schéma et de type d'annotation), ainsi que leur présentations à l'aide de vues (modèles appliqués aux données pour produire des hypervidéos) et de requêtes. + + + Ce modèle a été développé par les partenaires du projet Cinelab (2007-2008, financé par l'ANR), et utilisé par la suite dans plusieurs projets et applications, dont Advene (LIRIS) et Ligne de temps (IRI). + homepage: http://advene.org/ns/cinelab/ld + id: lov.cl + name: Cinelab ontology + prefix: cl + source: lov.linkeddata.es + subjects: [] + uri_format: http://advene.org/ns/cinelab/ld#$1 +lov.cld: + authority: lov + description: An expression in RDF of the application profile for collection-level description developed by the Dublin Core Collection Description Task Group. + homepage: http://purl.org/cld/terms/ + id: lov.cld + name: The Collection Description Terms + prefix: cld + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/cld/terms/$1 +lov.cmo: + authority: lov + description: An ontology to tie classes and properties to SKOS concepts + homepage: http://purl.org/twc/ontologies/cmo.owl + id: lov.cmo + name: Conceptual Model Ontology + prefix: cmo + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://purl.org/twc/ontologies/cmo.owl#$1 +lov.cnt: + authority: lov + description: Representing Content in RDF as defined by http://www.w3.org/TR/Content-in-RDF/ + homepage: http://www.w3.org/2011/content + id: lov.cnt + name: Representing Content in RDF + prefix: cnt + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2011/content#$1 +lov.co: + authority: lov + description: The Counter Ontology specification provides basic concepts and properties for describing a general counter concept and some important sub counters + homepage: http://purl.org/ontology/co/core# + id: lov.co + name: Counter Ontology + prefix: co + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/co/core#$1 +lov.cochrane: + authority: lov + description: The Cochrane Core ontology describes the entities and concepts that exist in the domain of evidence based healthcare. It is used for the construction of the Cochrane Linked Data Vocabulary containing some 400k terms including Interventions (Drugs, Procedures etc), Populations (Age, Sex, Condition), and clinical Outcomes. + homepage: http://data.cochrane.org/ontologies/core/ + id: lov.cochrane + name: Cochrane Core Vocabulary Ontology + prefix: cochrane + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://data.cochrane.org/ontologies/core/$1 +lov.cocoon: + authority: lov + description: Simple ontology for Cloud Computing Services. This ontology allows to define model of prices used in large cloud computing providers such as Google, Amazon, Azure, etc., including options for regions, type of instances, prices specification, etc. + homepage: https://w3id.org/cocoon/v1.0 + id: lov.cocoon + name: Cloud Computing Services Ontology + prefix: cocoon + source: lov.linkeddata.es + subjects: + - law + uri_format: https://w3id.org/cocoon/v1.0#$1 +lov.cogs: + authority: lov + description: Vocabulary for describing ETL and data transformation activities. + homepage: http://vocab.deri.ie/cogs + id: lov.cogs + name: COGS Vocabulary + prefix: cogs + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.deri.ie/cogs#$1 +lov.cold: + authority: lov + description: Ontology for the description of customizable products. It models the configuration process as the traversal of a graph of partially defined products, or "Configurations" + homepage: http://purl.org/configurationontology + id: lov.cold + name: "'Configuration as Linked Data' ontology" + prefix: cold + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/configurationontology#$1 +lov.coll: + authority: lov + description: 'The Collections Ontology (CO) defines unordered collections (Set and Bag) and ordered collections (or List). This ontology has been inspired by the work "Putting OWL in Order: Patterns for Sequences in OWL" by Drummond et al. (OWL-ED 2006).' + homepage: http://purl.org/co + id: lov.coll + name: Collections Ontology + prefix: coll + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/co/$1 +lov.comm: + authority: lov + description: This vocabulary is intended to describe all the aspects which are needed to communicate incident related information for fire department services + homepage: http://vocab.resc.info/communication + id: lov.comm + name: Vocabulary related to incident communication + prefix: comm + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.resc.info/communication#$1 +lov.common: + authority: lov + description: The Delivery Context Ontology models the knowledge of the environment in which devices interact with the Web or other services + homepage: http://www.w3.org/2007/uwa/context/deliverycontext.owl + id: lov.common + name: The Delivery Context Ontology + prefix: common + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2007/uwa/context/common.owl#$1 +lov.con: + authority: lov + description: Utility concepts for everyday life + homepage: http://www.w3.org/2000/10/swap/pim/contact + id: lov.con + name: Contact + prefix: con + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2000/10/swap/pim/contact#$1 +lov.contax: + authority: lov + description: An ontology containing additional terminology for structuring and annotating RDFS/OWL taxonomies for describing constructions (components, materials, spatial zones, damages, construction tasks and properties). It also functions as an index for known taxonomies starting from root classes and properties. + homepage: https://w3id.org/con-tax + id: lov.contax + name: ConTax ontology + prefix: contax + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/con-tax#$1 +lov.conversion: + authority: lov + description: Ontology used to describe interpretations of tabular literals to produce RDF + homepage: http://purl.org/twc/vocab/conversion/ + id: lov.conversion + name: Conversion Ontology + prefix: conversion + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/twc/vocab/conversion/$1 +lov.coo: + authority: lov + description: The COO provides a vocabulary for exposing available configuration options for car models. It allows indicating choices that can be made as well as compatibility, dependency, and inclusion information. The ontology imports and extends the GoodRelations ontology for e-commerce + homepage: http://purl.org/coo/ns# + id: lov.coo + name: Car Options Ontology + prefix: coo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/coo/ns#$1 +lov.core: + authority: lov + description: This is the core module in Materials Design Ontology. + homepage: https://w3id.org/mdo/core/ + id: lov.core + name: Materials Design Ontology - Core Module + prefix: core + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/mdo/core/$1 +lov.coun: + authority: lov + description: Basic properties of a country as defined by ISO 3166 (code and name) + homepage: http://www.daml.org/2001/09/countries/iso-3166-ont + id: lov.coun + name: ISO 3166 Country Codes + prefix: coun + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://www.daml.org/2001/09/countries/iso-3166-ont#$1 +lov.cpa: + authority: lov + description: A set of annotation properties to be used for ontology design patterns + homepage: http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl + id: lov.cpa + name: Content Pattern Annotations + prefix: cpa + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/schemas/cpannotationschema.owl#$1 +lov.cpmeta: + authority: lov + description: 'OWL vocabulary describing metadata of two environmental research infrastructures: ICOS and SITES' + homepage: http://meta.icos-cp.eu/ontologies/cpmeta/ + id: lov.cpmeta + name: Ontology of Integrated Carbon Observation System (ICOS) + prefix: cpmeta + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://meta.icos-cp.eu/ontologies/cpmeta/$1 +lov.crm: + authority: lov + description: This is the encoding approved by CRM-SIG in the meeting 21/11/2012 as the official current version for the CIDOC CRM namespace. Note that this is NOT a definition of the CIDOC CRM, but an encoding derived from the authoritative release of the CIDOC CRM v5.0.4 on http://www.cidoc-crm.org/official_release_cidoc.html + homepage: http://www.cidoc-crm.org/cidoc-crm/ + id: lov.crm + name: CIDOC Conceptual Reference Model + prefix: crm + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.cidoc-crm.org/cidoc-crm/$1 +lov.cro: + authority: lov + description: The Copyright Ontology is a contribution geared towards the development of copyright-aware Digital Rights Management (DRM) systems. + homepage: http://rhizomik.net/ontologies/copyrightonto.owl + id: lov.cro + name: Copyright Ontology + prefix: cro + source: lov.linkeddata.es + subjects: [] + uri_format: http://rhizomik.net/ontologies/copyrightonto.owl#$1 +lov.crsw: + authority: lov + description: The ReSIST Courseware Ontology represents the various educational courses and resources within the ReSIST project + homepage: http://courseware.rkbexplorer.com/ontologies/courseware + id: lov.crsw + name: ReSIST Courseware Ontology + prefix: crsw + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://courseware.rkbexplorer.com/ontologies/courseware#$1 +lov.cs: + authority: lov + description: This vocabulary defines a set of terms for describing changes to resource descriptions. + homepage: http://purl.org/vocab/changeset/schema + id: lov.cs + name: Changeset + prefix: cs + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocab/changeset/schema#$1 +lov.csp: + authority: lov + description: A vocabulary to represent Constraint Satisfaction Problems (CSPs) in which constraints are expressed by Boolean expressions on fluents. + homepage: http://vocab.deri.ie/csp + id: lov.csp + name: Constraint Satisfaction Problems Vocabulary + prefix: csp + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.deri.ie/csp#$1 +lov.csvw: + authority: lov + description: This document describes the RDFS vocabulary description used in the Metadata Vocabulary for Tabular Data along with the default JSON-LD Context. + homepage: http://www.w3.org/ns/csvw# + id: lov.csvw + name: CSV on the Web Vocabulary + prefix: csvw + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/csvw#$1 +lov.ct: + authority: lov + description: Defines types of connectivity used in communication and bearer services accessible in certain connectivity. + homepage: http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl + id: lov.ct + name: Connectivity types + prefix: ct + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.tele.pw.edu.pl/~sims-onto/ConnectivityType.owl#$1 +lov.ctag: + authority: lov + description: Common Tags are references to unique, well-defined concepts, complete with metadata and their own URLs. + homepage: http://commontag.org/ns# + id: lov.ctag + name: Common Tag Vocabulary + prefix: ctag + source: lov.linkeddata.es + subjects: [] + uri_format: http://commontag.org/ns#$1 +lov.ctlog: + authority: lov + description: The Catalogue module allows the description of concepts related to the Italian General Catalogue of Cultural Heritage (ICCD-MiBAC), and in particular catalogue records, that is XML files recording all data gathered by a cataloguer on a particular cultural property. + homepage: https://w3id.org/arco/ontology/catalogue + id: lov.ctlog + name: Catalogue Ontology (ArCo network) + prefix: ctlog + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: https://w3id.org/arco/ontology/catalogue/$1 +lov.cto: + authority: lov + description: >- + The Construction Tasks Ontology (CTO) describes tasks operating on + construction elements, spatial zones and/or damages. The tasks are either + planned or executed depending on the dataset metadata context of the dataset + its used in. Five different types of tasks are defined: instalment, removal, + modification, repair and inspection. + + Consequences of tasks on the dataset, i.e. added and/or deleted triples, are modeled using reified statements. The tasks can link to a reified statement using the CTO relations. + homepage: https://w3id.org/cto + id: lov.cto + name: 'CTO: Construction Tasks Ontology' + prefix: cto + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/cto#$1 +lov.ctorg: + authority: lov + description: El objetivo de este vocabulario es la creación de un esquema que permita definir los contenidos de la información relacionada con los órganos de gobierno y los centros públicos que ofrecen servicios. Se identifican ciertas variables en el dominio de los centros públicos, que se modelan a través de ciertos tipos de datos y de propiedades relacionadas entre los recursos. Se utiliza Ontologies for e-Government para modelar las principales características. + homepage: http://purl.org/ctic/infraestructuras/organizacion + id: lov.ctorg + name: Vocabulario de la estructura de organismos públicos + prefix: ctorg + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://purl.org/ctic/infraestructuras/organizacion#$1 +lov.ctrl: + authority: lov + description: CTRLont specifies concepts and relationships of control actors on a high level + homepage: https://w3id.org/ibp/CTRLont + id: lov.ctrl + name: CTRLont - An ontology to formally specify the control domain + prefix: ctrl + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/ibp/CTRLont#$1 +lov.ctxdesc: + authority: lov + description: OWL pattern for describing activity models as abstract dependencies among classes. + homepage: http://www.demcare.eu/ontologies/contextdescriptor.owl + id: lov.ctxdesc + name: Context Descriptor Pattern + prefix: ctxdesc + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.demcare.eu/ontologies/contextdescriptor.owl#$1 +lov.cwmo: + authority: lov + description: Creative Workshop Management Ontology (CWMO) - an ontology designed to describe the creative workshop domain, to permit reasoning on creative method and to describe resources gathered inside Creative Support System. The primary goal of the ontology is to cover all knowledge about creative workshop and creative method necessary for Creative support system. The second goal is to provide interoperability between distributed Creative Support System. + homepage: http://purl.org/cwmo/# + id: lov.cwmo + name: Creative Workshop Management Ontology (CWMO) + prefix: cwmo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/cwmo/#$1 +lov.cwork: + authority: lov + description: This ontology defines the terms required to describe the creative works produced by the BBC and their associated metadata. + homepage: http://www.bbc.co.uk/ontologies/creativework + id: lov.cwork + name: Creative Work Ontology + prefix: cwork + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.bbc.co.uk/ontologies/creativework/$1 +lov.cwrc: + authority: lov + description: L'Ontologie CWRC est l'ontologie du Collaboratoire scientifique des écrits du Canada. + homepage: http://sparql.cwrc.ca/ontologies/cwrc + id: lov.cwrc + name: L'Ontologie CWRC + prefix: cwrc + source: lov.linkeddata.es + subjects: [] + uri_format: http://sparql.cwrc.ca/ontologies/cwrc#$1 +lov.d2rq: + authority: lov + description: This document specifies the D2RQ mapping language. D2RQ is a declarative language to describe mappings between relational database schemata and OWL/RDFS ontologies. + homepage: http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1 + id: lov.d2rq + name: D2RQ - Language Specification + prefix: d2rq + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#$1 +lov.dady: + authority: lov + description: A vocabulary that allows for coarse-grained descriptions of the data-source dynamics as well as the discovery of change notification mechanism(s). + homepage: http://vocab.deri.ie/dady + id: lov.dady + name: Dataset Dynamics (dady) vocabulary + prefix: dady + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/NET/dady#$1 +lov.daia: + authority: lov + description: The Document Availability Information Ontology (DAIA) describes the current availability of documents in libraries and similar institutions. Availability can be expressed in terms of specific services. + homepage: http://purl.org/ontology/daia + id: lov.daia + name: Document Availability Information Ontology + prefix: daia + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/ontology/daia/$1 +lov.daq: + authority: lov + description: Quality metrics can be (in principle) calculated on various forms of data (such as datasets, graphs, set of triples etc...). This vocabulary allow the owner/user of such RDF data to calculate metrics on multiple (and different) resources. + homepage: http://purl.org/eis/vocab/daq# + id: lov.daq + name: Dataset Quality Vocabulary + prefix: daq + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/eis/vocab/daq#$1 +lov.dataid: + authority: lov + description: DBpedia Data ID is an ontology with the goal of describing LOD datasets via RDF files in a uniform way. Established vocabularies like DCAT, VoID, Prov-O and SPARQL Service Description are used for maximum compatibility. + homepage: http://dataid.dbpedia.org/ns/core# + id: lov.dataid + name: DataID + prefix: dataid + source: lov.linkeddata.es + subjects: [] + uri_format: http://dataid.dbpedia.org/ns/core#$1 +lov.date: + authority: lov + description: OntoMedia (Ontology for Media) Date Component has been designed to describe the different ways of marking time in media. + homepage: http://contextus.net/ontology/ontomedia/misc/date# + id: lov.date + name: OntoMedia Date Part Representation + prefix: date + source: lov.linkeddata.es + subjects: [] + uri_format: http://contextus.net/ontology/ontomedia/misc/date#$1 +lov.datex: + authority: lov + description: This document gives URIs to all terms used within Datex II. the Datex standard was developed for information exchange between traffic management centres, traffic information centres and service providers in Europe + homepage: http://vocab.datex.org/terms# + id: lov.datex + name: Linked Datex II + prefix: datex + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://vocab.datex.org/terms#$1 +lov.dave: + authority: lov + description: The Data Value Vocabulary (DaVe) is an extensible core vocabulary that allows user to use custom data value dimensions and metrics to characterise data value in a specific context. This flexibility allows for the comprehensive modelling of data value. As a data value model, DaVe allows users to monitor data value as it occurs within a data exploitation or value creation process (data value chain) + homepage: http://theme-e.adaptcentre.ie/dave/dave.ttl + id: lov.dave + name: Data Value Vocabulary (DaVe) + prefix: dave + source: lov.linkeddata.es + subjects: + - generic + - mathematics + - computer and information sciences + uri_format: http://theme-e.adaptcentre.ie/dave#$1 +lov.dba: + authority: lov + description: "The ontology, presented here in a beta version, is based on the analysis of the documentation and descriptive requirements of the Intesa Sanpaolo Historical Archive and is intended to describe the content of historical banking documents and of some of the activities carried out by the bank, particularly in relation to third parties (loans, charity donations, seizures and confiscations, etc.), which involve the initiation of processes or the production of documents. The focal point of the descriptive model is the bank - an entity that initiates different types of processes, whose common feature is that they are structured into various stages/events - and the relationship between the documentation produced and the information it contains. In fact, this ontology is based on information collected from archived documents which describe various processes and activities carried out by banking institutions: the starting point for its construction were the inventories and databases of documentation stored in the Historical Archive which was produced by the various banks that over time were merged into Intesa Sanpaolo. The ontology was created to provide a sufficiently abstract representation and model for describing the processes of various banking activities from which the documentation was produced - from a company's request for financing and its outcome, to the preparation of seizure, confiscation and asset restitution filings, to charitable contributions, just to mention a few examples - reusing models that were already well established and widely used. The structure of the proposed ontology is in fact intended to adapt to the various activities, described in the archive files that a banking institution performs in relation to third parties. The proposed ontology is therefore not an ontology on banking activity in general, but on the relationship between this activity and the documents that are produced. Moreover, its objective is not to describe the documents in the strict sense of the term, for which reference is made to OAD ontology. The purpose of this project is to lay the initial, and fundamental, building blocks for describing the complexity, variety, and breadth of the domain of archiving bank records and the data they contain. Despite having data from different banks relating to different activities and having already made arrangements for the integration of third-party datasets and ontologies, before completing the project we will have to wait for the processing of representations based on other types of documents and banking institutions, including non-Italian ones." + homepage: https://w3id.org/dba/ontology/ + id: lov.dba + name: Description Banking Archives Ontology + prefix: dba + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: https://w3id.org/dba/ontology/$1 +lov.dbm: + authority: lov + description: An ontology for the Drug Bureau of Macedonia (DBM). + homepage: http://purl.org/net/dbm/ontology# + id: lov.dbm + name: DBM Ontology + prefix: dbm + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://purl.org/net/dbm/ontology#$1 +lov.dbowl: + authority: lov + description: Primitive ontology for database to Semantic Web mapping which subsumes classes that represent mappings to explicit OWL constructs, such as OWL class, object property, data property, etc. Classes in this ontology are populated by individuals representing components of the database schema being mapped. + homepage: http://ontology.cybershare.utep.edu/dbowl + id: lov.dbowl + name: Relational to Ontology Mapping Primitive + prefix: dbowl + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.cybershare.utep.edu/dbowl/relational-to-ontology-mapping-primitive.owl#$1 +lov.dbpedia-owl: + authority: lov + description: The DBpedia ontology provides the classes and properties used in the DBpedia data set. + homepage: http://dbpedia.org/ontology/ + id: lov.dbpedia-owl + name: The DBpedia Ontology + prefix: dbpedia-owl + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://dbpedia.org/ontology/$1 +lov.dbug: + authority: lov + description: An extension of DOAP for the description of bugs + homepage: http://ontologi.es/doap-bugs# + id: lov.dbug + name: DOAP Bugs + prefix: dbug + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontologi.es/doap-bugs#$1 +lov.dcam: + authority: lov + description: An abstract model for Dublin Core metadata + homepage: http://purl.org/dc/dcam/ + id: lov.dcam + name: DCMI Abstract Model + prefix: dcam + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://purl.org/dc/dcam/$1 +lov.dcat: + authority: lov + description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web + homepage: http://www.w3.org/ns/dcat + id: lov.dcat + name: Data Catalog Vocabulary + prefix: dcat + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/dcat#$1 +lov.dce: + authority: lov + description: The Dublin Core Metadata Element Set is a vocabulary of fifteen properties for use in resource description. The name "Dublin" is due to its origin at a 1995 invitational workshop in Dublin, Ohio; "core" because its elements are broad and generic, usable for describing a wide range of resources. + homepage: http://purl.org/dc/elements/1.1/ + id: lov.dce + name: Dublin Core Metadata Element Set + prefix: dce + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/dc/elements/1.1/$1 +lov.dcite: + authority: lov + description: The DataCite Ontology is an ontology written in OWL 2 DL to enable certain metadata properties of the DataCite Metadata Specification version 2.0 (http://datacite.org/schema/DataCite-MetadataKernel_v2.0.pdf) to be described in RDF. + homepage: http://purl.org/spar/datacite + id: lov.dcite + name: The DataCite Ontology + prefix: dcite + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/datacite/$1 +lov.dcndl: + authority: lov + description: RDF Schema declaration for Japan NDL Metadata Terms + homepage: http://ndl.go.jp/dcndl/terms/ + id: lov.dcndl + name: NDL Metadata Terms + prefix: dcndl + source: lov.linkeddata.es + subjects: [] + uri_format: http://ndl.go.jp/dcndl/terms/$1 +lov.dco: + authority: lov + description: domOS Common Ontology (dCO) represents a common information model to share a unified understanding for humans and machines and to ensure semantic interoperability in a heterogeneous IoT infrastructure. This ontology allows the decoupling of the infrastructure from the software services and applications. + homepage: https://w3id.org/dco + id: lov.dco + name: domOS Common Ontology + prefix: dco + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/dco#$1 +lov.dcterms: + authority: lov + description: an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. + homepage: http://purl.org/dc/terms/ + id: lov.dcterms + name: DCMI Metadata Terms + prefix: dcterms + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/dc/terms/$1 +lov.dctype: + authority: lov + description: The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource. + homepage: http://purl.org/dc/dcmitype/ + id: lov.dctype + name: DCMI Type Vocabulary + prefix: dctype + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://purl.org/dc/dcmitype/$1 +lov.ddesc: + authority: lov + description: >- + The Denotative Description module encodes the characteristics of a cultural + property, as detectable and/or detected during the cataloguing process and + measurable according to a reference system. Examples include measurements + e.g. length, constituting materials e.g. clay, employed techniques e.g. + melting, conservation status e.g. good, decent, bad. + + In this module are used as template the following Ontology Design Patterns: + + - http://www.ontologydesignpatterns.org/cp/owl/collectionentity.owl + + - http://www.ontologydesignpatterns.org/cp/owl/classification.owl + + - http://www.ontologydesignpatterns.org/cp/owl/descriptionandsituation.owl + + - http://www.ontologydesignpatterns.org/cp/owl/situation.owl + homepage: https://w3id.org/arco/ontology/denotative-description + id: lov.ddesc + name: Denotative Description Ontology (ArCo network) + prefix: ddesc + source: lov.linkeddata.es + subjects: + - generic + uri_format: https://w3id.org/arco/ontology/denotative-description/$1 +lov.decision: + authority: lov + description: Decision-making is a process that can result in some decision and decision is a situation of indicating one of the considered options. Decision Ontology provides means for precise distinguishing and distinct treatment of these two aspects. + homepage: https://decision-ontology.googlecode.com/svn/trunk/decision.owl + id: lov.decision + name: Decision ontology + prefix: decision + source: lov.linkeddata.es + subjects: [] + uri_format: https://decision-ontology.googlecode.com/svn/trunk/decision.owl#$1 +lov.demlab: + authority: lov + description: The ontology has been developed in the framework of the Dem@Care project for representing the experimentation protocol towards diagnostic support and assessment of Dementia in a controlled environment. The aim of the protocol is to provide a brief overview of their health status of the participants during consultation (cognition, behaviours and function), and to correlate the system (sensor) data with the data collected using typical dementia care assessment tools. + homepage: http://www.demcare.eu/ontologies/demlab.owl + id: lov.demlab + name: Dem@Care Lab Ontology for Dementia Assessment + prefix: demlab + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://www.demcare.eu/ontologies/demlab.owl#$1 +lov.deo: + authority: lov + description: The Discourse Elements Ontology is an ontology for describing the major rhetorical elements of a document such as a journal article. It is a subsidiary ontology that is imported into the Document Components Ontology, itself part of SPAR, the Semantic Publishing and Referencing Ontologies + homepage: http://purl.org/spar/deo + id: lov.deo + name: The Discourse Elements Ontology + prefix: deo + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/deo/$1 +lov.deps: + authority: lov + description: An extension to DOAP for describing a project's requirements + homepage: http://ontologi.es/doap-deps# + id: lov.deps + name: DOAP Dependencies + prefix: deps + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontologi.es/doap-deps#$1 +lov.dfc: + authority: lov + description: A common vocabulary for digital food platforms + homepage: http://static.datafoodconsortium.org/ontologies/DFC_FullModel.owl + id: lov.dfc + name: Data Food Consortium Ontology + prefix: dfc + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://static.datafoodconsortium.org/ontologies/DFC_FullModel.owl#$1 +lov.dfc-b: + authority: lov + description: DFC Business Ontology + homepage: http://static.datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl + id: lov.dfc-b + name: DFC Business Ontology + prefix: dfc-b + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://static.datafoodconsortium.org/ontologies/DFC_BusinessOntology.owl#$1 +lov.dfc-p: + authority: lov + description: A common vocabulary for digital food platforms (Product Glossary Part) + homepage: http://static.datafoodconsortium.org/ontologies/DFC_ProductGlossary.owl + id: lov.dfc-p + name: A common vocabulary for digital food platforms (Product Glossary Part) + prefix: dfc-p + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://static.datafoodconsortium.org/ontologies/DFC_ProductGlossary.owl#$1 +lov.dfc-t: + authority: lov + description: A common vocabulary for digital food platforms (Technical Part) + homepage: http://static.datafoodconsortium.org/ontologies/DFC_TechnicalOntology.owl + id: lov.dfc-t + name: A common vocabulary for digital food platforms (Technical Part) + prefix: dfc-t + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://static.datafoodconsortium.org/ontologies/DFC_TechnicalOntology.owl#$1 +lov.dg: + authority: lov + description: 'The DINGO ontology (Data Integration for Grant Ontology) defines the terms of the DINGO vocabulary and provides a machine readable extensible framework to model data relative to projects, funding, project and funding actors, and, notably, funding policies. It is designed to yield high modeling power and elasticity to cope with the huge variety in funding and project practices, which makes it applicable to many areas where funding is an important aspect: first of all research, but also the arts, cultural conservation, and many others.' + homepage: https://w3id.org/dingo/ + id: lov.dg + name: DINGO Ontology + prefix: dg + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/dingo#$1 +lov.dicom: + authority: lov + description: "Ontology for healthcare metadata - especially metadata found in DICOM files (Digital Imaging and Communications in Medicine, see http://dicom.nema.org/). Author: Michael Brunnbauer, Bonubase GmbH (www.bonubase.com). The author's email address is brunni@netestate.de. See http://purl.org/healthcarevocab/v1help for explanations." + homepage: http://purl.org/healthcarevocab/v1 + id: lov.dicom + name: Healthcare metadata - DICOM ontology + prefix: dicom + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://purl.org/healthcarevocab/v1#$1 +lov.dio: + authority: lov + description: The scope of the DIO is the domain of design intent or design rationale that needs to be documented while undertaking the design of any artifact + homepage: https://w3id.org/dio + id: lov.dio + name: The Design Intent Ontology + prefix: dio + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/dio#$1 +lov.disco: + authority: lov + description: A metadata vocabulary for documenting research and survey data + homepage: http://rdf-vocabulary.ddialliance.org/discovery + id: lov.disco + name: DDI-RDF Discovery Vocabulary + prefix: disco + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdf-vocabulary.ddialliance.org/discovery#$1 +lov.dita: + authority: lov + description: The DITA RDF ontology translates the semantics of a subset of the vocabulary described in the DITA 1.2 specification in a format that can be understood in the semantic Web of data. By Colin Maudry, licensed under the terms of the Unlicense (public domain). + homepage: http://purl.org/dita/ns# + id: lov.dita + name: DITA RDF ontology + prefix: dita + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/dita/ns#$1 +lov.dk: + authority: lov + description: The Data Knowledge Vocabulary allows for a comprehensive description of data assets and enterprise data management. It covers a business data dictionary, data quality management, data governance, the technical infrastructure and many other aspects of enterprise data management. The vocabulary represents a linked data implementation of the Data Knowledge Model which resulted from extensive applied research. + homepage: http://www.data-knowledge.org/dk/ + id: lov.dk + name: The Data Knowledge Vocabulary + prefix: dk + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.data-knowledge.org/dk/$1 +lov.dm2e: + authority: lov + description: The DM2E model is a specialisation of the Europeana Data Model (EDM) and can be used for the description of manuscripts in the cultural heritage domain. + homepage: http://onto.dm2e.eu/schemas/dm2e + id: lov.dm2e + name: DM2E model + prefix: dm2e + source: lov.linkeddata.es + subjects: [] + uri_format: http://onto.dm2e.eu/schemas/dm2e/$1 +lov.dnbt: + authority: lov + description: The DNB RDF Vocabulary (dnb:) is a collection of classes, properties and datatypes used within the DNB's linked data service.It complements the GND Ontology (gndo:) which is specifically geared towards authority data from the Integrated Authority File (GND), whereas this vocabulary is more general-purpose. + homepage: http://d-nb.info/standards/elementset/dnb + id: lov.dnbt + name: DNB Metadata Terms + prefix: dnbt + source: lov.linkeddata.es + subjects: [] + uri_format: http://d-nb.info/standards/elementset/dnb#$1 +lov.doap: + authority: lov + description: The Description of a Project (DOAP) vocabulary, described using W3C RDF Schema and the Web Ontology Language. + homepage: http://usefulinc.com/ns/doap# + id: lov.doap + name: Description of a Project vocabulary + prefix: doap + source: lov.linkeddata.es + subjects: [] + uri_format: http://usefulinc.com/ns/doap#$1 +lov.doc: + authority: lov + description: Defines properties and relationships between works. + homepage: http://www.w3.org/2000/10/swap/pim/doc + id: lov.doc + name: Works, licences, derivatives and dependencies + prefix: doc + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.w3.org/2000/10/swap/pim/doc#$1 +lov.doco: + authority: lov + description: An ontology for describing the component parts of a bibliographic document + homepage: http://purl.org/spar/doco + id: lov.doco + name: DoCO, the Document Components Ontology + prefix: doco + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/doco/$1 +lov.docso: + authority: lov + description: A micro-ontology that defines a set of typical document-related services such as provided by libraries, museums and archives. + homepage: http://purl.org/ontology/dso + id: lov.docso + name: Document Service Ontology + prefix: docso + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/dso#$1 +lov.dogont: + authority: lov + description: The DogOnt ontology supports device/network independent description of houses, including both controllable and architectural elements. + homepage: http://elite.polito.it/ontologies/dogont.owl + id: lov.dogont + name: Ontology Modeling for Intelligent Domotic Environments + prefix: dogont + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: http://elite.polito.it/ontologies/dogont$1 +lov.donto: + authority: lov + description: >- + The data.gov.au Dataset Ontology is an OWL ontology designed to describe the + characteristics of datasets published on data.gov.au. + + + The ontology contains elements which describe the publication, update, origin, governance, spatial and temporal coverage and other contextual information about the dataset. The ontology also covers aspects of organisational custodianship and governance. + + By using this ontology to describe datasets on data.gov.au publishers increase discoverability and enable the consumption of this information in other applications/systems as Linked Data. It further enables decentralised publishing of catalogs and facilitates federated dataset search across sites, e.g. in datasets that are published by the States. + + Other publishers of Linked Data may make assertions about data published using this ontology, e.g. they may publish information about the use of the dataset in other applications. + homepage: http://reference.data.gov.au/def/ont/dataset + id: lov.donto + name: Dataset Ontology + prefix: donto + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://reference.data.gov.au/def/ont/dataset#$1 +lov.dot: + authority: lov + description: >- + - Version 0.8: + + * completed ontology metadata wrt LOV + + * added classes dot:ClassifiedDamage and dot:UnclassifiedDamage (subclasses of dot:Damage) + + * made dot:StructuralDamage and dot:Defect subclasses of dot:Damage + homepage: https://w3id.org/dot# + id: lov.dot + name: Damage Topology Ontology + prefix: dot + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://w3id.org/dot#$1 +lov.dpn: + authority: lov + description: This ontology is being developed by CSIRO under the eReefs project for describing data provider nodes, web services available and datasets that are hosted by them. This ontology features a module for describing Datasets. It does not however describe geospatial, temporal, organisational or domain concepts as these are intended to be included from other ontologies via the imports statement. Other modules complementary to the DPN ontology are http://purl.org/dpn/dataset and http://purl.org/dpn/services. This version aligns DCAT and DC terms and imports DPN services. + homepage: http://purl.org/dpn + id: lov.dpn + name: Data Provider Node ontology + prefix: dpn + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/dpn#$1 +lov.dprov: + authority: lov + description: >- + This ontology is a reduced-in-scope version of the [W3C Decisions and + Decision-Making Incubator + Group](https://www.w3.org/2005/Incubator/decision/)'s Decision Ontology (DO) + which can be found at . It has + been re-worked to align entirely with the W3C's [PROV + ontology](https://www.w3.org/TR/prov-o/) since it is widely recognised that + analysing the elements of decisions *post hoc* is an exercise in provenance. + + + Unlike the original DO, this ontology cannot be used for *normative* scenarios: it is only capable of recording decisions that have already been made (so-called *data-driven* use in the DO). This is because PROV, to which this ontology is completely mapped, does not have a templating system which can indicate what *should* occur in future scenarios. + + + This ontology introduces only one new element for decision modelling over that which was present in the DO: an Agent which allows agency in decision making to be recorded. + homepage: http://promsns.org/def/decprov + id: lov.dprov + name: Decision Provenance ontology (DecPROV) + prefix: dprov + source: lov.linkeddata.es + subjects: [] + uri_format: http://promsns.org/def/do#$1 +lov.dq: + authority: lov + description: An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - DQ Package + homepage: http://def.seegrid.csiro.au/isotc211/iso19115/2003/dataquality + id: lov.dq + name: OWL representation of ISO 19115 (Geographic Information - Metadata - Data quality package) + prefix: dq + source: lov.linkeddata.es + subjects: [] + uri_format: http://def.seegrid.csiro.au/isotc211/iso19115/2003/dataquality#$1 +lov.dqc: + authority: lov + description: This RDF document contains a library of data quality constraints represented as SPARQL query templates based on the SPARQL Inferencing Framework (SPIN). The data quality constraint templates are especially useful for the identification of data quality problems during data entry and for periodic quality checks during data usage. + homepage: http://semwebquality.org/ontologies/dq-constraints + id: lov.dqc + name: The Data Quality Constraints Library + prefix: dqc + source: lov.linkeddata.es + subjects: [] + uri_format: http://semwebquality.org/ontologies/dq-constraints#$1 +lov.dqm: + authority: lov + description: The Data Quality Management Vocabulary - An Ontology for Data Requirements Management, Data Quality Monitoring, Data Quality Assessment, and Data Cleansing + homepage: http://purl.org/dqm-vocabulary/v1/dqm + id: lov.dqm + name: The Data Quality Management Vocabulary + prefix: dqm + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/dqm-vocabulary/v1/dqm#$1 +lov.dqv: + authority: lov + description: The Data Quality Vocabulary (DQV) is seen as an extension to DCAT to cover the quality of the data, how frequently is it updated, whether it accepts user corrections, persistence commitments etc. When used by publishers, this vocabulary will foster trust in the data amongst developers. + homepage: http://www.w3.org/ns/dqv + id: lov.dqv + name: Data Quality Vocabulary + prefix: dqv + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/dqv#$1 +lov.dr: + authority: lov + description: Relationships without range and domains meant to be reused in different contexts + homepage: http://purl.org/swan/2.0/discourse-relationships/ + id: lov.dr + name: Discourse relationships vocabulary + prefix: dr + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/swan/2.0/discourse-relationships/$1 +lov.drama: + authority: lov + description: >- + Designed with the goals to describe and encode the core dramatic qualities + and to serve as a knowledge base underlying a number of applications, + Drammar is a comprehensive ontology of drama, realized through a + collaboration of computer scientists and drama scholars. It makes the + knowledge about drama available as a vocabulary for the linked interchange + of drama encodings and readily usable by automatic reasoners. + + By avoinding references to style and artistic qualities Drammar aims at representing the elements shared by different, cross-media manifestations of drama, the so–called intangible elements of drama as an intangible cultural heritage form. + homepage: http://www.purl.org/drammar + id: lov.drama + name: 'Drammar: a comprehensive ontology of drama' + prefix: drama + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.purl.org/drammar#$1 +lov.drm: + authority: lov + description: A metamodel for government data + homepage: http://vocab.data.gov/def/drm + id: lov.drm + name: Data Reference Model + prefix: drm + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://vocab.data.gov/def/drm#$1 +lov.ds: + authority: lov + description: Este vocabulario se utiliza para modelar los catálogos de conjuntos de datos y las relaciones con los datasets + homepage: http://purl.org/ctic/dcat# + id: lov.ds + name: Dataset Catalog Vocabulary + prefix: ds + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/ctic/dcat#$1 +lov.dsd: + authority: lov + description: To ensure comparability between schemas from different data models, the Description of a Data Source (DSD) vocabulary has been developed. + homepage: https://w3id.org/dsd + id: lov.dsd + name: Description of a Data Source + prefix: dsd + source: lov.linkeddata.es + subjects: + - other humanities + - computer and information sciences + uri_format: https://w3id.org/dsd#$1 +lov.dsn: + authority: lov + description: DSNotify Eventsets is a vocabulary for events that change resources in linked data sources. + homepage: http://purl.org/dsnotify/vocab/eventset/ + id: lov.dsn + name: 'DSNotify Eventsets: A vocabulary for change events in linked data sources' + prefix: dsn + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/dsnotify/vocab/eventset/$1 +lov.dso: + authority: lov + description: This ontology offers OWL-Lite definition for object list. It is a restricted version of OWL-S ObjectList + homepage: http://inference-web.org/2.0/ds.owl + id: lov.dso + name: Data Structure Ontology + prefix: dso + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://inference-web.org/2.0/ds.owl#$1 +lov.dtx_srti: + authority: lov + description: 'An RDF/OWL vocabulary to represent SRTI DATEX II profile (according the Commission Delegated Regulation (EU) No 886/2013) within the European LOD-RoadTran18 action "Supporting the cross-border use of Road Traffic Data with Linked Open Data based on DATEX II (LOD-RoadTran18)" (Agreement No: INEA/CEF/ICT/A2018/1803421, Action No: 2018-EU-IA-0088). The vocabulary is used for mapping between DATEX II and LOD formats.' + homepage: http://cef.uv.es/lodroadtran18/def/transporte/dtx_srti + id: lov.dtx_srti + name: LOD SRTI DATEX II + prefix: dtx_srti + source: lov.linkeddata.es + subjects: [] + uri_format: http://cef.uv.es/lodroadtran18/def/transporte/dtx_srti#$1 +lov.dtype: + authority: lov + description: The ontology 'dtype' provides a specification of simple data types such as enumerations. These are needed in support of the conversion of XML Schemas and UML Models to OWL. Codelists are also defined in 'dtype'. + homepage: http://www.linkedmodel.org/schema/dtype + id: lov.dtype + name: Datatype Ontology + prefix: dtype + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.linkedmodel.org/schema/dtype#$1 +lov.dul: + authority: lov + description: The DOLCE+DnS Ultralite ontology. It is a simplification of some parts of the DOLCE Lite-Plus library (cf. http://www.ontologydesignpatterns.org/ont/dul/DLP397.owl) + homepage: http://www.ontologydesignpatterns.org/ont/dul/DUL.owl + id: lov.dul + name: DOLCE+DnS Ultralite + prefix: dul + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.ontologydesignpatterns.org/ont/dul/DUL.owl#$1 +lov.duv: + authority: lov + description: The Dataset Usage Vocabulary (DUV) is used to describe consumer experiences, citations, and feedback about datasets from the human perspective. + homepage: http://www.w3.org/ns/duv + id: lov.duv + name: Dataset Usage Vocabulary + prefix: duv + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/duv#$1 +lov.dvia: + authority: lov + description: dvia is an RDF vocabulary designed to facilitate interoperability between visualization applications published on the Web. + homepage: http://purl.org/ontology/dvia + id: lov.dvia + name: The visualization vocabulary for LOD applications + prefix: dvia + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/ontology/dvia#$1 +lov.eac-cpf: + authority: lov + description: Derive from the EAC-CPF original XML schema. Encoded Archival Context for Corporate Bodies, Persons, and Families provides a grammar for encoding names of creators of archival materials and related information. + homepage: http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/ + id: lov.eac-cpf + name: 'EAC-CPF Descriptions Ontology for Linked Archival Data:' + prefix: eac-cpf + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://archivi.ibc.regione.emilia-romagna.it/ontology/eac-cpf/$1 +lov.earl: + authority: lov + description: EARL is a vocabulary, the terms of which are defined across a set of specifications and technical notes, and that is used to describe test results. The primary motivation for developing this vocabulary is to facilitate the exchange of test results between Web accessibility evaluation tools in a vendor-neutral and platform-independent format. It also provides reusable terms for generic quality assurance and validation purposes. + homepage: http://www.w3.org/ns/earl + id: lov.earl + name: Evaluation and Report Language + prefix: earl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/earl#$1 +lov.earth: + authority: lov + description: The Linked Earth Ontology aims to provide a common vocabulary for annotating paleoclimatology data + homepage: http://linked.earth/ontology# + id: lov.earth + name: The Linked Earth Ontology + prefix: earth + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://linked.earth/ontology#$1 +lov.ebg: + authority: lov + description: >- + The euBusinessGraph (`ebg:`) ontology represents companies, + type/status/economic classification, addresses, identifiers, company + officers (e.g., directors and CEOs), and dataset offerings. + + + It uses `schema:domainIncludes/rangeIncludes` (which are polymorphic) to describe which properties are applicable to a class, + + rather than `rdfs:domain/range` (which are monomorphic) to prescribe what classes must be applied to each node using a property. + + We find that this enables more flexible reuse and combination of different ontologies. + + We reuse the following ontologies and nomenclatures, and extend them where appropriate with classes and properties: + + + - W3C Org, W3C RegOrg (basic company data), + + + - W3C Time (officer membership), + + + - W3C Locn (addresses), + + + - schema.org (domain/rangeIncludes and various properties) + + + - DBpedia ontology (jurisdiction) + + + - NGEO and Spatial (NUTS administrative divisions) + + + - ADMS (identifiers), + + + - FOAF, SIOC (blog posts), + + + - RAMON, SKOS (NACE economic classifications and various nomenclatures), + + + - VOID (dataset descriptions). + + + This is only a reference. See more detail in the [EBG Semantic Model](https://docs.google.com/document/d/1dhMOTlIOC6dOK_jksJRX0CB-GIRoiYY6fWtCnZArUhU/edit) google document, which includes an informative description of classes and properties, gives examples and data provider rules, and provides more schema and instance diagrams. + homepage: http://data.businessgraph.io/ontology# + id: lov.ebg + name: euBusinessGraph ontology + prefix: ebg + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.businessgraph.io/ontology#$1 +lov.ebucore: + authority: lov + description: Combined with the EBU Class Conceptual Data Model (CCDM) of simple business objects, EBUCore provides the appropriate framework for descriptive and technical metadata for use in Service Oriented Architectures and also in audiovisual ontologies for semantic web and linked data developments. + homepage: http://www.ebu.ch/metadata/ontologies/ebucore/ebucore + id: lov.ebucore + name: EBU Ontology + prefix: ebucore + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#$1 +lov.eccrev: + authority: lov + description: A vocabulary & data model for describing RDF changes and revisions. It defines the Commit & Revision classes together with their expected properties. + homepage: https://vocab.eccenca.com/revision/ + id: lov.eccrev + name: RDF changes and revisions vocabulary + prefix: eccrev + source: lov.linkeddata.es + subjects: [] + uri_format: https://vocab.eccenca.com/revision/$1 +lov.ecfo: + authority: lov + description: This ontology defines a vocabulary for describing carbon emission conversion factors (CF). These are values typically used to calculate carbon emissions where the CF multiplies a quantified estimate of the energy (e.g., kWh of electricity, litters of fuel, etc.) used by a particular activity. + homepage: https://w3id.org/ecfo + id: lov.ecfo + name: The Emission Conversion Factor Ontology + prefix: ecfo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://w3id.org/ecfo#$1 +lov.eclap: + authority: lov + description: The ECLAP vocabulary provide classes and properties for the description of multimedia content related with performing arts. + homepage: http://www.eclap.eu/schema/eclap/ + id: lov.eclap + name: ECLAP, Performing Arts Vocabulary + prefix: eclap + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.eclap.eu/schema/eclap/$1 +lov.ecpo: + authority: lov + description: Defines the common bibliographic terms for the description of enumeration and chronology of periodicals + homepage: http://purl.org/ontology/ecpo + id: lov.ecpo + name: Enumeration and Chronology of Periodicals Ontology + prefix: ecpo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/ecpo#$1 +lov.ecrm: + authority: lov + description: >- + Erlangen CRM / OWL - An OWL DL 1.0 implementation of the CIDOC Conceptual + Reference Model, based on: Nick Crofts, Martin Doerr, Tony Gill, Stephen + Stead, Matthew Stiff (eds.): Definition of the CIDOC Conceptual Reference + Model (http://cidoc-crm.org/). + + This implementation has been originally created by Bernhard Schiemann, Martin Oischinger and Günther Görz at the Friedrich-Alexander-University of Erlangen-Nuremberg, Department of Computer Science, Chair of Computer Science 8 (Artificial Intelligence) in cooperation with the Department of Museum Informatics of the Germanisches Nationalmuseum Nuremberg and the Department of Biodiversity Informatics of the Zoologisches Forschungsmuseum Alexander Koenig Bonn. + + The Erlangen CRM / OWL implementation of the CIDOC Conceptual Reference Model is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License. + homepage: http://erlangen-crm.org/current/ + id: lov.ecrm + name: Erlangen CRM / OWL + prefix: ecrm + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://erlangen-crm.org/current/$1 +lov.edac: + authority: lov + description: >- + The ELSEWeb EDAC ontology describes datasets published by EDAC. This project + provides foundational support for the ELSEWeb + project(http://elseweb.cybershare.utep.edu/). + + website: http://elseweb.cybershare.utep.edu/ontologies + + email: nvillanuevarosales@utep.edu + homepage: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl + id: lov.edac + name: ELSEWeb EDAC Ontology + prefix: edac + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-edac.owl#$1 +lov.edm: + authority: lov + description: The Europeana Data Model (EDM) is aimed at being an integration medium for collecting, connecting and enriching the descriptions provided by Europeana data providers. + homepage: http://www.europeana.eu/schemas/edm/ + id: lov.edm + name: Europeana Data Model vocabulary + prefix: edm + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.europeana.eu/schemas/edm/$1 +lov.edu: + authority: lov + description: Ontoloogia kirjeldab hariduse valdkonna peamised m?isted ja seosed nende vahel. Praeguses versioonis on r?hk pandud ?ppematerjali, ?piv?ljundite ja ?ppekavaga seotud detailidele. + homepage: https://schema.edu.ee/ + id: lov.edu + name: Education Ontology + prefix: edu + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: https://schema.edu.ee/$1 +lov.edupro: + authority: lov + description: The EduProgression ontology formalizes the educational progressions of the French educational system, making possible to represent the existing progressions in a standard formal model, searchable and understandable by machines (OWL). + homepage: http://ns.inria.fr/semed/eduprogression/ + id: lov.edupro + name: EduProgression Ontology + prefix: edupro + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://ns.inria.fr/semed/eduprogression#$1 +lov.eem: + authority: lov + description: This vocabulary is based on the EPC Information Services Specification http://www.gs1.org/sites/default/files/docs/epc/epcis_1_0_1-standard-20070921.pdf + homepage: http://purl.org/eem + id: lov.eem + name: The EPCIS Event Model + prefix: eem + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/eem#$1 +lov.eeo: + authority: lov + description: An ontology to describe experiments, evaluations and their relation. + homepage: https://w3id.org/eeo + id: lov.eeo + name: Experimental Evaluation Ontology + prefix: eeo + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/eeo#$1 +lov.ei2a: + authority: lov + description: >- + The initiative Aragón Open Data was initiated by agreement of 17 of July of + 2012 of the Government of Aragon. Under the same was ordered the start of + the project to open public data and on February 6, 2013 was implemented + through the Portal opendata.aragon.es + . + + + Throughout this time there have been numerous works to achieve automation in the publication of information to ensure that third parties can reuse it in the best way. Given the volume of data that begins to exist, within the line of work of automation in information management, all those elements that help in the improvement of the structuring of information and the standardization of the data contained in the databases are beginning to have a special relevance. + + + Based on this, within the General Directorate of Electronic Administration and Information Society, the idea arises of generating a set of technical and legal rules that allow to deepen in that standardization and that lead to think in the creation of the Interoperable Information Scheme Of Aragon (E2IA). The E2IA thus emerges as the framework in which the open data and in general the information of the Government of Aragon can begin to be automated in a much more profound way. The E2IA has to have a number of technical, organizational and legal elements that need to be developed. + + + For this reason, the Technological Institute of Aragon (ITAINNOVA) has been entrusted with carrying out actions consisting in identifying, studying and analyzing current research trends and technological development in relation to ontologies and dictionaries of data interoperability, defining the ontological proposal, performing The necessary tests to validate the ontological proposal and generate the text and web versions of the ontology. + homepage: https://opendata.aragon.es/def/ei2a/ei2a.owl + id: lov.ei2a + name: |- + Aragon Interoperable Information Structure Ontology + EI2A + prefix: ei2a + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://opendata.aragon.es/def/ei2a#$1 +lov.elec: + authority: lov + description: El objetivo de este vocabulario es la creación de un esquema que permita definir los contenidos de información relacionada con procesos electorales y sus resultados. Se identifican ciertas variables en el dominio de las elecciones, que se modelan a través de ciertos tipos de datos y de propiedades relacionadas entre los recursos. + homepage: http://purl.org/ctic/sector-publico/elecciones + id: lov.elec + name: Vocabulario de Resultados Electorales + prefix: elec + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://purl.org/ctic/sector-publico/elecciones#$1 +lov.eli: + authority: lov + description: Transposition of the ELI metadata fields into an OWL ontology + homepage: http://data.europa.eu/eli/ontology + id: lov.eli + name: The European Legislation Identifier + prefix: eli + source: lov.linkeddata.es + subjects: + - other humanities + - law + uri_format: http://data.europa.eu/eli/ontology#$1 +lov.emotion: + authority: lov + description: EmOCA is used to contextualize dimensionnal emotion and to categorize it for human readability. + homepage: http://ns.inria.fr/emoca + id: lov.emotion + name: Emotion Ontology for Context Awareness + prefix: emotion + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/emoca#$1 +lov.emp: + authority: lov + description: El objetivo de este vocabulario es la creación de un esquema que permita definir los contenidos de la información relacionada con la oferta de empleo público. Se identifican ciertas variables en el dominio de la oferta de empleo público, que se modelan a través de ciertos tipos de datos y de propiedades relacionadas entre los recursos. + homepage: http://purl.org/ctic/empleo/oferta + id: lov.emp + name: Vocabulario de Ofertas de Empleo + prefix: emp + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ctic/empleo/oferta#$1 +lov.ends: + authority: lov + description: Endpoint Status vocabulary intends to describe endpoint availability + homepage: http://labs.mondeca.com/vocab/endpointStatus + id: lov.ends + name: Vocabulary of endpoint status (availability, responseTime) + prefix: ends + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://labs.mondeca.com/vocab/endpointStatus#$1 +lov.ep: + authority: lov + description: Describes the main classes and properties which EPrints adds to voID, DC, BIBO and SKOS etc + homepage: http://eprints.org/ontology/ + id: lov.ep + name: EPrints Ontology + prefix: ep + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://eprints.org/ontology/$1 +lov.eppl: + authority: lov + description: PROV extension for linking Plans and parts of plans to their respective executions. + homepage: https://w3id.org/ep-plan + id: lov.eppl + name: The EP-Plan ontology + prefix: eppl + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/ep-plan#$1 +lov.eqp: + authority: lov + description: Defines aircraft models, aircraft systems / subsystems, and aircraft characteristics + homepage: https://data.nasa.gov/ontologies/atmonto/equipment# + id: lov.eqp + name: Aircraft Equipment Vocabulary + prefix: eqp + source: lov.linkeddata.es + subjects: [] + uri_format: https://data.nasa.gov/ontologies/atmonto/equipment#$1 +lov.era: + authority: lov + description: >- + This is the human and machine readable Vocabulary/Ontology governed by the + European Union Agency for Railways. It represents the concepts and + relationships linked to the sectorial legal framework and the use cases + under the Agency´s remit. Currently, this vocabulary covers the European + railway infrastructure and the vehicles authorized to operate over it. It is + a semantic/browsable representation of the + [RINF](https://www.era.europa.eu/sites/default/files/registers/docs/rinf_application_guide_for_register_en.pdf) + and + [ERATV](https://www.era.europa.eu/sites/default/files/registers/docs/iu-eratv_application_guide_for_register_2016-797_en.pdf) + application guides that were built by domain experts in the RINF and ERATV + working parties. + + Since version 2.6.0, the ontology includes the routebook concepts described in appendix D2 \"Elements the infrastructure manager has to provide to the railway undertaking for the Route Book\" (https://eur-lex.europa.eu/eli/reg_impl/2019/773/oj) and the appendix D3 \"ERTMS trackside engineering information relevant to operation that the infrastructure manager shall provide to the railway undertaking\". + homepage: http://data.europa.eu/949/ + id: lov.era + name: ERA vocabulary + prefix: era + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.europa.eu/949/$1 +lov.esco: + authority: lov + description: >- + The ontology of the taxonomy "European Skills, Competences, qualifications + and Occupations". + + + The ontology considers three ESCO pillars (or taxonomy) and 2 registers. + + The three pillars are: + + - Occupation + + - Skill (and competences) + + - Qualification + + + For the construction and use of the ESCO pillars, the following modelling artefacts are used: + + - Facetting support to specialize ESCO pillar concepts based on bussiness relevant Concept Groups (e.g. species, languages, ...) + + - Conept Groups, Thesaurus array and Compound terms (as detailed in ISO 25964) to organize faceted concepts + + - SKOS mapping properties to relate ESCO pillar concepts to concepts in other (external) taxonomies (e.g. FoET, ISCO88 and ISCO08. More mappings can be added in the future.) + + - Tagging ESCO pillar concepts by other (external) taxonomies (NUTS, EQF, NACE, ...) + + - Capture gender specifics on the labels of the ESCO pillar concepts + + - Rich ESCO concept relationships holding a description and other specific characteristics of the relation between two ESCO pillar concepts. + + + ESCO maintains two additional registers: + + - Awarding Body + + - Work Context + + Awarding Bodies typically are referenced by ESCO qualifications. + + Occupations can have one or more work context. + homepage: http://data.europa.eu/esco/model + id: lov.esco + name: The ESCO ontology + prefix: esco + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.europa.eu/esco/model#$1 +lov.essglobal: + authority: lov + description: 'Un vocabulario para la Economia Social y Solidária (ESS). Este vocabulario es concebido para ser conjugado con los esquemas de metadados/vocabularios/ontologias: dcterms, good relations, foaf, vcard, organization e schema.org - esto esta definido em el Perfil de Aplicación Dublin Core de la ESS. Vocabulario desarollado por el grupo ESSGlobal de la Red Intercontinental para la promoción de Economia Social y Solidaria (RIPESS).' + homepage: http://purl.org/essglobal/vocab/ + id: lov.essglobal + name: ESSGlobal Vocabulary + prefix: essglobal + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/essglobal/vocab/$1 +lov.eupont: + authority: lov + description: EUPont is an ontology to model high level rules for Internet of Things End User Programming (IoT-EUP). + homepage: http://elite.polito.it/ontologies/eupont.owl + id: lov.eupont + name: 'EUPont: an ontology for End User Programming of the IoT' + prefix: eupont + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://elite.polito.it/ontologies/eupont.owl#$1 +lov.event: + authority: lov + description: This ontology deals with the notion of reified events - events seen as first-class objects. + homepage: http://purl.org/NET/c4dm/event.owl + id: lov.event + name: The Event Ontology + prefix: event + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/NET/c4dm/event.owl#$1 +lov.ex: + authority: lov + description: スキーマにサンプルコードを埋め込むための語彙。XSLTを使って、XHTMLの中で例を表示させることができる。 + homepage: http://purl.org/net/ns/ex + id: lov.ex + name: Example vocabulary + prefix: ex + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/ns/ex#$1 +lov.exif: + authority: lov + description: Vocabulary to describe an Exif format picture data. All Exif 2.2 tags are defined as RDF properties, as well as several terms to help this schema. + homepage: http://www.w3.org/2003/12/exif/ns + id: lov.exif + name: Exif data description vocabulary + prefix: exif + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2003/12/exif/ns#$1 +lov.ext: + authority: lov + description: An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - EX Package + homepage: http://def.seegrid.csiro.au/isotc211/iso19115/2003/extent + id: lov.ext + name: OWL representation of ISO 19115 (Geographic Information - Metadata - Extent package) + prefix: ext + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://def.seegrid.csiro.au/isotc211/iso19115/2003/extent#$1 +lov.fabio: + authority: lov + description: FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web bibliographic records of scholarly endeavours. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies. + homepage: http://purl.org/spar/fabio + id: lov.fabio + name: FRBR-aligned Bibliographic Ontology + prefix: fabio + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/fabio/$1 +lov.faldo: + authority: lov + description: Used to describe a location that consists of a number of Regions but where the order is not known. e.g. the oddly named order() keyword in a INSDC file. + homepage: http://biohackathon.org/resource/faldo + id: lov.faldo + name: Feature Annotation Location Description Ontology + prefix: faldo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://biohackathon.org/resource/faldo#$1 +lov.fea: + authority: lov + description: To facilitate efforts to transform the Federal Government to one that is citizen-centered, results-oriented, and market-based, the Office of Management and Budget (OMB) is developing the Federal Enterprise Architecture (FEA), a business-based framework for Governmentwide improvement. + homepage: http://vocab.data.gov/def/fea + id: lov.fea + name: Federal Enterprise Architecture Vocabulary + prefix: fea + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://vocab.data.gov/def/fea#$1 +lov.fel: + authority: lov + description: This RDF vocabulary can be use to describe and categorize annotations involving entity mentions (sub-strings of text) that link to knowledgebase identifiers + homepage: http://w3id.org/vcb/fel# + id: lov.fel + name: A Fine-grained Entity Linking vocabulary + prefix: fel + source: lov.linkeddata.es + subjects: [] + uri_format: http://w3id.org/vcb/fel#$1 +lov.fiesta-iot: + authority: lov + description: The FIESTA-IoT ontology takes inspiration from the well-known Noy et al. methodology for reusing and interconnecting existing ontologies. To build the ontology, we leverage a number of core concepts from various mainstream ontologies and taxonomies, such as Semantic Sensor Network (SSN), M3-lite (a lite version of M3 ontology), WGS84, IoT-lite, Time, and DUL ontology. + homepage: http://purl.org/iot/ontology/fiesta-iot + id: lov.fiesta-iot + name: FIESTA-IoT Ontology + prefix: fiesta-iot + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/iot/ontology/fiesta-iot#$1 +lov.fiesta-priv: + authority: lov + description: FIESTA-Priv Ontology + homepage: http://purl.org/iot/ontology/fiesta-priv# + id: lov.fiesta-priv + name: FIESTA-Priv Ontology + prefix: fiesta-priv + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/iot/ontology/fiesta-iot#$1 +lov.foaf: + authority: lov + description: FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. + homepage: http://xmlns.com/foaf/0.1/ + id: lov.foaf + name: Friend of a Friend vocabulary + prefix: foaf + source: lov.linkeddata.es + subjects: [] + uri_format: http://xmlns.com/foaf/0.1/$1 +lov.fog: + authority: lov + description: >- + The File Ontology for Geometry formats (FOG) describes meaningful relations + towards geometry snippets in RDF literals, geometry files on relative or + absolute URLs and ontology-based geometry descriptions. The defined + properties in this ontology are related towards each other and additional + metadata is provided, such as file extension and related + specifications/sources (incl. entries in dbpedia and Wikidata). + + + The initial version of the ontology (v0.0.1) was documented in: + + + Bonduel, Mathias, Wagner, Anna, Pauwels, Pieter, Vergauwen, Maarten, & Klein, Ralf (2019). Including Widespread Geometry Formats in Semantic Graphs Using RDF Literals. In Proceedings of the European Conference on Computing in Construction (EC3 2019). Chania, Greece. + homepage: https://w3id.org/fog + id: lov.fog + name: 'FOG: File Ontology for Geometry formats' + prefix: fog + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: https://w3id.org/fog#$1 +lov.foio: + authority: lov + description: >- + This ontology defines feature of interest and their properties, as an + extension of the core classes of the SSN ontology + (https://www.w3.org/ns/ssn/). + + + A feature of interest is an abstraction of a real world phenomena (thing, person, event, etc). A feature of interest is then defined in terms of its properties, which are qualifiable, quantifiable, observable or operable qualities of the feature of interest. + + + Alignments to other ontologies are proposed in external documents: + + + - [SSNAlignment](https://w3id.org/seas/SSNAlignment) proposes an alignment to the [SSN ontology](http://www.w3.org/ns/ssn/). + + - [QUDTAlignment](https://w3id.org/seas/QUDTAlignment) proposes an alignment to the [QUDT ontology](http://qudt.org/). + homepage: https://w3id.org/seas/FeatureOfInterestOntology + id: lov.foio + name: The SEAS Feature of Interest ontology. + prefix: foio + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/seas/FeatureOfInterestOntology/$1 +lov.food: + authority: lov + description: This ontology models the Food domain. It allows to describe ingredients and food products. Ontology used by the Open Food Facts dataset + homepage: http://data.lirmm.fr/ontologies/food + id: lov.food + name: Food Ontology + prefix: food + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://data.lirmm.fr/ontologies/food#$1 +lov.fowl: + authority: lov + description: Along with Wine Ontology, was used as example in the first OWL Recommendation (February 2004) + homepage: http://www.w3.org/TR/2003/PR-owl-guide-20031215/food + id: lov.fowl + name: Food Ontology in OWL + prefix: fowl + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://www.w3.org/TR/2003/PR-owl-guide-20031209/food#$1 +lov.frad: + authority: lov + description: This is the element set of native RDF classes and properties described in the Functional Requirements for Authority Data model. The model also uses elements previously described in the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. + homepage: http://iflastandards.info/ns/fr/frad/ + id: lov.frad + name: FRAD model + prefix: frad + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://iflastandards.info/ns/fr/frad/$1 +lov.frapo: + authority: lov + description: FRAPO, the Funding, Research Administration and Projects Ontology, is a CERIF-compliant ontology written in OWL 2 DL for describing research project administrative information. + homepage: http://purl.org/cerif/frapo/ + id: lov.frapo + name: Funding, Research Administration and Projects Ontology + prefix: frapo + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://purl.org/cerif/frapo/$1 +lov.frappe: + authority: lov + description: FraPPE is a vocabulary to enable Visual Analytics operations on geo-spatial time varying data. By enabling Visual Analytics instruments FraPPE ease the capture, correlation and comparison operations on geo-spatial data from different sources evolving over time + homepage: http://streamreasoning.org/ontologies/frappe# + id: lov.frappe + name: 'FraPPE: Frame, Pixel, Place, Event vocabulary' + prefix: frappe + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://streamreasoning.org/ontologies/frappe#$1 +lov.frbr: + authority: lov + description: An expression in RDF of the concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR) + homepage: http://purl.org/vocab/frbr/core + id: lov.frbr + name: Expression of Core FRBR Concepts in RDF + prefix: frbr + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/vocab/frbr/core#$1 +lov.frbre: + authority: lov + description: Expression of Extended FRBR Concepts in RDF + homepage: http://purl.org/vocab/frbr/extended + id: lov.frbre + name: Extended FRBR + prefix: frbre + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/vocab/frbr/extended#$1 +lov.frbrer: + authority: lov + description: This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. + homepage: http://iflastandards.info/ns/fr/frbr/frbrer/ + id: lov.frbrer + name: FRBRer model + prefix: frbrer + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://iflastandards.info/ns/fr/frbr/frbrer/$1 +lov.fresnel: + authority: lov + description: OWL Full vocabulary for defining lenses and formats on RDF models. + homepage: http://www.w3.org/2004/09/fresnel + id: lov.fresnel + name: Fresnel Lens and Format Core Vocabulary + prefix: fresnel + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2004/09/fresnel#$1 +lov.g50k: + authority: lov + description: A vocabulary developed to describe the Ordance Survey 50k Gazetteer linked data + homepage: http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/ + id: lov.g50k + name: 50K Gazetteer Vocabulary + prefix: g50k + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://data.ordnancesurvey.co.uk/ontology/50kGazetteer/$1 +lov.game: + authority: lov + description: This schema describes games with a known state, and few or no random elements. + homepage: http://data.totl.net/game/ + id: lov.game + name: TotL Game Ontology + prefix: game + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.totl.net/game/$1 +lov.gc: + authority: lov + description: The Government Core Ontology establishes a foundation for all oegov ontologies. + homepage: http://www.oegov.org/core/owl/gc + id: lov.gc + name: oeGOV Government Core Ontology + prefix: gc + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://www.oegov.org/core/owl/gc#$1 +lov.gci: + authority: lov + description: >- + Global City Indicator Foundation Ontology developed by the Information + Engineering Group, Mechanical & Industrial Engineering, University of + Toronto. Contains the foundation ontologies required to represent ISO 37120 + city indicators, including Placenames, Time, Measurement, Provenance, + Statistics, Validity and Trust. See: Fox, M.S., (2013), "A Foundation + Ontology for Global City Indicators", Global City Institute Working Paper, + Vol. 1, No.4, pp. 1-45. Global Cities Institute, University of Toronto. + Updated 24 June 2014: http://www.eil. Based on the Global City Indicators + Facility, University of Toronto: + http://www.cityindicators.org/Deliverables/Core%20and%20Supporting%20Indicators%20Table%20SEPTEMBER%202011.pdf. + + + Contact: Mark S. Fox, msf@eil.utoronto.ca + homepage: http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl + id: lov.gci + name: Global City Indicator Foundation Ontology + prefix: gci + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl#$1 +lov.gcon: + authority: lov + description: GConsent provides concepts and relationships for defining consent and its associated information or metadata with a view towards GDPR compliance. It is the outcome of an analysis of consent and requirements associated with obtaining, using, and changes in consent as per the GDPR. The ontology also provides an approach to using its terms in various scenarios and use-cases (see more information in the documentation) which is intended to assist in its adoption. + homepage: https://w3id.org/GConsent + id: lov.gcon + name: GConsent - a consent ontology based on the GDPR + prefix: gcon + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/GConsent#$1 +lov.gd: + authority: lov + description: A RDF Schema that defines concepts and relationships common to all Open Government Data + homepage: http://vocab.data.gov/gd + id: lov.gd + name: Government Data Vocabulary + prefix: gd + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://reference.data.gov/def/govdata/$1 +lov.gdprov: + authority: lov + description: GDPRov is an OWL2 ontology to express provenance metadata of consent and data lifecycles towards documenting compliance for GDPR. + homepage: https://w3id.org/GDPRov + id: lov.gdprov + name: The GDPR Provenance ontology + prefix: gdprov + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/GDPRov#$1 +lov.gdprt: + authority: lov + description: The General Data Protection Regulation (GDPR) is comprised of several articles, each with points that refer to specific concepts. The general convention of referring to these points and concepts is to quote the specific article or point using a human-readable reference. This ontology provides a way to refer to the points within the GDPR using the EurLex ontology published by the European Publication Office. It also defines the concepts defined, mentioned, and requried by the GDPR using the Simple Knowledge Organization System (SKOS) ontology. + homepage: https://w3id.org/GDPRtEXT + id: lov.gdprt + name: GDPR text EXTensions + prefix: gdprt + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/GDPRtEXT#$1 +lov.gen: + authority: lov + description: A simple RDF vocabulary containing terms to facilitate the linking of genealogical data. + homepage: http://purl.org/gen/0.1# + id: lov.gen + name: Vocabulary for Linked Genealogical Data + prefix: gen + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/gen/0.1#$1 +lov.geo: + authority: lov + description: A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum. + homepage: http://www.w3.org/2003/01/geo/wgs84_pos + id: lov.geo + name: WGS84 Geo Positioning + prefix: geo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://www.w3.org/2003/01/geo/wgs84_pos#$1 +lov.geod: + authority: lov + description: Vocabulary describing the administrative subdivision of Norway + homepage: http://vocab.lenka.no/geo-deling + id: lov.geod + name: Landinndelingen i Norge + prefix: geod + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://vocab.lenka.no/geo-deling#$1 +lov.geof: + authority: lov + description: This ontology contains geographic feature classes and associated properties including classes and properties for describing the spatial location of the geographic feature. The classes and properties have been defined based on an ESRI dataset. + homepage: http://www.mindswap.org/2003/owl/geo/geoFeatures20040307.owl + id: lov.geof + name: Geo Features + prefix: geof + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://www.mindswap.org/2003/owl/geo/geoFeatures20040307.owl#$1 +lov.geofla: + authority: lov + description: Ontologie décrivant le découpage administratif de la France métropolitaine, des départements d'outre mer, ou de la collectivité départementale de Mayotte, représentée comme une hiérarchie de classes OWL + homepage: http://data.ign.fr/def/geofla + id: lov.geofla + name: Ontologie des unités administratives de l'IGN + prefix: geofla + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://data.ign.fr/def/geofla#$1 +lov.geom: + authority: lov + description: Ontologie des primitives géométriques représentant la forme et la localisation d'entités topographiques. + homepage: http://data.ign.fr/def/geometrie + id: lov.geom + name: Ontologie des primitives géométriques + prefix: geom + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://data.ign.fr/def/geometrie#$1 +lov.geop: + authority: lov + description: FAO's geopolitical ontology version 1.1 was populated with FAO, UN and internationally recognized data sources. + homepage: http://aims.fao.org/aos/geopolitical.owl + id: lov.geop + name: FAO Geopolitical Ontology + prefix: geop + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://aims.fao.org/aos/geopolitical.owl#$1 +lov.geosp: + authority: lov + description: The GeoSpecies Ontology is used to describe geographical distribution of living species. + homepage: http://rdf.geospecies.org/ont/geospecies + id: lov.geosp + name: GeoSpecies Ontology + prefix: geosp + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://rdf.geospecies.org/ont/geospecies#$1 +lov.gf: + authority: lov + description: An OWL representation of part of the General Feature Model described in ISO 19109 and the General Feature Instance model described in Annex C of ISO 19156:2011. + homepage: http://def.seegrid.csiro.au/isotc211/iso19109/2005/feature + id: lov.gf + name: OWL representation of ISO 19109 (General Feature Model) + prefix: gf + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://def.seegrid.csiro.au/isotc211/iso19109/2005/feature#$1 +lov.gleif-base: + authority: lov + description: Ontology defining generic concepts for reuse by other Global Legal Entity Identifier Foundation (GLEIF) ontologies. It defines generic classes for (legal) Entities and their relationships and statuses; and generic properties for different types of name and address. It makes use of the OMG Languages Countries and Codes (LCC) ontology (based on the ISO 3166 standard) for country and region information. + homepage: https://www.gleif.org/ontology/Base/ + id: lov.gleif-base + name: Global Legal Entity Identifier Foundation Base Ontology + prefix: gleif-base + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://www.gleif.org/ontology/Base/$1 +lov.gleif-elf: + authority: lov + description: Ontology defining concepts for Entity Legal Forms and their abbreviations by jurisdiction, based on ISO 20275. Though used by Global Legal Entity Identifier Foundation (GLEIF) for Legal Entity Identifier registration, it is more broadly applicable. + homepage: https://www.gleif.org/ontology/EntityLegalForm/ + id: lov.gleif-elf + name: Entity Legal Form Ontology + prefix: gleif-elf + source: lov.linkeddata.es + subjects: + - law + uri_format: https://www.gleif.org/ontology/EntityLegalForm/$1 +lov.gleif-geo: + authority: lov + description: Ontology defining concepts for Geocoding of addresses. It is based on the geocoding used in the Global Legal Entity Identifier Foundation (GLEIF) Golden Copy Data, but is more broadly applicable. + homepage: https://www.gleif.org/ontology/Geocoding/ + id: lov.gleif-geo + name: Global Legal Entity Identifier Foundation Geocoding Ontology + prefix: gleif-geo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://www.gleif.org/ontology/Geocoding/$1 +lov.gleif-l1: + authority: lov + description: 'Ontology for legal entity identifier registration. It was designed for Global Legal Entity Identifier Foundation (GLEIF) Level 1 data corresponding to the Common Data Format version 2.1. It covers key reference data for a legal entity identifiable with an LEI. The ISO 17442 standard developed by the International Organization for Standardization defines a set of attributes or LEI reference data that comprises the most essential elements of identification. It specifies the minimum reference data, which must be supplied for each LEI: The official name of the legal entity as recorded in the official registers. The registered address of that legal entity. The country of formation. The codes for the representation of names of countries and their subdivisions. The date of the first LEI assignment; the date of last update of the LEI information; and the date of expiry, if applicable.' + homepage: https://www.gleif.org/ontology/L1/ + id: lov.gleif-l1 + name: Global Legal Entity Identifier Foundation Level 1 Ontology - Who Is Who + prefix: gleif-L1 + source: lov.linkeddata.es + subjects: [] + uri_format: https://www.gleif.org/ontology/L1/$1 +lov.gleif-l2: + authority: lov + description: Ontology for legal entity parent relationships. It was designed for Global Legal Entity Identifier Foundation (GLEIF) Level 2 data corresponding to the Relationship Record format, version 1.1. Legal entities that have or acquire an LEI report their ‘direct accounting consolidating parent’ as well as their ‘ultimate accounting consolidating parent’, or for International Branches ‘is an International Branch of'. Otherwise they must provide a Reporting Exception. + homepage: https://www.gleif.org/ontology/L2/ + id: lov.gleif-l2 + name: Global Legal Entity Identifier Foundation Level 2 Ontology - Who Owns Whom + prefix: gleif-L2 + source: lov.linkeddata.es + subjects: [] + uri_format: https://www.gleif.org/ontology/L2/$1 +lov.gleif-ra: + authority: lov + description: Ontology defining concepts for Business Registries, including the jurisdictions served. This is based on the Registration Authority Code List (RAL) used for Global Legal Entity Identifier Foundation (GLEIF) registration, but is more broadly applicable. + homepage: https://www.gleif.org/ontology/RegistrationAuthority/ + id: lov.gleif-ra + name: Global Legal Entity Identifier Foundation Registration Authority Ontology + prefix: gleif-ra + source: lov.linkeddata.es + subjects: + - law + uri_format: https://www.gleif.org/ontology/RegistrationAuthority/$1 +lov.gleif-repex: + authority: lov + description: Ontology for representing exceptions to reporting of parents, for entities registered with a Legal Entity Identifier. The Global Legal Identifier System (GLEIS) requires that legal entities with an LEI provide information on their ultimate and direct accounting consolidating parents. Relationship reporting is mandatory with exceptions allowed for certain well-defined reasons. This ontology provides a simple structure for recording reasons for each exception by LEI. + homepage: https://www.gleif.org/ontology/ReportingException/ + id: lov.gleif-repex + name: Global Legal Entity Identifier Foundation Reporting Exception Ontology + prefix: gleif-repex + source: lov.linkeddata.es + subjects: [] + uri_format: https://www.gleif.org/ontology/ReportingException/$1 +lov.gm: + authority: lov + description: An OWL representation of part of the model for geometry and space from ISO 19107:2003 Geographic Information - Spatial Schema + homepage: http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry + id: lov.gm + name: OWL representation of ISO 19107 (Geographic Information) + prefix: gm + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://def.seegrid.csiro.au/isotc211/iso19107/2003/geometry#$1 +lov.gml: + authority: lov + description: A specialization of GeoSPARQL defining specific subtypes of Geometry + homepage: http://www.opengis.net/ont/gml + id: lov.gml + name: OGC Geometry + prefix: gml + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://www.opengis.net/ont/gml#$1 +lov.gn: + authority: lov + description: The Geonames ontology provides elements of description for geographical features defined in the geonames.org data base + homepage: http://www.geonames.org/ontology + id: lov.gn + name: The Geonames ontology + prefix: gn + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://www.geonames.org/ontology#$1 +lov.gndo: + authority: lov + description: GND stands for "Gemeinsame Normdatei" (Integrated Authority File) and offers a broad range of elements to describe authorities. The GND originates from the German library community and aims to solve the name ambiguity problem in the library world. + homepage: http://d-nb.info/standards/elementset/gnd# + id: lov.gndo + name: GND Ontology + prefix: gndo + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://d-nb.info/standards/elementset/gnd#$1 +lov.gold: + authority: lov + description: The General Ontology for Linguistic Description (GOLD) was created primarily for applications involving descriptive linguistics. + homepage: http://purl.org/linguistics/gold + id: lov.gold + name: General Ontology for Linguistic Description + prefix: gold + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/linguistics/gold/$1 +lov.gom: + authority: lov + description: '- Version 0.0.1: initial version' + homepage: https://w3id.org/gom + id: lov.gom + name: 'GOM: Geometry Metadata Ontology' + prefix: gom + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: https://w3id.org/gom#$1 +lov.gov: + authority: lov + description: The Genealogisches Orts-Verzeichnis (GOV) contains information about current and historical political, ecclesiastical and legal administrative affiliations of settlements and administrative units. In addition several time-dependent values (such as names, population numbers, postal codes etc.) are given. + homepage: http://gov.genealogy.net/ontology.owl + id: lov.gov + name: Ontology for modelling historic administrative information. + prefix: gov + source: lov.linkeddata.es + subjects: [] + uri_format: http://gov.genealogy.net/ontology.owl#$1 +lov.gr: + authority: lov + description: The GoodRelations ontology provides the vocabulary for annotating e-commerce offerings (1) to sell, lease, repair, dispose, or maintain commodity products and (2) to provide commodity services. + homepage: http://purl.org/goodrelations/v1 + id: lov.gr + name: The GoodRelations Ontology for Semantic Web-based E-Commerce + prefix: gr + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/goodrelations/v1#$1 +lov.grddl: + authority: lov + description: Gleaning Resource Descriptions from Dialects of Languages Vocabulary + homepage: http://www.w3.org/2003/g/data-view + id: lov.grddl + name: Gleaning Resource Descriptions from Dialects of Languages Vocabulary + prefix: grddl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2003/g/data-view#$1 +lov.gso: + authority: lov + description: Ontology for Relating Generic and Specific Information Resources + homepage: http://www.w3.org/2006/gen/ont + id: lov.gso + name: Generic Specific Ontology + prefix: gso + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2006/gen/ont#$1 +lov.gsp: + authority: lov + description: A Geographic Query Language for RDF Data OGC 11-052r5 + homepage: http://www.opengis.net/ont/geosparql + id: lov.gsp + name: OGC GeoSPARQL + prefix: gsp + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://www.opengis.net/ont/geosparql#$1 +lov.gtfs: + authority: lov + description: This ontology is a translation of the General Transit Feed Specification towards URIs. Its intended use is creating an exchange platform where the Linked GTFS model can be used as a start to get the right data into the right format. + homepage: http://vocab.gtfs.org/terms# + id: lov.gtfs + name: General Transit Feed Specification + prefix: gtfs + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.gtfs.org/terms#$1 +lov.gts: + authority: lov + description: This is an RDF/OWL representation of the GeoSciML Geologic Timescale model, which has been adapted from the model described in Cox, S.J.D, & Richard, S.M. (2005) A formal model for the geologic timescale and GSSP, compatible with geospatial information transfer standards, Geosphere, Geological Society of America 1/3, 119–137. + homepage: http://resource.geosciml.org/ontology/timescale/gts + id: lov.gts + name: Geologic Timescale model + prefix: gts + source: lov.linkeddata.es + subjects: [] + uri_format: http://resource.geosciml.org/ontology/timescale/gts#$1 +lov.gufo: + authority: lov + description: >- + The objective of gUFO is to provide a lightweight implementation of the + Unified Foundational Ontology (UFO) [1-5] suitable for Semantic Web OWL 2 DL + applications. + + + Intended users are those implementing UFO-based lightweight ontologies that reuse gUFO by specializing and instantiating its elements. + + + There are three implications of the use of the term lightweight. First of all, we have employed little expressive means in an effort to retain computational properties for the resulting OWL ontology. Second, we have selected a subset of UFO-A [1, 2] and UFO-B [3] to include here. In particular, there is minimalistic support for UFO-B (only that which is necessary to establish the participation of objects in events and to capture historical dependence between events). Third, a lightweight ontology, differently from a reference ontology, is designed with the purpose of providing an implementation artifact to structure a knowledge base (or knowledge graph). This has driven a number of pragmatic implementation choices which are discussed in comments annotated to the various elements of this implementation. + + + The 'g' in gUFO stands for gentle. At the same time, "gufo" is the Italian word for "owl". + + + + For the source repository, see: + homepage: http://purl.org/nemo/gufo# + id: lov.gufo + name: 'gUFO: A Lightweight Implementation of the Unified Foundational Ontology (UFO)' + prefix: gufo + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://purl.org/nemo/gufo#$1 +lov.gvp: + authority: lov + description: The GVP Ontology defines classes, properties and values (skos:Concepts) used in GVP LOD. It is complete regarding AAT and TGN (as of version 2.0), and will be extended in time with more elements needed for the other GVP vocabularies (ULAN, CONA). + homepage: http://vocab.getty.edu/ontology + id: lov.gvp + name: Getty Vocabulary Program ontology + prefix: gvp + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.getty.edu/ontology#$1 +lov.h2o: + authority: lov + description: This ontology establishes classes corresponding to stereotypes used in ISO-conformant models, as used in the rules for conversion of the ISO TC 211 Harmonized Model from the UML to OWL representations + homepage: http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic + id: lov.h2o + name: Ontology for conversion of ISO/TC 211 + prefix: h2o + source: lov.linkeddata.es + subjects: [] + uri_format: http://def.seegrid.csiro.au/isotc211/iso19150/-2/2012/basic#$1 +lov.ha: + authority: lov + description: An ontology to detect activity in a smart home + homepage: http://sensormeasurement.appspot.com/ont/home/homeActivity# + id: lov.ha + name: Home Activity + prefix: ha + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://sensormeasurement.appspot.com/ont/home/homeActivity#$1 +lov.hctl: + authority: lov + description: Ontology designed to provide an RDF representation of Hypermedia Controls, in particular links and forms. + homepage: https://www.w3.org/2019/wot/hypermedia# + id: lov.hctl + name: Hypermedia Controls Ontology + prefix: hctl + source: lov.linkeddata.es + subjects: [] + uri_format: https://www.w3.org/2019/wot/hypermedia#$1 +lov.hdo: + authority: lov + description: Simple ontology developed for integration purposes. Describe helpdesk entities used to record support tickets for diagnosis and resolve purpuses. The ontology re-uses a) W3C ORG and REGORG ontologies, b) DUL upper ontology, and c) GoodRelations ontology. + homepage: http://www.samos.gr/ontologies/helpdeskOnto.owl + id: lov.hdo + name: HelpDesk support Ontology + prefix: hdo + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.samos.gr/ontologies/helpdeskOnto.owl#$1 +lov.hifm: + authority: lov + description: An ontology for describing brand-name drugs. + homepage: http://purl.org/net/hifm/ontology# + id: lov.hifm + name: HIFM Ontology + prefix: hifm + source: lov.linkeddata.es + subjects: + - biological sciences + - health sciences + uri_format: http://purl.org/net/hifm/ontology#$1 +lov.holding: + authority: lov + description: A vocabulary to express (library) holdings in RDF + homepage: http://purl.org/ontology/holding + id: lov.holding + name: Holding Ontology + prefix: holding + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/ontology/holding#$1 +lov.holy: + authority: lov + description: This is the Hydrogen Ontology (HOLY). HOLY is a domain ontology for describing the complex structure of hydrogen-based markets. HOLY contributes to the systemic modeling of the hydrogen domain with a focus on its value chain. Hence, it provides a foundation for retrieval, storage, and delivery of market insights. + homepage: http://purl.org/holy/ns# + id: lov.holy + name: Hydrogen Ontology + prefix: holy + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://purl.org/holy/ns#$1 +lov.hosp: + authority: lov + description: A RDF Schema that defines concepts and relationships used for Hospital data. + homepage: http://vocab.data.gov/hosp + id: lov.hosp + name: Hospital Vocabulary + prefix: hosp + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://health.data.gov/def/hospital/$1 +lov.hpont: + authority: lov + description: >- + The Heat Pump Ontology (HPOnt) aims to formalize and represent all the + relevant information of Heat Pumps. + + + The HPOnt has been developed as part of the REACT project which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 824395. + homepage: https://w3id.org/hpont + id: lov.hpont + name: The Heat Pump Ontology (HPOnt). + prefix: hpont + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/hpont#$1 +lov.hr: + authority: lov + description: hRESTS is a vocabulary for describing RESTful Web services + homepage: http://iserve.kmi.open.ac.uk/ns/hrests + id: lov.hr + name: hRESTS Ontology + prefix: hr + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://iserve.kmi.open.ac.uk/ns/hrests#$1 +lov.hto: + authority: lov + description: The Haystack Tagging Ontology is an OWL ontology for Project Haystack, a domain vocabulary for Building Automation Systems. + homepage: http://vcharpenay.github.io/hto/hto.xml + id: lov.hto + name: Haystack Tagging Ontology + prefix: hto + source: lov.linkeddata.es + subjects: [] + uri_format: http://vcharpenay.github.io/hto/hto.xml#$1 +lov.http: + authority: lov + description: A namespace for describing HTTP messages (http://www.w3.org/Protocols/rfc2616/rfc2616.html) + homepage: http://www.w3.org/2011/http + id: lov.http + name: HTTP in RDF + prefix: http + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3.org/2011/http#$1 +lov.hw: + authority: lov + description: Smart home ontology for weather phenomena and exterior conditions + homepage: https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl + id: lov.hw + name: Home Weather + prefix: hw + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://www.auto.tuwien.ac.at/downloads/thinkhome/ontology/WeatherOntology.owl$1 +lov.hydra: + authority: lov + description: A lightweight vocabulary for hypermedia-driven Web APIs + homepage: http://www.w3.org/ns/hydra/core + id: lov.hydra + name: The Hydra Core Vocabulary + prefix: hydra + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/hydra/core#$1 +lov.iadopt: + authority: lov + description: The I-ADOPT Framework ontology + homepage: https://w3id.org/iadopt/ont + id: lov.iadopt + name: I-ADOPT Framework ontology + prefix: iadopt + source: lov.linkeddata.es + subjects: + - biological sciences + - earth and related environmental sciences + uri_format: https://w3id.org/iadopt/ont/$1 +lov.ibis: + authority: lov + description: This document specifies a vocabulary for describing an IBIS (issue-based information system). + homepage: https://privatealpha.com/ontology/ibis/1# + id: lov.ibis + name: IBIS Vocabulary + prefix: ibis + source: lov.linkeddata.es + subjects: [] + uri_format: https://privatealpha.com/ontology/ibis/1#$1 +lov.ic: + authority: lov + description: This ontology provides basic classes and more detailed properties for representating international street addresses, phone numbers and emails. Rather than using existing ontologies, such as vcard, it was decided to create a new one as the vcard and foaf ignore the details of international addresses, phone numbers, etc. + homepage: http://ontology.eil.utoronto.ca/icontact.owl + id: lov.ic + name: 'International Contact Ontology: Addresses, phone numbers and emails.' + prefix: ic + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.eil.utoronto.ca/icontact.owl#$1 +lov.iddo: + authority: lov + description: The interconnected data dictionary ontology maps the data model of the ISO 23386 for the describing, creating, and maintenance of properties in interconnected data dictionaries. + homepage: https://w3id.org/iddo + id: lov.iddo + name: The Interconnected Data Dictionary Ontology (IDDO) + prefix: iddo + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: https://w3id.org/iddo#$1 +lov.idemo: + authority: lov + description: Ontologie des classes et propriétés utilisées pour la démographie, notamment le recensement de la population + homepage: http://rdf.insee.fr/def/demo + id: lov.idemo + name: Ontologie démographique de l'INSEE + prefix: idemo + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdf.insee.fr/def/demo#$1 +lov.identity: + authority: lov + description: v.2.0 based on P3P1.0 Specification http://www.w3.org/TR/P3P/ + homepage: http://www.identity.org/ontologies/identity.owl + id: lov.identity + name: Ontology of digital identity. + prefix: identity + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.identity.org/ontologies/identity.owl#$1 +lov.ids: + authority: lov + description: This ontology defines classes and properties for describing participants, infrastructure, data and services of the International Data Spaces (formerly known as Industrial Data Space). + homepage: https://w3id.org/idsa/core + id: lov.ids + name: IDS Information Model + prefix: ids + source: lov.linkeddata.es + subjects: + - other humanities + - law + - computer and information sciences + uri_format: https://w3id.org/idsa/core/$1 +lov.ifc: + authority: lov + description: OWL ontology for the IFC conceptual data schema and exchange file format for Building Information Model (BIM) data + homepage: https://w3id.org/ifc/IFC4_ADD1 + id: lov.ifc + name: IFC4_ADD1 + prefix: ifc + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://w3id.org/ifc/IFC4_ADD1#$1 +lov.igeo: + authority: lov + description: Ontologie des objets géographiques de l'INSEE, en particulier des territoires administratifs de la France + homepage: http://rdf.insee.fr/def/geo + id: lov.igeo + name: Ontologie géographique de l'INSEE + prefix: igeo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://rdf.insee.fr/def/geo#$1 +lov.ignf: + authority: lov + description: 'Codes for describing coordinates reference systems consistently with ISO TC/211. French translations of terms and definitions are mainly taken from the multilingual glossary of ISO/TC 211 available online: http://www.isotc211.org/Terminology.htm' + homepage: http://data.ign.fr/def/ignf + id: lov.ignf + name: Ontologie des systèmes de coordonnées de référence + prefix: ignf + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://data.ign.fr/def/ignf#$1 +lov.imo: + authority: lov + description: La Ontologia de IMGpedia provee terminos para referirse a descriptores visuales y relaciones de similitud entre imagenes + homepage: http://imgpedia.dcc.uchile.cl/ontology + id: lov.imo + name: The IMGpedia Ontology + prefix: imo + source: lov.linkeddata.es + subjects: [] + uri_format: http://imgpedia.dcc.uchile.cl/ontology#$1 +lov.incident: + authority: lov + description: >- + Vocabulary to describe the response to a incident by emergency services. + + This is NOT intended to describe the incident itself, it describes the response + homepage: http://vocab.resc.info/incident + id: lov.incident + name: Vocabulary to describe incident response by emergency services + prefix: incident + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.resc.info/incident#$1 +lov.infor: + authority: lov + description: Allows designers to model information objects and their realizations. This allows to reason about physical objects and the information they realize, by keeping them distinguished. + homepage: http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl + id: lov.infor + name: Information Realization + prefix: infor + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl#$1 +lov.inno: + authority: lov + description: One key use case for this ontology is to facilitate the matching of needs and innovations. + homepage: http://purl.org/innovation/ns + id: lov.inno + name: Ontology for Innovation + prefix: inno + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/innovation/ns#$1 +lov.interval: + authority: lov + description: An ontology for time intervals + homepage: http://reference.data.gov.uk/def/intervals + id: lov.interval + name: Intervals Ontology + prefix: interval + source: lov.linkeddata.es + subjects: [] + uri_format: http://reference.data.gov.uk/def/intervals/$1 +lov.iol: + authority: lov + description: An ontology of information objects, encodings and realizations, as a plugin to DOLCE-Ultralite + homepage: http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl + id: lov.iol + name: Information Objects ontology + prefix: iol + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.ontologydesignpatterns.org/ont/dul/IOLite.owl#$1 +lov.iot-lite: + authority: lov + description: iot-lite is a lightweight ontology based on SSN to describe Internet of Things (IoT) concepts and relationships. + homepage: http://purl.oclc.org/NET/UNIS/fiware/iot-lite# + id: lov.iot-lite + name: Iot-lite ontology + prefix: iot-lite + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: http://purl.oclc.org/NET/UNIS/fiware/iot-lite#$1 +lov.iot-tta: + authority: lov + description: The Internet of Things taxonomy is extended with semantic ontologies for IoT layers, containing classes, properties, individuals, and rules specific to IoT technologies, tools, and applications + homepage: https://w3id.org/iot-tta + id: lov.iot-tta + name: Ontology for Internet of Things Technologies, Tools, and Applications + prefix: iot-tta + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/iot-tta#$1 +lov.ioto: + authority: lov + description: >- + IoT-O is a core domain Internet of Things ontology. It is intended to model + horizontal knowledge about IoT systems and applications, and to be extended + with vertical, application specific knowledge. + + It is constituted of different modules : + - A sensing module, based on W3C's SSN (http://purl.oclc.org/NET/ssnx/ssn) + - An acting module, based on SAN (http://www.irit.fr/recherches/MELODI/ontologies/SAN) + - A service module, based on MSM (http://iserve.kmi.open.ac.uk/ns/msm/msm-2014-09-03.rdf) and hRest (http://www.wsmo.org/ns/hrests) + - A lifecycle module, based on a lifecycle vocabulary (http://vocab.org/lifecycle/schema-20080603.rdf) and an iot-specific extension (http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle) + - An energy module, based on powerOnt (ttp://elite.polito.it/ontologies/poweront.owl) + + IoT-O developping team also contributes to the oneM2M IoT interoperability standard. + homepage: http://www.irit.fr/recherches/MELODI/ontologies/IoT-O + id: lov.ioto + name: IoT-O + prefix: ioto + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.irit.fr/recherches/MELODI/ontologies/IoT-O#$1 +lov.iottaxolite: + authority: lov + description: The IoT-Taxonomy-lite is adapted from M3-lite taxonomy. This taxonomy is refactored and defines many other concepts such as subclasses of Feature-of-Interest and Quality-of-Observation. + homepage: http://purl.org/iot/vocab/iot-taxonomy-lite# + id: lov.iottaxolite + name: The IoTTaxonomy-lite Taxonomy + prefix: iottaxolite + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/iot/vocab/iot-taxonomy-lite#$1 +lov.ipo: + authority: lov + description: Vocabulary for describing issues (or problems) and corresponding symptoms and solutions to a broad variety of contexts. It is intended to provide a generic, reusable core ontology that can be extended or specialized for use in domain-specific situations, aimed at supporting linked data publishing. The solutions are represented by procedures, which are possible workflows for solving corresponding issues. + homepage: http://purl.org/ipo/core + id: lov.ipo + name: IPO - Issue Procedure Ontology + prefix: ipo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ipo/core#$1 +lov.irao: + authority: lov + description: Informatics Research Artifacts Ontology, described using W3C RDF Schema and the Web Ontology Language OWL. + homepage: http://ontology.ethereal.cz/irao + id: lov.irao + name: Informatics Research Artifacts Ontology + prefix: irao + source: lov.linkeddata.es + subjects: + - other humanities + - computer and information sciences + uri_format: http://ontology.ethereal.cz/irao/$1 +lov.irw: + authority: lov + description: This ontology is an evolution of IRE ontology. It describes identification of resources on the Web, through the definition of relationships between resources and their representations on the Web. The requirement is to describe what can be identified by URIs and how this is handled e.g. in form of HTTP requests and reponds. + homepage: http://www.ontologydesignpatterns.org/ont/web/irw.owl + id: lov.irw + name: The Identity of Resources on the Web ontology + prefix: irw + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/ont/web/irw.owl#$1 +lov.is: + authority: lov + description: The Information Service Ontology specification provides basic concepts and properties for describing different information services, e.g. Wikipedia, MusicBrainz, Freebase + homepage: http://purl.org/ontology/is/core# + id: lov.is + name: Info Service Ontology + prefix: is + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/is/core#$1 +lov.isbd: + authority: lov + description: This is a registration of classes and properties from International Standard Bibliographic Description (ISBD), consolidated edition, published by De Gruyter Saur in July 2011 (ISBN 978-3-11-026379-4). + homepage: http://iflastandards.info/ns/isbd/elements/ + id: lov.isbd + name: ISBD elements + prefix: isbd + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://iflastandards.info/ns/isbd/elements/$1 +lov.iso-thes: + authority: lov + description: This vocabulary aims at providing interoperability between SKOS and ISO 25964 ‐ 1:2011, the new standard for thesauri + homepage: http://purl.org/iso25964/skos-thes + id: lov.iso-thes + name: ISO 25964 SKOS extension + prefix: iso-thes + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/iso25964/skos-thes#$1 +lov.iso37120: + authority: lov + description: >- + ISO 37120 – Sustainable Development and Resilience of Communities – + Indicators for City Services and Quality of Life (under TC268) + + + http://ontology.eil.utoronto.ca/ISO37120.html + + + This OWL file defines a class for each indicator defined in the ISO 37120 standard. Names for each indicator are provided. Text definitions are provided only for Economy, Education and Energy indicators, due to copyright restrictions imposed by ISO. This file is meant to provide a single URI for each indicator. + + + An ontology for representing an indicator's supporting data plus meta information such as provenance, validity and trust can be found in: + + http://ontology.eil.utoronto.ca/GCI/Foundation/GCI-Foundation.owl + + + Documentation of the ontology can be found in: + + http://eil.utoronto.ca/smartcities/papers/GCI-Foundation-Ontology.pdf + homepage: http://ontology.eil.utoronto.ca/ISO37120.owl + id: lov.iso37120 + name: ISO 37120 indicator URIs + prefix: iso37120 + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://ontology.eil.utoronto.ca/ISO37120.owl#$1 +lov.isoadr: + authority: lov + description: "This ontology is a version of the ISO TC211, Group for Ontology Management (GOM)'s OWL ontology interpretation of the ISO19160-1:2015 \"Addressing -- Part 1: Conceptual model\" standard (see https://www.iso.org/standard/61710.html) taken from that ontology's source code, published at https://github.com/ISO-TC211/GOM/tree/master/isotc211_GOM_harmonizedOntology/19160-1/2015." + homepage: http://reference.data.gov.au/def/ont/iso19160-1-address + id: lov.isoadr + name: ISO19160-1:2015 Address ontology + prefix: isoadr + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://reference.data.gov.au/def/ont/iso19160-1-address#$1 +lov.ispra: + authority: lov + description: L'ontologia ISPRA nasce dall'esigenza di pubblicazione dei dataset LOD ed è finalizzata alla descrizione dei processi e delle attività dell'Istituto negli ambiti circoscritti dai primi dataset pubblicati. Al momento sono descritte in modo analitico le classi e le proprietà che insistono sul dominio specifico della rete ondametrica nazionale, della rete mareografica, del consumo del suolo e degli interventi di dissesto idrogeologico, ma l'obiettivo è di estenderla parallelamente alla pubblicazione di nuovi dataset. + homepage: http://dati.isprambiente.it/ontology/core# + id: lov.ispra + name: Ispra Ontology + prefix: ispra + source: lov.linkeddata.es + subjects: + - other humanities + - earth and related environmental sciences + uri_format: http://dati.isprambiente.it/ontology/core#$1 +lov.istex: + authority: lov + description: ISTEX est une plateforme qui a pour ambition d’offrir, à l’ensemble de la communauté de l’enseignement supérieur et de la recherche française qui le souhaite, un accès en ligne aux collections rétrospectives de la littérature scientifique dans toutes les disciplines. À ce réservoir inégalé en ressources multidisciplinaires s’ajoute un nombre important de services à valeur ajoutée permettant d’en optimiser l’exploitation grâce à des outils de fouille de contenus (TDM) et de valorisation interactive. + homepage: https://data.istex.fr/ontology/istex# + id: lov.istex + name: Ontologie du projet Istex pour la diffusion de la littérature scientifique + prefix: istex + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: https://data.istex.fr/ontology/istex#$1 +lov.itm: + authority: lov + description: A partir del estudio de las características de las herramientas de gestión de tareas o issue tracking systems, se ha elaborado este vocabulario. + homepage: http://spi-fm.uca.es/spdef/models/genericTools/itm/1.0 + id: lov.itm + name: Issue Tracking tool Model + prefix: itm + source: lov.linkeddata.es + subjects: [] + uri_format: http://spi-fm.uca.es/spdef/models/genericTools/itm/1.0#$1 +lov.itsmo: + authority: lov + description: IT Service Management Ontology (ITSMO) provides the vocabulary for annotating resources related to IT Service Management. ITSMO tries to be consistent with 2011 ITIL glossary. + homepage: http://ontology.it/itsmo/v1 + id: lov.itsmo + name: IT Service Management Ontology + prefix: itsmo + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.it/itsmo/v1#$1 +lov.ivoam: + authority: lov + description: |- + A vocabulary of particles used for observations in astronomy. + This list started its existence as the controlled vocabulary for + VODataService's vs:Waveband type; the machine-readable identifiers are in + upper case for backwards compatibility. + homepage: http://www.ivoa.net/rdf/messenger + id: lov.ivoam + name: Messengers + prefix: ivoam + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ivoa.net/rdf/messenger#$1 +lov.jsonsc: + authority: lov + description: Module for data schema specifications, part of the W3C Web of Things (WoT) Thing Description model + homepage: https://www.w3.org/2019/wot/json-schema# + id: lov.jsonsc + name: JSON Schema in RDF + prefix: jsonsc + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://www.w3.org/2019/wot/json-schema#$1 +lov.jup: + authority: lov + description: Slovnik prisupnosti budov vznikl v ramci projektu Mapy bez barier, ktery realizuje Nadace Charty 77 - Konto Bariery. Vychazi z Metodiky kategorizace pristupnosti objektu, je vsak doplnen i o entity vyplyvajici z pozadavku projektu. Tento slovnik je i tematem diplomove prace Ontologie pristupnosti budov. Projekt je spolufinancovan z prostredku Evropske unie, Evropskeho fondu pro regionalni rozvoj. + homepage: http://w3id.org/charta77/jup + id: lov.jup + name: Ontology of Building Accessibility + prefix: jup + source: lov.linkeddata.es + subjects: [] + uri_format: http://w3id.org/charta77/jup/$1 +lov.juso: + authority: lov + description: Juso Ontology is a Web vocabulary for describing geographical addresses and features. + homepage: http://rdfs.co/juso/ + id: lov.juso + name: Juso Ontology + prefix: juso + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - mathematics + uri_format: http://rdfs.co/juso/$1 +lov.juso.kr: + authority: lov + description: South Korea Extension to Juso Ontology is a Web vocabulary that extends Juso Ontology to describe geographical addresses and features in South Korea. + homepage: http://rdfs.co/juso/kr/ + id: lov.juso.kr + name: South Korea Extension to Juso Ontology + prefix: juso.kr + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - mathematics + uri_format: http://rdfs.co/juso/kr/$1 +lov.kdo: + authority: lov + description: The Knowledge Diversity Ontology aims at providing a vocabulary that describes different dimensions of knowledge diversity of the Web. To support the representation of diversity information, the conceptual model of the Knowledge Diversity Ontology includes concepts and relations that were identified and modelled by focusing on real world scenarios in context of customer feedback, news, and Wikipedia opinion mining as well as content and sentiment analysis. + homepage: http://kdo.render-project.eu/kdo# + id: lov.kdo + name: The Knowledge Diversity Ontology + prefix: kdo + source: lov.linkeddata.es + subjects: [] + uri_format: http://kdo.render-project.eu/kdo#$1 +lov.kees: + authority: lov + description: KEES (Knowledge Exchange Engine Schema ) ontology describes a knowledge base configuration in terms of ABox and TBox statements together with their accrual and reasoning policies. This vocabulary is designed to drive automatic data ingestion in a graph database according KEES and Linked (Open) Data principles. + homepage: http://linkeddata.center/kees/v1 + id: lov.kees + name: KEES Ontology + prefix: kees + source: lov.linkeddata.es + subjects: [] + uri_format: http://linkeddata.center/kees/v1#$1 +lov.keys: + authority: lov + description: A vocabulary for musical keys and notes + homepage: http://purl.org/NET/c4dm/keys.owl + id: lov.keys + name: Keys Ontology + prefix: keys + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/NET/c4dm/keys.owl#$1 +lov.km4c: + authority: lov + description: A Knowledge Model to describe a smart city, that interconnect data from infomobility service, Open Data and other source + homepage: http://www.disit.org/km4city/schema + id: lov.km4c + name: km4city, the DISIT Knowledge Model for City and Mobility + prefix: km4c + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://www.disit.org/km4city/schema#$1 +lov.label: + authority: lov + description: Term definitions for singular and plural label properties + homepage: http://purl.org/net/vocab/2004/03/label + id: lov.label + name: label + prefix: label + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/vocab/2004/03/label#$1 +lov.lawd: + authority: lov + description: The goal of LAWD is to fill in the cracks between the data used and published by projects with a focus on the ancient world and the standard Linked Data vocablary schemes, like Dublin Core, the Open Annotation Collaboration, and CIDOC-CRM. + homepage: http://lawd.info/ontology/ + id: lov.lawd + name: Linking Ancient World Data Ontology + prefix: lawd + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://lawd.info/ontology/$1 +lov.lc: + authority: lov + description: This ontology provides the predicates necessary to describe a connection or hop from one transit stop to another. + homepage: http://semweb.mmlab.be/ns/linkedconnections#Ontology + id: lov.lc + name: The Linked Connections ontology + prefix: lc + source: lov.linkeddata.es + subjects: [] + uri_format: http://semweb.mmlab.be/ns/linkedconnections#$1 +lov.lcy: + authority: lov + description: The Lifecycle Schema provides classes and properties that allow the specification of a lifecycle that any resource may pass through. + homepage: http://purl.org/vocab/lifecycle/schema + id: lov.lcy + name: Lifecycle Schema + prefix: lcy + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocab/lifecycle/schema#$1 +lov.ldp: + authority: lov + description: A set of best practices and simple approach for a read-write Linked Data architecture, based on HTTP access to web resources that describe their state using the RDF data model. + homepage: http://www.w3.org/ns/ldp# + id: lov.ldp + name: Linked Data Platform + prefix: ldp + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3.org/ns/ldp#$1 +lov.ldr: + authority: lov + description: The Linked Data Rights ontology provides the vocabulary for creating rights expressions for Linked Data resources. + homepage: http://purl.oclc.org/NET/ldr/ns# + id: lov.ldr + name: Linked Data Rights (LDR) + prefix: ldr + source: lov.linkeddata.es + subjects: + - law + uri_format: http://purl.oclc.org/NET/ldr/ns#$1 +lov.ldvm: + authority: lov + description: Vocabulary for Linked Data Visualization Model (LDVM) serves for description and configuration of components and pipelines according to LDVM + homepage: http://linked.opendata.cz/ontology/ldvm/ + id: lov.ldvm + name: Vocabulary for Linked Data Visualization Model + prefix: ldvm + source: lov.linkeddata.es + subjects: [] + uri_format: http://linked.opendata.cz/ontology/ldvm/$1 +lov.lemon: + authority: lov + description: 'Lemon: The lexicon model for ontologies is designed to allow for descriptions of lexical information regarding ontological elements and other RDF resources. Lemon covers mapping of lexical decomposition, phrase structure, syntax, variation, morphology, and lexicon-ontology mapping.' + homepage: http://lemon-model.net/lemon + id: lov.lemon + name: LExicon Model for ONtologies + prefix: lemon + source: lov.linkeddata.es + subjects: [] + uri_format: http://lemon-model.net/lemon#$1 +lov.lexdcp: + authority: lov + description: A model for the representation of lexical information relative to ontologies. Decomposition module. + homepage: http://www.w3.org/ns/lemon/decomp + id: lov.lexdcp + name: Lexicon Model for Ontologies - Decomp + prefix: lexdcp + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/lemon/decomp#$1 +lov.lexinfo: + authority: lov + description: Version 2.0 of LexInfo Ontology, based on Lemon + homepage: http://www.lexinfo.net/ontology/2.0/lexinfo + id: lov.lexinfo + name: LexInfo Ontology + prefix: lexinfo + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.lexinfo.net/ontology/2.0/lexinfo#$1 +lov.lgdo: + authority: lov + description: LinkedGeoData ontology has been derived from concepts defined by Open Street Map + homepage: http://linkedgeodata.org/ontology + id: lov.lgdo + name: LinkedGeoData ontology + prefix: lgdo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://linkedgeodata.org/ontology/$1 +lov.lh: + authority: lov + description: An ontology for metadata about legal texts represented using the LegalHTML format + homepage: https://w3id.org/legalhtml/ov + id: lov.lh + name: LegalHTML Ontology + prefix: lh + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/legalhtml/ov#$1 +lov.li: + authority: lov + description: An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - LI Package + homepage: http://def.seegrid.csiro.au/isotc211/iso19115/2003/lineage + id: lov.li + name: OWL representation of ISO 19115 (Geographic Information - Metadata - Lineage package) + prefix: li + source: lov.linkeddata.es + subjects: [] + uri_format: http://def.seegrid.csiro.au/isotc211/iso19115/2003/lineage#$1 +lov.lib: + authority: lov + description: Experimental "library" extension vocabulary for use with Schema.org + homepage: http://purl.org/library/ + id: lov.lib + name: Library extension of schema.org + prefix: lib + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/library/$1 +lov.lifecycle: + authority: lov + description: >- + This ontology is a specialization of the lifecycle vocabulary + (http://purl.org/vocab/lifecycle/schema) meant to be used in the context of + IoT. It is used as a module in the IoT core domain ontology IoT-O + (www.irit.fr/recherches/MELODI/ontologies/IoT-O). + + + IoT-Lifecycle adds a specific state definition (ParametrizedState) and a specific transition (Update) that is useful to model actuators. + homepage: http://www.irit.fr/recherches/MELODI/ontologies/IoT-Lifecycle + id: lov.lifecycle + name: IoT-Lifecycle + prefix: lifecycle + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocab/lifecycle/schema#$1 +lov.lime: + authority: lov + description: LIME (LInguistic MEtadata) is a vocabulary for expressing linguistic metadata about linguistic resources and linguistically grounded datasets. + homepage: http://www.w3.org/ns/lemon/lime + id: lov.lime + name: Lexicon Model for Ontologies - LIngusitic MEtadata (LIME) + prefix: lime + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.w3.org/ns/lemon/lime#$1 +lov.limo: + authority: lov + description: A Vocabulary for Incorporating Predictive Models into the Linked Data Web + homepage: http://purl.org/limo-ontology/limo/ + id: lov.limo + name: Linked Statistical Models Vocabulary + prefix: limo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/limo-ontology/limo#$1 +lov.limoo: + authority: lov + description: A vocabulary to describe licenses + homepage: http://purl.org/LiMo/0.1# + id: lov.limoo + name: License Model Ontology + prefix: limoo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/LiMo/0.1#$1 +lov.lingvo: + authority: lov + description: An ontology for using languages as resources + homepage: https://w3id.org/vocab/lingvoj + id: lov.lingvo + name: The Lingvoj Ontology + prefix: lingvo + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/vocab/lingvoj#$1 +lov.lio: + authority: lov + description: A Lightweight Ontology for Describing Images + homepage: http://purl.org/net/lio + id: lov.lio + name: Lightweight Image Ontology + prefix: lio + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/lio#$1 +lov.llont: + authority: lov + description: LinkLion - the Link Discovery Portal + homepage: http://www.linklion.org/ontology + id: lov.llont + name: LinkLion - the Link Discovery Portal + prefix: llont + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.linklion.org/ontology#$1 +lov.lmm1: + authority: lov + description: This ontology is a composition of some content design patterns for the semiotic triangle. Its structure is extracted from DOLCE-Ultralite (DOLCE+c.DnS), but it uses a different terminology, + homepage: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl + id: lov.lmm1 + name: Lexical MetaModel Level 1 + prefix: lmm1 + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L1.owl#$1 +lov.lmm2: + authority: lov + description: An ontology for aligning existing linguistic ontologies, and for describing the research objects of NLP. + homepage: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl + id: lov.lmm2 + name: Lexical MetaModel Level 2 + prefix: lmm2 + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/ont/lmm/LMM_L2.owl#$1 +lov.loc: + authority: lov + description: Este vocabulario se utiliza para modelar las localizaciones físicas de lugares públicos. Utiliza elementos de Geonames para identificar las distintas características geográficas. + homepage: http://purl.org/ctic/infraestructuras/localizacion + id: lov.loc + name: Vocabulario de Localizaciones + prefix: loc + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://purl.org/ctic/infraestructuras/localizacion#$1 +lov.locah: + authority: lov + description: This vocabulary derived from the Encoded Archival Description standard has been developed in 2010-2011 by the LOCAH project. + homepage: http://data.archiveshub.ac.uk/def/ + id: lov.locah + name: The LOCAH RDF Vocabulary + prefix: locah + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://data.archiveshub.ac.uk/def/$1 +lov.locn: + authority: lov + description: The ISA Programme Location Core Vocabulary provides a minimum set of classes and properties for describing any place in terms of its name, address or geometry. The vocabulary is specifically designed to aid the publication of data that is interoperable with EU INSPIRE Directive. + homepage: http://www.w3.org/ns/locn + id: lov.locn + name: ISA Programme Location Core Vocabulary + prefix: locn + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - mathematics + uri_format: http://www.w3.org/ns/locn#$1 +lov.lode: + authority: lov + description: An ontology for publishing descriptions of historical events as Linked Data, and for mapping between other event-related vocabularies and ontologies. + homepage: http://linkedevents.org/ontology/ + id: lov.lode + name: Linking Open Descriptions of Events + prefix: lode + source: lov.linkeddata.es + subjects: [] + uri_format: http://linkedevents.org/ontology/$1 +lov.log: + authority: lov + description: An historical ontology used by the cwm command-line tool back in the very early days of the semantic web (~ 2000- 2003 ?) + homepage: http://www.w3.org/2000/10/swap/log + id: lov.log + name: SWAP Logic Ontology + prefix: log + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2000/10/swap/log#$1 +lov.lom: + authority: lov + description: >- + An ontology and vocabulary used for exposing IEEE LOM, a metadata standard + for educational contents, as Linked Data. + + It is intended as a bridge for linkage of educational metadata into Linked Open Data (LOD). In this ontology, we designed a mapping of IEEE LOM elements to RDF based on Linked Data principles. + homepage: http://data.opendiscoveryspace.eu/lom_ontology_ods.owl + id: lov.lom + name: Learning Object Metadata Ontology + prefix: lom + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.opendiscoveryspace.eu/lom_ontology_ods.owl#$1 +lov.losp: + authority: lov + description: Ontology Specialties describes all possible specialties (directions) in the RF, in which the UGNS they are composed, as well as information about their old codes / groups / names. + homepage: http://sparql.sstu.ru:3030/speciality/ + id: lov.losp + name: Linked open specialities RF + prefix: losp + source: lov.linkeddata.es + subjects: [] + uri_format: http://sparql.sstu.ru:3030/speciality/$1 +lov.loted: + authority: lov + description: A vocabulary for European Calls for Tenders (in english, german, and french) + homepage: http://loted.eu/ontology + id: lov.loted + name: LOTED ontology + prefix: loted + source: lov.linkeddata.es + subjects: + - law + uri_format: http://loted.eu/ontology#$1 +lov.lsc: + authority: lov + description: LSC, the Linked Science Core Vocabulary, is a lightweight vocabulary providing terms to enable publishers and researchers to relate things in science to time, space, and themes. + homepage: http://linkedscience.org/lsc/ns# + id: lov.lsc + name: Linked Science Core Vocabulary + prefix: lsc + source: lov.linkeddata.es + subjects: [] + uri_format: http://linkedscience.org/lsc/ns#$1 +lov.lslife: + authority: lov + description: >- + The ELSEWeb Lifemapper ontology provides classes for describing biodiversity + modelling services provided by Lifemapper. This project provides support + for the ELSEWeb project(http://elseweb.cybershare.utep.edu/). + + website: http://elseweb.cybershare.utep.edu/ontologies + + email: nvillanuevarosales@utep.edu + homepage: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl + id: lov.lslife + name: ELSEWeb Lifemapper Ontology + prefix: lslife + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper.owl#$1 +lov.lsmap: + authority: lov + description: >- + The ELSEWeb mappings ontology imports related upper level ontologies and + vocabularies and aligns ELSEWeb ontologies to importec classes. This + ontology provides support for the ELSEWeb + project(http://elseweb.cybershare.utep.edu/). + + website: http://elseweb.cybershare.utep.edu/ontologies + + email: nvillanuevarosales@utep.edu + homepage: http://ontology.cybershare.utep.edu/ELSEWeb/mappings/elseweb-mappings.owl + id: lov.lsmap + name: ELSEWeb Mappings Ontology + prefix: lsmap + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl#$1 +lov.lsq: + authority: lov + description: The Linked SPARQL Queries Vocabulary (LSQ(V)), defined using RDF(S) and OWL, provides a machine readable vocabulary to help describe queries in SPARQL logs and their statistics. The vocabulary builds upon the SPIN vocabulary and the Service Description vocabulary. + homepage: http://lsq.aksw.org/vocab + id: lov.lsq + name: The Linked SPARQL Queries Vocabulary (LSQ(V)) + prefix: lsq + source: lov.linkeddata.es + subjects: [] + uri_format: http://lsq.aksw.org/vocab#$1 +lov.lsweb: + authority: lov + description: >- + The ELSEWeb Data ontology provides simple classes for describing datasets. + This project provides foundational support for the ELSEWeb + project(http://elseweb.cybershare.utep.edu/). + + website: http://elseweb.cybershare.utep.edu/ontologies + + email: nvillanuevarosales@utep.edu + homepage: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl + id: lov.lsweb + name: ELSEWeb Data Ontology + prefix: lsweb + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-data.owl#$1 +lov.lswmo: + authority: lov + description: >- + The ELSEWeb Modelling ontology provides simple classes for describing data + models. This project provides foundational support for the ELSEWeb + project(http://elseweb.cybershare.utep.edu/). + + website: http://elseweb.cybershare.utep.edu/ontologies + + email: nvillanuevarosales@utep.edu + homepage: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl + id: lov.lswmo + name: ELSEWeb Modelling Ontology + prefix: lswmo + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-modelling.owl#$1 +lov.lswpm: + authority: lov + description: >- + The ELSEWeb Lifemapper parameters ontology provides auxiliary classes and + instances that describe input parameters of Lifemapper modelling services. + This ontology provides support for the ELSEWeb + project(http://elseweb.cybershare.utep.edu/). + + website: http://elseweb.cybershare.utep.edu/ontologies + + email: nvillanuevarosales@utep.edu + homepage: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl + id: lov.lswpm + name: ELSEWeb Lifemapper Parameters Ontology + prefix: lswpm + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.cybershare.utep.edu/ELSEWeb/elseweb-lifemapper-parameters.owl#$1 +lov.ludo: + authority: lov + description: Ludo is an ontology created to enable the description and representation of Serious Games that use structured data published on the Web through the Linked Data as a knowledge base. From the representation of the players’ profile and their contextual information whithin the game, it is possible to generate personalized recommendations of related educational resources in order to stimulate the learning process while playing. + homepage: http://ns.inria.fr/ludo + id: lov.ludo + name: Ludo Ontology + prefix: ludo + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/ludo$1 +lov.ludo-gm: + authority: lov + description: Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics. + homepage: http://ns.inria.fr/ludo/v1/gamemodel# + id: lov.ludo-gm + name: Ludo Game Model Ontology + prefix: ludo-gm + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/ludo/v1/gamemodel#$1 +lov.ludo-gp: + authority: lov + description: Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics. + homepage: http://ns.inria.fr/ludo/v1/gamepresentation# + id: lov.ludo-gp + name: Ludo - Game Presentation + prefix: ludo-gp + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/ludo/v1/gamepresentation#$1 +lov.ludo-vc: + authority: lov + description: Given the increasing amount of structured data published on the Web, many possibilities are open for creating new types of games that use resources from the Web of Data. In particular, if we consider the subcategory of Serious Games in which the object of the game is to educate the user through the interactive discovery of real-life concepts (associated to Semantic Web resources), the inclusion of a semantic representation of the user profile and his contextual information becomes an important element to recommend the user more accurate concepts. Ludo is an ontology that allows the creation of Serious Games with those characteristics. + homepage: http://ns.inria.fr/ludo/v1/virtualcontext# + id: lov.ludo-vc + name: Ludo - Virtual Context + prefix: ludo-vc + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/ludo/v1/virtualcontext#$1 +lov.ludo-xapi: + authority: lov + description: This is an OWL formalization of the statements defined in the Experience API (xAPI) specification. It is a module of the LUDO ontology. + homepage: http://ns.inria.fr/ludo/v1/xapi + id: lov.ludo-xapi + name: Experience API (xAPI) + prefix: ludo-xapi + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://ns.inria.fr/ludo/v1/xapi#$1 +lov.lv: + authority: lov + description: Under this name space new properties and classes needed for the lobid.org service are defined . Already existing properties and classes which are (re)used in lobid.org aren't documented here. + homepage: http://purl.org/lobid/lv + id: lov.lv + name: lobid vocab + prefix: lv + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/lobid/lv#$1 +lov.lvont: + authority: lov + description: An ontology for natural language terms description, including scripts, languages and meanings. The Lexvo.org ontology is still under development and may not be able to address all needs. Please also consider using the Lingvoj Ontology and the GOLD ontology, whereever appropriate. + homepage: http://lexvo.org/ontology + id: lov.lvont + name: Lexvo.org Ontology + prefix: lvont + source: lov.linkeddata.es + subjects: [] + uri_format: http://lexvo.org/ontology#$1 +lov.lyou: + authority: lov + description: Vocabulary for describing common webpages provided by an organisation + homepage: http://purl.org/linkingyou/ + id: lov.lyou + name: Linking-you vocabulary + prefix: lyou + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/linkingyou/$1 +lov.m3lite: + authority: lov + description: 'M3 lite taxonomy is designed for the FIESTA-IOT H2020 EU project. We refactor, clean and simplify the M3 ontology designed by Eurecom (Amelie Gyrard). M3 ontology lite is currently aligned with the quantity taxonomy used by several testbeds: SmartSantander (Spain), University of Surrey (United Kingdom), KETI (Korea) and Com4Innov (France).' + homepage: http://purl.org/iot/vocab/m3-lite# + id: lov.m3lite + name: The Machine-to-Machine Measurement (M3) Lite Ontology + prefix: m3lite + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/iot/vocab/m3-lite#$1 +lov.m4i: + authority: lov + description: >- + Metadata4Ing defines classes and properties or reuses such classes and + properties from other ontologies to describe research processes and research + data management in NFDI4Ing. + + New concepts and properties are located in the namespace of Metadata4Ing. + + Metadata4Ing does not import complete ontologies for the sake of relevance, readability, understandability and usability by and for engineers. + + Instead, it tries to make re-use of existing identifiers for classes and properties by re-using all or a relevant subset of the axioms from the original ontology. + + These statements have been extracted in different ways, e.g. by using Protégé tools importing an ontology and copying axioms of relevant items to Metadata4Ing or by download from data services or raw files of ontologies and manual copypasting. + + In some cases there was a need to extend or modify the original set of statements about an entity, e.g. because labels and definitions were expressed with a different owl:AnnotationProperty than the rest of Metadata4Ing, or because a skos:preflabel or a skos:definition in any of the languages we would like to support was missing. + + Any editorial changes on elements from external ontologies are declared in Metadata4Ing by an annotation with skos:editorialNote at item-level. + + To get the original set of statements we encourage to visit the original namespace of the respective item. + + Metadata4Ing reuses elements from the following ontologies: + + - BIBO = Bibliographic Ontology + + - BIRO = Bibliographic Reference Ontology + + - DCAT = Data Catalog + + - DCTERMS = Dublin Core Terms + + - FOAF = Friend of a Friend + + - OWL = Web Ontology Language + + - PROV = Provenance Namespace + + - QUDT = Quantities, Units, Dimensions and Types + + - RDF = Resource Description Framework + + - RDFS = RDF Schema + + - SCHEMA = schema.org + + - SKOS = Simple Knowledge Organization System + + - SSN = Semantic Sensor Network Ontology + + - VANN = Vocabulary for Annotating vocabulary descriptions + + - XSD = XML Schema Definition + + - EMMO = European Materials and Modelling Ontology + + - BFO = Basic Formal Ontology + + - RO = Relation Ontology + + - PIMS-II = PIMS Interoperability Infrastructure + + - D-SI = Digital System of Units + homepage: http://w3id.org/nfdi4ing/metadata4ing# + id: lov.m4i + name: 'Metadata4Ing: An ontology for describing the generation of research data within a scientific activity.' + prefix: m4i + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://w3id.org/nfdi4ing/metadata4ing#$1 +lov.ma-ont: + authority: lov + description: The Ontology for Media Resources 1.0 describes a core vocabulary of properties and a set of mappings between different metadata formats of media resources hat describe media resources published on the Web (as opposed to local archives, museums, or other non-web related and non-shared collections of media resources). + homepage: http://www.w3.org/ns/ma-ont + id: lov.ma-ont + name: Ontology for Media Resources + prefix: ma-ont + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/ma-ont#$1 +lov.mads: + authority: lov + description: MADS/RDF (Metadata Authority Description Schema in RDF) is a knowledge organization system (KOS) designed for use with controlled values for names (personal, corporate, geographic, etc.), thesauri, taxonomies, subject heading systems, and other controlled value lists + homepage: http://www.loc.gov/mads/rdf/v1 + id: lov.mads + name: Metadata Authority Description Schema + prefix: mads + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.loc.gov/mads/rdf/v1#$1 +lov.marl: + authority: lov + description: Marl is a standardised data schema designed to annotate and describe subjective opinions expressed on the web or in particular Information Systems. + homepage: http://www.gsi.dit.upm.es/ontologies/marl/ns + id: lov.marl + name: Marl Ontology Specification + prefix: marl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.gsi.dit.upm.es/ontologies/marl/ns#$1 +lov.maso: + authority: lov + description: 'Ontologie pour le domaine de la sécurité: application aux agents mobiles' + homepage: http://securitytoolbox.appspot.com/MASO + id: lov.maso + name: Sécurité Agents Mobiles + prefix: maso + source: lov.linkeddata.es + subjects: [] + uri_format: http://securitytoolbox.appspot.com/MASO#$1 +lov.md: + authority: lov + description: An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - MD Package. + homepage: http://def.seegrid.csiro.au/isotc211/iso19115/2003/metadata + id: lov.md + name: OWL representation of ISO 19115 + prefix: md + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://def.seegrid.csiro.au/isotc211/iso19115/2003/metadata#$1 +lov.mdi: + authority: lov + description: An RDF vocabulary to describe and facilitate the usage of a Multidimensional Interface. + homepage: https://w3id.org/multidimensional-interface/ontology + id: lov.mdi + name: RDF vocabulary to describe a Multidimensional Interface. + prefix: mdi + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/multidimensional-interface/ontology#$1 +lov.mdo: + authority: lov + description: This is the Materials Design Ontology. + homepage: https://w3id.org/mdo/full/ + id: lov.mdo + name: Materials Design Ontology - Full + prefix: mdo + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: https://w3id.org/mdo/full/$1 +lov.mdo-calc: + authority: lov + description: This is the calculation module of Materials Design Ontology. + homepage: https://w3id.org/mdo/calculation/ + id: lov.mdo-calc + name: Materials Design Ontology - Calculation Module + prefix: mdo-calc + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: https://w3id.org/mdo/calculation/$1 +lov.mdo-struc: + authority: lov + description: This is the structure module in Materials Design Ontology. + homepage: https://w3id.org/mdo/structure/ + id: lov.mdo-struc + name: Materials Design Ontology - Structure Module + prefix: mdo-struc + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: https://w3id.org/mdo/structure/$1 +lov.mdoprov: + authority: lov + description: This is the provenance module of Materials Design Ontology. + homepage: https://w3id.org/mdo/provenance/ + id: lov.mdoprov + name: Materials Design Ontology - Provenance Module + prefix: mdoprov + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/mdo/provenance/$1 +lov.mdr: + authority: lov + description: >- + An application profile of DCAT combining it with other metadata vocabularies + (e.g. VoID, DCTERMS, LIME) + to meet requirements elicited in various use cases of the Semantic Web platform Semantic Turkey + homepage: http://semanticturkey.uniroma2.it/ns/mdr + id: lov.mdr + name: The Semantic Turkey metadata registry ontology + prefix: mdr + source: lov.linkeddata.es + subjects: [] + uri_format: http://semanticturkey.uniroma2.it/ns/mdr#$1 +lov.meb: + authority: lov + description: This ontology provides the base elements required by myExperiment for content management, social networking and object annotation. + homepage: http://rdf.myexperiment.org/ontologies/base/ + id: lov.meb + name: The myExperiment Base Ontology + prefix: meb + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://rdf.myexperiment.org/ontologies/base/$1 +lov.media: + authority: lov + description: In order to enable and encourage the sharing, distribution, syndication, and aggregation of media content, the authors propose the Media RDF vocabulary, an open standard for distributed media metadata. + homepage: http://purl.org/media + id: lov.media + name: The Media RDF Vocabulary + prefix: media + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/media#$1 +lov.medred: + authority: lov + description: This ontology aims to model generic Medical Data Acquisition Instruments, which can be interoperable across different clinical data management systems. The ontology is developed in the context of the MedRed project (https://www.hevs.ch/en/rad-institutes/institute-of-information-systems/projects/medical-research-data-acquisition-platform-14092) + homepage: http://w3id.org/medred/medred# + id: lov.medred + name: 'MedRed ontology: clinical data acquisition model' + prefix: medred + source: lov.linkeddata.es + subjects: + - biological sciences + - health sciences + uri_format: http://w3id.org/medred/medred#$1 +lov.mexalgo: + authority: lov + description: MEX is an RDF vocabulary designed to facilitate interoperability between published machine learning experiments results on the Web. The mex-algo layer represents the algorithm information existing into a basic machine learning experiment. + homepage: http://mex.aksw.org/mex-algo + id: lov.mexalgo + name: MEX Algorithm Ontology + prefix: mexalgo + source: lov.linkeddata.es + subjects: [] + uri_format: http://mex.aksw.org/mex-algo#$1 +lov.mexcore: + authority: lov + description: MEX e um vocabulario modelado para facilitar a interoperabilidade entre resultados de experimentos de aprendizado de maquinas publicados na Web. A camada mex-core representa a principal informacao obtida de um experimento de aprendizado de maquina. + homepage: http://mex.aksw.org/mex-core + id: lov.mexcore + name: MEX Core Vocabulary + prefix: mexcore + source: lov.linkeddata.es + subjects: [] + uri_format: http://mex.aksw.org/mex-core#$1 +lov.mexperf: + authority: lov + description: MEX e um vocabulario modelado para facilitar a interoperabilidade entre resultados de experimentos de aprendizado de maquinas publicados na Web. A camada mex-perf e o 3o. nivel na abordagem MEX para representar performances de algoritmos de aprendizado de maquinas + homepage: http://mex.aksw.org/mex-perf + id: lov.mexperf + name: MEX Performance Ontology + prefix: mexperf + source: lov.linkeddata.es + subjects: [] + uri_format: http://mex.aksw.org/mex-perf#$1 +lov.mil: + authority: lov + description: The Muninn Military Ontology marks up information about military people, organizations and events. + homepage: http://rdf.muninn-project.org/ontologies/military + id: lov.mil + name: Military Ontology Specification + prefix: mil + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdf.muninn-project.org/ontologies/military#$1 +lov.mls: + authority: lov + description: ML-Schema is a collaborative, community effort with a mission to develop, maintain, and promote standard schemas for data mining and machine learning algorithms, datasets, and experiments + homepage: http://www.w3.org/ns/mls + id: lov.mls + name: Machine Learning Schema + prefix: mls + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/mls#$1 +lov.mo: + authority: lov + description: The Music Ontology Specification provides main concepts and properties fo describing music (i.e. artists, albums and tracks) on the Semantic Web + homepage: http://purl.org/ontology/mo/ + id: lov.mo + name: Music Ontology + prefix: mo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/mo/$1 +lov.moac: + authority: lov + description: MOAC, the Management of a Crisis Vocabulary, is a lightweight vocabulary aiming to provide terms to enable practitioners to relate different "things" in crisis management activities together as Linked Data. The initial MOAC terms originated from the Inter Agency Standing Committee (IASC), Emergency Shelter Cluster in Haiti, UNOCHA 3W Who What Where Contact Database + homepage: http://www.observedchange.com/moac/ns# + id: lov.moac + name: Management of a Crisis Vocabulary + prefix: moac + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://observedchange.com/moac/ns#$1 +lov.moat: + authority: lov + description: An ontology that let users define relationships between Tag objects and URIs of Semantic Web resources + homepage: http://moat-project.org/ns# + id: lov.moat + name: Meaning of a Tag Ontology + prefix: moat + source: lov.linkeddata.es + subjects: [] + uri_format: http://moat-project.org/ns#$1 +lov.mod: + authority: lov + description: This specification describes MOD, a metadata vocabulary to describe and publish ontologies + homepage: http://www.isibang.ac.in/ns/mod + id: lov.mod + name: 'MOD: Metadata for Ontology Description and publication' + prefix: mod + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.isibang.ac.in/ns/mod#$1 +lov.modsci: + authority: lov + description: ModSci is a reference ontology for modelling different types of modern sciences and related entities, such as scientific discoveries, renowned scientists, instruments, phenomena ... etc. + homepage: https://w3id.org/skgo/modsci# + id: lov.modsci + name: ModSci, Modern Science Ontology. + prefix: modsci + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: https://w3id.org/skgo/modsci#$1 +lov.mrel: + authority: lov + description: MARC relators are defined as both RDF properties and SKOS concepts + homepage: http://id.loc.gov/vocabulary/relators + id: lov.mrel + name: MARC Code List for Relators + prefix: mrel + source: lov.linkeddata.es + subjects: [] + uri_format: http://id.loc.gov/vocabulary/relators/$1 +lov.msm: + authority: lov + description: A simple RDF(S) ontology able to capture (part of) the semantics of both Web services and Web APIs + homepage: http://iserve.kmi.open.ac.uk/ns/msm + id: lov.msm + name: Minimal Service Model + prefix: msm + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://iserve.kmi.open.ac.uk/ns/msm#$1 +lov.msr: + authority: lov + description: The Measurement Ontology is an ontology in which measurements may be rendered + homepage: http://www.telegraphis.net/ontology/measurement/measurement# + id: lov.msr + name: Measurement Ontology + prefix: msr + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.telegraphis.net/ontology/measurement/measurement#$1 +lov.mtlo: + authority: lov + description: MarineTLO is a top-level ontology for the marine domain (also applicable to the terrestrial domain). + homepage: http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl + id: lov.mtlo + name: MarineTLO Ontology + prefix: mtlo + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://www.ics.forth.gr/isl/MarineTLO/v4/marinetlo.owl#$1 +lov.munc: + authority: lov + description: An OWL vocabulary for describing uncertainty metadata. + homepage: http://ns.inria.fr/munc/ + id: lov.munc + name: Meta-Uncertainty + prefix: munc + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/munc#$1 +lov.mus: + authority: lov + description: DOREMUS is an extension of the FRBRoo model for describing the music. + homepage: http://data.doremus.org/ontology# + id: lov.mus + name: DOREMUS is an extension of the FRBRoo model for describing the music. + prefix: mus + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://data.doremus.org/ontology#$1 +lov.music: + authority: lov + description: A vocabulary, or music ontology, to describe classical music and performances. Classes (categories) for musical works, events, instruments and performers, as well as related properties are defined. Make sure to distinguish musical works (e.g. Opera) from performance events (Opera_Event), or works (String_Quartette) from performer (StringQuartetEnsemble in this vocab), whose natural language terms are used interchangeblly. The present version experiments more precise model to describe a musical work, its representations (performances, scores, etc) and a musical event to present a representation (a concert). Includes 30 keys as individuals. + homepage: http://www.kanzaki.com/ns/music + id: lov.music + name: Music Vocabulary + prefix: music + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.kanzaki.com/ns/music#$1 +lov.muto: + authority: lov + description: The Modular and Unified Tagging Ontology (MUTO) is an ontology for tagging and folksonomies. It is based on a thorough review of earlier tagging ontologies and unifies core concepts in one consistent schema. It supports different forms of tagging, such as common, semantic, group, private, and automatic tagging, and is easily extensible. + homepage: http://purl.org/muto/core + id: lov.muto + name: Modular Unified Tagging Ontology (MUTO) + prefix: muto + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/muto/core#$1 +lov.mv: + authority: lov + description: Our goal is to significantly improve the data mobility between all stakeholders by providing a standardized vocabulary using Semantic Web technologies and ontologies. For the open vocabulary covering various mobility aspects we use RDF (Resource Description Framework) - a recommended specification of the World Wide Web Consortium (W3C) and the so-called lingua franca for the integration of data and web. We invite everyone who is interested to join our MobiVoc initiative and to participate in the development of the Open Mobility Vocabulary. + homepage: http://schema.mobivoc.org/ + id: lov.mv + name: 'MobiVoc: Open Mobility Vocabulary' + prefix: mv + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://schema.mobivoc.org/$1 +lov.mvco: + authority: lov + description: The Media Value Chain Ontology (MVCO) is an ontology for formalizing the representation of the Media Value Chain. It couples naturally with the MPEG-21 multimedia framework, and its standardization as Part 19 of this ISO/IEC standard is underway (at the editing time of this document). + homepage: http://purl.oclc.org/NET/mvco.owl + id: lov.mvco + name: Media Value Chain Ontology + prefix: mvco + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.oclc.org/NET/mvco.owl#$1 +lov.nao: + authority: lov + description: The NEPOMUK Annotation Ontology is an ontology for annotation, providing vocabulary which is commonly required to annotate resources on the semantic desktop. + homepage: http://www.semanticdesktop.org/ontologies/2007/08/15/nao + id: lov.nao + name: NEPOMUK Annotation Ontology + prefix: nao + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.semanticdesktop.org/ontologies/2007/08/15/nao#$1 +lov.nas: + authority: lov + description: Defines concepts related to the structure of the US National Airspace System (NAS) + homepage: https://data.nasa.gov/ontologies/atmonto/NAS# + id: lov.nas + name: US National Airspace System (NAS) vocabulary + prefix: nas + source: lov.linkeddata.es + subjects: [] + uri_format: https://data.nasa.gov/ontologies/atmonto/NAS#$1 +lov.ncal: + authority: lov + description: The NEPOMUK Calendaring Ontology intends to provide vocabulary for describing calendaring data (events, tasks, journal entries) which is an important part of the body of information usually stored on a desktop. It is an adaptation of the ICALTZD ontology created by the W3C RDF Calendar Task Force of the Semantic Web Interest Group in the Semantic Web Activity. + homepage: http://www.semanticdesktop.org/ontologies/2007/04/02/ncal + id: lov.ncal + name: NEPOMUK Calendar Ontology + prefix: ncal + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.semanticdesktop.org/ontologies/2007/04/02/ncal#$1 +lov.nco: + authority: lov + description: NEPOMUK Contact Ontology describes contact information, common in many places on the desktop. It evolved from the VCARD specification (RFC 2426) and has been inspired by the Vcard Ontology by Renato Ianella. The scope of NCO is much broader though. This document gives an overview of the classes, properties and intended use cases of the NCO ontology. + homepage: http://www.semanticdesktop.org/ontologies/2007/03/22/nco + id: lov.nco + name: NEPOMUK Contact Ontology + prefix: nco + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.semanticdesktop.org/ontologies/2007/03/22/nco#$1 +lov.nen2660: + authority: lov + description: Ontology which is a normative part of the Dutch NEN 2660-2 standard + homepage: https://w3id.org/nen2660/ + id: lov.nen2660 + name: "NEN 2660-2:2022 'Rules for information modelling of the built environment - Part 2: Practical configuration, extension and implementation of NEN 2660-1''" + prefix: nen2660 + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/nen2660/def#$1 +lov.nfo: + authority: lov + description: Part of Nepomuk Information Element Ontology Framework + homepage: http://www.semanticdesktop.org/ontologies/2007/03/22/nfo + id: lov.nfo + name: NEPOMUK File Ontology + prefix: nfo + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#$1 +lov.ngeo: + authority: lov + description: A vocabulary for specifying geographical regions in RDF + homepage: http://geovocab.org/geometry + id: lov.ngeo + name: NeoGeo Geometry Ontology + prefix: ngeo + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://geovocab.org/geometry#$1 +lov.nie: + authority: lov + description: The Core Ontology of the NEPOMUK suite defines basic elements such as Data Object, Information Element ... + homepage: http://www.semanticdesktop.org/ontologies/2007/01/19/nie + id: lov.nie + name: NEPOMUK Information Element Core Ontology + prefix: nie + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.semanticdesktop.org/ontologies/2007/01/19/nie#$1 +lov.nif: + authority: lov + description: The NLP Interchange Format (NIF) is an RDF/OWL-based format that aims to achieve interoperability between Natural Language Processing (NLP) tools, language resources and annotations. + homepage: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core# + id: lov.nif + name: NLP Interchange Format + prefix: nif + source: lov.linkeddata.es + subjects: [] + uri_format: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#$1 +lov.nlon: + authority: lov + description: This specification describes National Library of Korea Ontology vocaburaries using W3C's RDF and OWL technology. + homepage: http://lod.nl.go.kr/ontology/ + id: lov.nlon + name: National Library of Korea Ontology + prefix: nlon + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://lod.nl.go.kr/ontology/$1 +lov.nno: + authority: lov + description: This is the Neural Network Ontology. Designed by the AIFB (http://www.aifb.kit.edu/web/Web_Science) + homepage: https://w3id.org/nno/ontology + id: lov.nno + name: The Neural Network Ontology + prefix: nno + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/nno/ontology#$1 +lov.noria: + authority: lov + description: >- + The NORIA-O project is a data model for IT networks, events and operations + information. + + The ontology is developed using web technologies (e.g. RDF, OWL, SKOS) and is intended as a structure for realizing an IT Service Management (ITSM) Knowledge Graph (KG) for Anomaly Detection (AD) and Risk Management applications. + + The model has been developed in collaboration with operational teams, and in connection with third parties linked vocabularies. + + + Alignment with third parties vocabularies is implemented on a per class or per property basis when relevant (e.g. with `rdfs:subClassOf`, `owl:equivalentClass`). + + Directions for direct instanciation of these vocabularies are provided for cases where implementing a class/property alignment is redundant. + + Alignment holds for the following vocabulary releases: + + - [BBO](https://hal.archives-ouvertes.fr/hal-02365012/) 1.0.0 + + - [BOT](https://w3id.org/bot/) 0.3.2 + + - [DevOps-Infra](https://oeg-upm.github.io/devops-infra/) 1.0.0 + + - [FOLIO](https://github.com/IBCNServices/Folio-Ontology) 1.0.0 + + - [ORG](https://www.w3.org/TR/vocab-org/) 0.8 + + - [PEP](https://w3id.org/pep/) 1.1 + + - [SEAS](https://w3id.org/seas/) 1.1 + + - [SLOGERT](https://sepses.ifs.tuwien.ac.at/ns/log/index-en.html) 1.1.0 + + - [UCO](https://github.com/ucoProject/uco) Release-0.8.0 + homepage: https://w3id.org/noria/ontology/ + id: lov.noria + name: The NORIA Ontology + prefix: noria + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/noria/ontology/$1 +lov.np: + authority: lov + description: The nanopub ontology + homepage: http://www.nanopub.org/nschema + id: lov.np + name: Nano publication ontology + prefix: np + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.nanopub.org/nschema#$1 +lov.npg: + authority: lov + description: The Core Ontology is a formal model providing definitions for the key concepts of interest to content publishing at Macmillan Science and Education. + homepage: http://ns.nature.com/terms/ + id: lov.npg + name: Nature.com Core Ontology + prefix: npg + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.nature.com/terms/$1 +lov.nrl: + authority: lov + description: Designed on top of RDF, it addresses certain limitations on the part of RDF/S. In particular it includes support for Named Graphs + homepage: http://www.semanticdesktop.org/ontologies/2007/08/15/nrl + id: lov.nrl + name: NEPOMUK Representational Language + prefix: nrl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.semanticdesktop.org/ontologies/2007/08/15/nrl#$1 +lov.nrv: + authority: lov + description: An OWL vocabulary for describing normative requirements. + homepage: http://ns.inria.fr/nrv + id: lov.nrv + name: Normative Requirements Vocabulary + prefix: nrv + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/nrv#$1 +lov.nsl: + authority: lov + description: The News Storyline Ontology is a generic model for describing and organising the stories news organisations tell. The ontology is intended to be flexible to support any given news or media publisher's approach to handling news stories. At the heart of the ontology, is the concept of Storyline. + homepage: http://purl.org/ontology/storyline + id: lov.nsl + name: A News Storyline Ontology + prefix: nsl + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/storyline/$1 +lov.ntag: + authority: lov + description: NiceTag Ontology is an ontology which describes as generally as possible tags or rather tag actions understood as a speech acts occurring on the Web + homepage: http://ns.inria.fr/nicetag/2010/09/09/voc + id: lov.ntag + name: Nice Tag Ontology + prefix: ntag + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/nicetag/2010/09/09/voc#$1 +lov.oa: + authority: lov + description: The Open Annotation Core Data Model specifies an interoperable framework for creating associations between related resources, annotations, using a methodology that conforms to the Architecture of the World Wide Web. This ontology is a non-normative OWL formalization of the textual OA specification at http://www.openannotation.org/spec/core/20130208/index.html + homepage: http://www.w3.org/ns/oa# + id: lov.oa + name: Open Annotation Data Model + prefix: oa + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/oa#$1 +lov.oad: + authority: lov + description: An ontology for the description of archival data (OAD, “Ontology of Archival Description”) using the Web Ontology Language (OWL). This ontology represents the classes and properties needed to expose the archival resources as linked data. + homepage: http://culturalis.org/oad# + id: lov.oad + name: Ontology for archival description + prefix: oad + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://culturalis.org/oad#$1 +lov.oae: + authority: lov + description: The Open NEE Model defines an extension of the Open Annotation Data Model (http://www.openannotation.org/spec/core) that allows describing in RDF the result of a Named Entity Extraction (NEE) process, enabling thereby an application to run advanced (SPARQL) queries over the annotated data. The model also exploits the Open NEE Configuration Model (http://www.ics.forth.gr/isl/oncm) for relating the output of a NEE process with an applied configuration (serving provenance information to the output of the entire NEE process). + homepage: http://www.ics.forth.gr/isl/oae/core + id: lov.oae + name: Open NEE Model + prefix: oae + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ics.forth.gr/isl/oae/core#$1 +lov.oan: + authority: lov + description: Description of French National Assembly + homepage: http://data.lirmm.fr/ontologies/oan + id: lov.oan + name: Ontologie de l'Assemblée Nationale + prefix: oan + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://data.lirmm.fr/ontologies/oan/$1 +lov.obo: + authority: lov + description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. + homepage: http://purl.obolibrary.org/obo/obi.owl + id: lov.obo + name: Ontology for Biomedical Investigation + prefix: obo + source: lov.linkeddata.es + subjects: + - biological sciences + - health sciences + uri_format: http://purl.obolibrary.org/obo/$1 +lov.obsm: + authority: lov + description: This is a taxonomy of some observation methods. It is incomplete + homepage: http://rdf.geospecies.org/methods/observationMethod.rdf + id: lov.obsm + name: Observation Method Ontology + prefix: obsm + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://rdf.geospecies.org/methods/observationMethod#$1 +lov.obws: + authority: lov + description: Ontology including the content ontology design pattern for modelling objects with states. + homepage: http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl + id: lov.obws + name: Object with states ontology + prefix: obws + source: lov.linkeddata.es + subjects: [] + uri_format: http://delicias.dia.fi.upm.es/ontologies/ObjectWithStates.owl#$1 +lov.oc: + authority: lov + description: OntoMedia (Ontology for Media) has been designed to describe the interactions occurring in multimedia. + homepage: http://contextus.net/ontology/ontomedia/core/expression# + id: lov.oc + name: OntoMedia Core + prefix: oc + source: lov.linkeddata.es + subjects: [] + uri_format: http://contextus.net/ontology/ontomedia/core/expression#$1 +lov.ocd: + authority: lov + description: L'ontologia Camera dei deputati è stata creata per descrivere tutte le risorse (persone, eventi, documenti) sia storiche che correnti, connesse alla Camera e alla sua attività + homepage: http://dati.camera.it/ocd/ + id: lov.ocd + name: Ontologia Camera dei Deputati + prefix: ocd + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://dati.camera.it/ocd/$1 +lov.ocds: + authority: lov + description: The OCDS is a data model that aims at structuring and publishing contracting data (tenders, procurements, awards, transactions, etc.). It got international adoption and is one of the leading models in this domain. + homepage: http://purl.org/onto-ocds/ocds + id: lov.ocds + name: Schema for an Open Contracting Release (OCDS) + prefix: ocds + source: lov.linkeddata.es + subjects: + - law + uri_format: http://purl.org/onto-ocds/ocds#$1 +lov.odapp: + authority: lov + description: This is an early version of a vocabulary to describe "open data applications" i.e. applications built using open data. Examples of such applications are listed on government open data catalogues and participant on open data competitions. + homepage: http://vocab.deri.ie/odapp + id: lov.odapp + name: Open Data Applications Vocabulary + prefix: odapp + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://vocab.deri.ie/odapp#$1 +lov.odapps: + authority: lov + description: odapps is an RDF vocabulary defined to facilitate the description of Open-Data-based ideas and applications published on the Web. + homepage: http://semweb.mmlab.be/ns/odapps + id: lov.odapps + name: The vocabulary for (L)OD ideas and applications + prefix: odapps + source: lov.linkeddata.es + subjects: [] + uri_format: http://semweb.mmlab.be/ns/odapps#$1 +lov.odpart: + authority: lov + description: The basic participation pattern, without temporal indexing. It clones equivalent elements from DOLCE-UltraLite. + homepage: http://www.ontologydesignpatterns.org/cp/owl/participation.owl + id: lov.odpart + name: Ontology Design Pattern Participation + prefix: odpart + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/cp/owl/participation.owl#$1 +lov.odrl: + authority: lov + description: The Open Digital Rights Language (ODRL) provides flexible and interoperable mechanisms to support transparent and innovative use of digital content in publishing, distribution, and consumption of of digital media across all sectors and communities. The ODRL Policy model is broad enough to support traditional rights expressions for commercial transaction, open access expressions for publicly distributed content, and privacy expressions for social media. + homepage: http://www.w3.org/ns/odrl/2/ + id: lov.odrl + name: The Open Digital Rights Language (ODRL) Ontology + prefix: odrl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/odrl/2/$1 +lov.odrs: + authority: lov + description: A vocabulary that supports the publication of Open Data by providing the means to capture machine-readable "rights statements", e.g. the licensing information, copyright notices and attribution requirements that are associated with the publication and re-use of a dataset. + homepage: http://schema.theodi.org/odrs + id: lov.odrs + name: Open Data Rights Statement Vocabulary + prefix: odrs + source: lov.linkeddata.es + subjects: [] + uri_format: http://schema.theodi.org/odrs#$1 +lov.odv: + authority: lov + description: Extension of data cube for civil service junior posts + homepage: http://reference.data.gov.uk/def/organogram + id: lov.odv + name: Organogram Data Vocabulary + prefix: odv + source: lov.linkeddata.es + subjects: [] + uri_format: http://reference.data.gov.uk/def/organogram/$1 +lov.oecc: + authority: lov + description: Creative Commons Ontology, extending RDF file at http://creativecommons.org/schema.rdf + homepage: http://www.oegov.org/core/owl/cc + id: lov.oecc + name: Extended Creative Commons Ontology + prefix: oecc + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.oegov.org/core/owl/cc#$1 +lov.of: + authority: lov + description: Ontology for Open Fridge project + homepage: http://owlrep.eu01.aws.af.cm/fridge + id: lov.of + name: Open Fridge vocabulary + prefix: of + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://owlrep.eu01.aws.af.cm/fridge#$1 +lov.ofo: + authority: lov + description: The aim of the Occupant Feedback Ontology is to semantically describe passive and active occupant feedback and to enable integration of this feedback with linked building data. + homepage: https://w3id.org/ofo# + id: lov.ofo + name: Occupant Feedback Ontology + prefix: ofo + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/ofo#$1 +lov.ofrd: + authority: lov + description: Vocabulary to describe fridges and freezers + homepage: http://purl.org/opdm/refrigerator# + id: lov.ofrd + name: Fridge and Freezer Vocabulary + prefix: ofrd + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/opdm/refrigerator#$1 +lov.og: + authority: lov + description: The Open Graph protocol enables any web page to become a rich object in a social graph. For instance, this is used on Facebook to enable any web page to have the same functionality as a Facebook Page. + homepage: http://ogp.me/ns + id: lov.og + name: Open Graph Protocol Vocabulary + prefix: og + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://ogp.me/ns#$1 +lov.oh: + authority: lov + description: 'A vocabulary to describe opening hours using calendars (recommended: iCal, RDFCal or schema.org) published on the Web.' + homepage: http://semweb.mmlab.be/ns/oh + id: lov.oh + name: The Opening Hours vocabulary + prefix: oh + source: lov.linkeddata.es + subjects: [] + uri_format: http://semweb.mmlab.be/ns/oh#$1 +lov.olca: + authority: lov + description: A vocabulary defining annotations enabling loose coupling between classes and properties in ontologies. Those annotations define with some accuracy the expected use of properties, in particular across vocabularies, without the formal constraints entailed by the use of OWL or RDFS constructions + homepage: https://w3id.org/vocab/olca + id: lov.olca + name: Ontology Loose Coupling Annotation + prefix: olca + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/vocab/olca#$1 +lov.olo: + authority: lov + description: The Ordered List Ontology Specification provides basic concepts and properties for describing ordered lists as semantic graphs. + homepage: http://purl.org/ontology/olo/core# + id: lov.olo + name: Ordered List Ontology + prefix: olo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/olo/core#$1 +lov.om: + authority: lov + description: An OWL representation of the Observation Schema described in clause 6 of ISO 19156:2011 Geographic Information - Observations and Measurements + homepage: http://def.seegrid.csiro.au/isotc211/iso19156/2011/observation + id: lov.om + name: ISO 19156 Observation Model + prefix: om + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://def.seegrid.csiro.au/isotc211/iso19156/2011/observation#$1 +lov.omg: + authority: lov + description: >- + The Ontology for Managing Geometry (OMG) is an ontology for describing + geometry descriptions of objects. It provides means to support the + application of multiple geometry descriptions of the same object as well as + the description of the geometry evolution over time. The OMG is based the + concepts introduced in the Ontology for Property Management (OPM) ontology. + + + This ontology was created within the research project SCOPE, funded by the German Federal Ministry for Economic Affairs and Energy (BMWi). + + + The initial version of the ontology (v0.0.1) is documented in: + + Wagner, Anna, Bonduel, Mathias, Pauwels, Pieter & Rüppel, Uwe(2019). Relating Geometry Descroptions to its Derivatives on the Web. In Proceedings of the European Conference on Computing in Construction (EC3 2019). Chania, Greece. + homepage: https://w3id.org/omg + id: lov.omg + name: 'OMG: Ontology for Managing Geometry' + prefix: omg + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: https://w3id.org/omg#$1 +lov.oml: + authority: lov + description: An OWL representation of the Observation Schema described in clauses 7-8 of ISO 19156:2011 Geographic Information - Observations and Measurements / OGC Abstract Specification - Topic 20. + homepage: http://def.seegrid.csiro.au/ontology/om/om-lite + id: lov.oml + name: OWL for Observations + prefix: oml + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://def.seegrid.csiro.au/ontology/om/om-lite#$1 +lov.omn: + authority: lov + description: This ontology defines the most abstract concepts and properties that are needed to semantically manage resource within federated infrastructures + homepage: http://open-multinet.info/ontology/omn + id: lov.omn + name: Open-Multinet Upper Ontology + prefix: omn + source: lov.linkeddata.es + subjects: [] + uri_format: http://open-multinet.info/ontology/omn#$1 +lov.omnfed: + authority: lov + description: This ontology defines concepts related to federation of internet infrastructures. + homepage: http://open-multinet.info/ontology/omn-federation + id: lov.omnfed + name: Open-Multinet Upper Federation Ontology + prefix: omnfed + source: lov.linkeddata.es + subjects: [] + uri_format: http://open-multinet.info/ontology/omn-federation#$1 +lov.omnlc: + authority: lov + description: This ontology defines generic concepts related to the life cycle of resource or service. + homepage: http://open-multinet.info/ontology/omn-lifecycle + id: lov.omnlc + name: Open-Multinet Upper Lifecycle Ontology + prefix: omnlc + source: lov.linkeddata.es + subjects: [] + uri_format: http://open-multinet.info/ontology/omn-lifecycle#$1 +lov.onc: + authority: lov + description: The Open NEE Configuration Model defines a Linked Data-based model for describing a configuration supported by a Named Entity Extraction (NEE) service. It is based on the model proposed in "Configuring Named Entity Extraction through Real-Time Exploitation of Linked Data" (http://dl.acm.org/citation.cfm?doid=2611040.2611085) for configuring such services, and allows a NEE service to describe and publish as Linked Data its entity mining capabilities, but also to be dynamically configured. + homepage: http://www.ics.forth.gr/isl/oncm/core + id: lov.onc + name: Open NEE Configuration Model + prefix: onc + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ics.forth.gr/isl/oncm/core#$1 +lov.ont: + authority: lov + description: Vocabulary to define some annotation properties as subproperties of common Dublin Core terms + homepage: http://purl.org/net/ns/ontology-annot + id: lov.ont + name: Ontology annotation DLiser vocabulary + prefix: ont + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/ns/ontology-annot#$1 +lov.ontolex: + authority: lov + description: A model for the representation of lexical information relative to ontologies. Core module. + homepage: http://www.w3.org/ns/lemon/ontolex + id: lov.ontolex + name: Lexicon Model for Ontologies - Core + prefix: ontolex + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/lemon/ontolex#$1 +lov.ontopic: + authority: lov + description: An ontology of topics as used in thesauri, subject directories, etc. + homepage: http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl + id: lov.ontopic + name: Ontopic Ontology + prefix: ontopic + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/ont/dul/ontopic.owl#$1 +lov.ontosec: + authority: lov + description: This ontology covers the domain of security in the field of mobile applications. + homepage: http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl + id: lov.ontosec + name: Ontology Security + prefix: ontosec + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.semanticweb.org/ontologies/2008/11/OntologySecurity.owl#$1 +lov.ontouml: + authority: lov + description: A reference implementation of the OntoUML metamodel in OWL. + homepage: https://w3id.org/ontouml + id: lov.ontouml + name: OntoUML Metamodel Vocabulary + prefix: ontouml + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/ontouml#$1 +lov.onyx: + authority: lov + description: Onyx is a vovabulary designed designed to annotate and describe the emotions expressed by user-generated content on the web or in particular Information Systems. + homepage: http://www.gsi.dit.upm.es/ontologies/onyx/ns + id: lov.onyx + name: Onyx Emotion Ontology + prefix: onyx + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.gsi.dit.upm.es/ontologies/onyx/ns#$1 +lov.oo: + authority: lov + description: This vocabulary provides supplementary terms for organisations wishing to publish open data about themselves. + homepage: http://purl.org/openorg/ + id: lov.oo + name: Open Organisations + prefix: oo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/openorg/$1 +lov.op: + authority: lov + description: A general purpose ontology for observable properties. The ontology supports description of both qualitative and quantitative properties. The allowed scale or units of measure may be specified. A property may be linked to substances-or-taxa and to features or realms, if they play a role in the definition. + homepage: http://environment.data.gov.au/def/op + id: lov.op + name: Observable properties + prefix: op + source: lov.linkeddata.es + subjects: [] + uri_format: http://environment.data.gov.au/def/op#$1 +lov.open311: + authority: lov + description: >- + Open 311 Ontology + + + This ontology generalizes the concepts that appear in 311 open data files published by several cities (Toronto, New York, Chicago, Vancouver) across North America. It provides a generis representation of 311 data that other cities can map their data onto and be used as a means of achieving interoperability. + homepage: http://ontology.eil.utoronto.ca/open311.owl + id: lov.open311 + name: "Open 311 Ontology: An Ontology for publishing a city's non-emergency events." + prefix: open311 + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontology.eil.utoronto.ca/open311#$1 +lov.opm: + authority: lov + description: The Ontology for Property Management (OPM) extends the concepts introduced in the Smart Energy Aware Systems (SEAS) Evaluations ontology. + homepage: https://w3id.org/opm + id: lov.opm + name: 'OPM: Ontology for Property Management' + prefix: opm + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://w3id.org/opm#$1 +lov.opmo: + authority: lov + description: "The Open Provenance Model is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any 'thing', whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation." + homepage: http://openprovenance.org/model/opmo + id: lov.opmo + name: Open Provenance Model + prefix: opmo + source: lov.linkeddata.es + subjects: [] + uri_format: http://openprovenance.org/model/opmo#$1 +lov.opmv: + authority: lov + description: OPMV, the Open Provenance Model Vocabulary, provides terms to enable practitioners of data publishing to publish their data responsibly. + homepage: http://purl.org/net/opmv/ns# + id: lov.opmv + name: Open Provenance Model Vocabulary + prefix: opmv + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/opmv/ns#$1 +lov.opmw: + authority: lov + description: OPMW is a OPMV profile to model the executions and definitions of scientific workflows. + homepage: http://www.opmw.org/ontology/ + id: lov.opmw + name: The OPMW Ontology + prefix: opmw + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.opmw.org/ontology/$1 +lov.opo: + authority: lov + description: Ontology for representing Online Presence + homepage: http://online-presence.net/opo/ns# + id: lov.opo + name: Online Presence Ontology + prefix: opo + source: lov.linkeddata.es + subjects: [] + uri_format: http://online-presence.net/opo/ns#$1 +lov.opus: + authority: lov + description: This file specifies in RDF Schema format the classes and properties for SwetoDblp. These classes and properties are based on the internal LSDIS Library portal engine. + homepage: http://lsdis.cs.uga.edu/projects/semdis/opus# + id: lov.opus + name: SwetoDblp Ontology of Computer Science Publications + prefix: opus + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://lsdis.cs.uga.edu/projects/semdis/opus#$1 +lov.orca: + authority: lov + description: orca, the Ontology of Reasoning, Certainty and Attribution, is an ontology for characterizing the certainty of information, how it is known, and its source + homepage: http://vocab.deri.ie/orca + id: lov.orca + name: orca, the Ontology of Reasoning, Certainty and Attribution + prefix: orca + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.deri.ie/orca#$1 +lov.ore: + authority: lov + description: Open Archives Initiative Object Reuse and Exchange (OAI-ORE) defines standards for the description and exchange of aggregations of Web resources. + homepage: http://www.openarchives.org/ore/terms/ + id: lov.ore + name: The OAI ORE terms vocabulary + prefix: ore + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.openarchives.org/ore/terms/$1 +lov.org: + authority: lov + description: Vocabulary for describing organizational structures, specializable to a broad variety of types of organization. + homepage: http://www.w3.org/ns/org# + id: lov.org + name: Core organization ontology + prefix: org + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/org#$1 +lov.orges: + authority: lov + description: Extensión de la ontología de Organizaciones para adecuarla al Directorio Común de entidades públicas en España. + homepage: http://datos.gob.es/def/sector-publico/organizacion# + id: lov.orges + name: Ontology about Spanish public organizations + prefix: orges + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://datos.gob.es/def/sector-publico/organizacion#$1 +lov.osadm: + authority: lov + description: An ontology describing the administrative and voting area geography of Great Britain + homepage: http://data.ordnancesurvey.co.uk/ontology/admingeo/ + id: lov.osadm + name: The administrative geography and civil voting area ontology + prefix: osadm + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://data.ordnancesurvey.co.uk/ontology/admingeo/$1 +lov.osgeom: + authority: lov + description: A provisional small geometry vocabulary used by Ordnance Survey vocabularies and datasets. Likely to change when some standard way of representing geometries in RDF is agreed. + homepage: http://data.ordnancesurvey.co.uk/ontology/geometry/ + id: lov.osgeom + name: Ordnance Survey Geometry Ontology + prefix: osgeom + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://data.ordnancesurvey.co.uk/ontology/geometry/$1 +lov.oslc: + authority: lov + description: The Open Services for Lifecycle Collaboration (OSLC) initiative is creating a family of web services specifications for products, services and other tools that support all phases of the software and product lifecycle. This OSLC Core Specification sets out the common features that every OSLC Service can be expected to support + homepage: http://open-services.net/ns/core# + id: lov.oslc + name: OSLC Core Vocabulary + prefix: oslc + source: lov.linkeddata.es + subjects: [] + uri_format: http://open-services.net/ns/core#$1 +lov.oslo: + authority: lov + description: This version of the OSLO Exchange Standard provides a minimum set of classes and properties for describing a natural person, i.e. the individual as opposed to any role they may play in society or the relationships they have to other people, organisations and property; all of which contribute significantly to the broader concept of identity. The vocabulary is closely integrated with the Person, Organisation and Location Vocabularies published by the W3C in the Gov Linked Data Project. The OSLO specification is the result of a public-private partnership initiated by V-ICT-OR, the Flemish Organization for ICT in Local Government. + homepage: http://purl.org/oslo/ns/localgov + id: lov.oslo + name: OSLO Exchange Standard + prefix: oslo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/oslo/ns/localgov#$1 +lov.osp: + authority: lov + description: Ontologie d'une organisation publique, plus particulièrement d'un tribunal, d'une organisation internationale ou d'un pays. + homepage: http://data.lirmm.fr/ontologies/osp + id: lov.osp + name: Ontologie du Service Public + prefix: osp + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.lirmm.fr/ontologies/osp#$1 +lov.osr: + authority: lov + description: The OntoMedia Space representation denotes areas of landscape. Expands on the AKT location ontology + homepage: http://contextus.net/ontology/ontomedia/core/space# + id: lov.osr + name: OntoMedia Space Representation + prefix: osr + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://contextus.net/ontology/ontomedia/core/space#$1 +lov.osspr: + authority: lov + description: An ontology describing basic spatial relations. + homepage: http://data.ordnancesurvey.co.uk/ontology/spatialrelations/ + id: lov.osspr + name: Spatial Relations Ontology + prefix: osspr + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://data.ordnancesurvey.co.uk/ontology/spatialrelations/$1 +lov.ostop: + authority: lov + description: The general purpose of this ontology is to provide a library of high level concepts that are used by the other modules within the whole OS Topographic ontology. The ontology also describes the relationships and instances common to more than one module. + homepage: http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl + id: lov.ostop + name: Ordnance Survey Topography Ontology + prefix: ostop + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://www.ordnancesurvey.co.uk/ontology/Topography/v0.1/Topography.owl#$1 +lov.otl: + authority: lov + description: This ontology provides the terms necessary to describe the status of traffic lights. + homepage: https://w3id.org/opentrafficlights + id: lov.otl + name: The Open Traffic Lights ontology + prefix: otl + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/opentrafficlights#$1 +lov.oum: + authority: lov + description: The Ontology of units of Measure (OM) 2.0 models concepts and relations important to scientific research. It has a strong focus on units, quantities, measurements, and dimensions. + homepage: http://www.ontology-of-units-of-measure.org/resource/om-2/ + id: lov.oum + name: Ontology of units of Measure (OM) + prefix: oum + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.ontology-of-units-of-measure.org/resource/om-2/$1 +lov.ov: + authority: lov + description: OpenVocab is a community maintained vocabulary intended for use on the Semantic Web, ideal for properties and classes that don't warrant the effort of creating or maintaining a full schema. OpenVocab allows anyone to create and modify vocabulary terms using their web browser. + homepage: http://open.vocab.org/terms + id: lov.ov + name: OpenVocab + prefix: ov + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://open.vocab.org/terms/$1 +lov.owl: + authority: lov + description: This ontology partially describes the built-in classes and properties that together form the basis of the RDF/XML syntax of OWL 2. + homepage: http://www.w3.org/2002/07/owl + id: lov.owl + name: The OWL 2 Schema vocabulary + prefix: owl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2002/07/owl#$1 +lov.p-plan: + authority: lov + description: The Ontology for Provenance and Plans (P-Plan) is an extension of the PROV-O ontology [PROV-O] created to represent the plans that guided the execution of scientific processes. P-Plan describes how the plans are composed and their correspondence to provenance records that describe the execution itself. + homepage: http://purl.org/net/p-plan# + id: lov.p-plan + name: The P-PLAN Ontology + prefix: p-plan + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/p-plan#$1 +lov.parl: + authority: lov + description: An ontology of UK Parliament + homepage: http://reference.data.gov.uk/def/parliament + id: lov.parl + name: Parliament Ontology + prefix: parl + source: lov.linkeddata.es + subjects: + - political sciences + uri_format: http://reference.data.gov.uk/def/parliament/$1 +lov.part: + authority: lov + description: The participation ontology is a simple model for describing the roles that people play within groups. It is intended that specific domains will create subclasses of roles within their own areas of expertise. + homepage: http://purl.org/vocab/participation/schema + id: lov.part + name: Participation Schema + prefix: part + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocab/participation/schema#$1 +lov.passim: + authority: lov + description: Description of the operation of a transport information service + homepage: http://data.lirmm.fr/ontologies/passim + id: lov.passim + name: PASSIM ontology + prefix: passim + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.lirmm.fr/ontologies/passim#$1 +lov.pat: + authority: lov + description: The Patch Request Ontology provides a schema to describe desired changes in Linked Data. By wrapping the Graph Update Ontology (guo) patch requests can be formulated to add, modify or delete particular triples (or subgraphs) within a dataset. + homepage: http://purl.org/hpi/patchr# + id: lov.pat + name: Patch Request Ontology + prefix: pat + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/hpi/patchr#$1 +lov.pattern: + authority: lov + description: An ontology defining formally patterns for segmenting a document into atomic components, in order to be manipulated independently and re-flowed in different contexts. + homepage: http://www.essepuntato.it/2008/12/pattern + id: lov.pattern + name: The Pattern Ontology + prefix: pattern + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.essepuntato.it/2008/12/pattern#$1 +lov.pav: + authority: lov + description: PAV is a lightweight ontology for tracking Provenance, Authoring and Versioning. PAV specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. + homepage: http://purl.org/pav/ + id: lov.pav + name: Provenance, Authoring and Versioning + prefix: pav + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/pav/$1 +lov.pay: + authority: lov + description: Vocabulary for representing payments, such as government expenditures, using the data cube representation. + homepage: http://reference.data.gov.uk/def/payment# + id: lov.pay + name: Payments ontology + prefix: pay + source: lov.linkeddata.es + subjects: + - law + uri_format: http://reference.data.gov.uk/def/payment#$1 +lov.pbo: + authority: lov + description: The Play Back Ontology specification provides basic concepts and properties for describing concepts that are related to the play back domain. + homepage: http://purl.org/ontology/pbo/core# + id: lov.pbo + name: Play Back Ontology + prefix: pbo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/pbo/core#$1 +lov.pc: + authority: lov + description: Ontologie pro veřejné zakázky poskytuje vyjadřovací prostředky pro popis zakázek zadávaných institucemi veřejné správy. + homepage: http://purl.org/procurement/public-contracts + id: lov.pc + name: Public Contracts Ontology + prefix: pc + source: lov.linkeddata.es + subjects: + - law + uri_format: http://purl.org/procurement/public-contracts#$1 +lov.pdo: + authority: lov + description: The Project Documents Ontology models the inherent structure and concepts of various documents in a project-specific setting, like meeting minutes, status reports etc. + homepage: http://vocab.deri.ie/pdo + id: lov.pdo + name: Project Documents Ontology + prefix: pdo + source: lov.linkeddata.es + subjects: [] + uri_format: http://ontologies.smile.deri.ie/pdo#$1 +lov.peco: + authority: lov + description: This ontology defines a vocabulary for describing provenance traces of carbon emission calculations by capturing the quantifiable measurements of carbon emission sources used by some activities (e.g., electricity used by a machinery to produce a product, petrol used to make a car journey, etc.) and emission conversion factors used to estimate the carbon emissions produced by these. In addition, the ontology provides the ability to capture various data transformations that occurred before energy estimates may be used with relevant conversion factors. For example, sensors may provide raw readings about a water flow of an irrigation rig in an agri-food operation which is then used as a proxy to estimate the total volume of fertilisers used. + homepage: https://w3id.org/peco + id: lov.peco + name: The Provenance of Emission Calculations Ontology + prefix: peco + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://w3id.org/peco#$1 +lov.pep: + authority: lov + description: The process execution ontology is a proposal for a simple extension of both the [W3C Semantic Sensor Network](https://www.w3.org/TR/vocab-ssn/) and the [Semantic Actuator Network](https://www.irit.fr/recherches/MELODI/ontologies/SAN.owl) ontology cores. + homepage: https://w3id.org/pep/ + id: lov.pep + name: Process Execution ontology. + prefix: pep + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/pep/$1 +lov.person: + authority: lov + description: The Person Core Vocabulary provides a minimum set of classes and properties for describing a natural person + homepage: http://www.w3.org/ns/person + id: lov.person + name: ISA Programme Person Core Vocabulary + prefix: person + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/person#$1 +lov.pext: + authority: lov + description: Upper-level ontology with extensions to handle Linked Open Data (LOD) + homepage: http://www.ontotext.com/proton/protonext + id: lov.pext + name: PROTON Extent module + prefix: pext + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontotext.com/proton/protonext#$1 +lov.phdd: + authority: lov + description: Physical data description (PHDD) of existing or published data (tables) in a rectangular format. The data could be either represented in records with character-separated values (CSV) or in records with fixed length. + homepage: http://rdf-vocabulary.ddialliance.org/phdd + id: lov.phdd + name: Physical Data Description + prefix: phdd + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdf-vocabulary.ddialliance.org/phdd#$1 +lov.pico: + authority: lov + description: The PICO ontology provides a machine accessible version of the PICO framework. It essentially provides a model for describing evidence in a consistent way. The model allows the specifying of complex populations, detailed interventions and their comparisons as well as the outcomes considered. The PICO ontology was originally designed to model the questions asked and answered in Cochrane's systematic reviews. As a leader in the field of evidence based healthcare Cochrane uses the PICO model when framing and publishing evidence based questions. The PICO model is widely adopted for describing healthcare evidence, furthermore is equally applicable in other evidence-based domains. It essentially provides a model for describing evidence in a consistent way. + homepage: http://data.cochrane.org/ontologies/pico/ + id: lov.pico + name: Cochrane PICO Ontology + prefix: pico + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://data.cochrane.org/ontologies/pico/$1 +lov.pimsii: + authority: lov + description: The Physicalistic Interpretation of Modelling and Simulation - Interoperability Infrastructure (PIMS-II) is a mid-level ontology with a focus on documenting cognitive processes and epistemic metadata + homepage: http://www.molmod.info/semantics/pims-ii.ttl + id: lov.pimsii + name: Physicalistic Interpretation of Modelling and Simulation - Interoperability Infrastructure (PIMS-II) + prefix: pimsii + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.molmod.info/semantics/pims-ii.ttl#$1 +lov.place: + authority: lov + description: The Places Ontology is a simple lightweight ontology for describing places of geographic interest. + homepage: http://purl.org/ontology/places + id: lov.place + name: The Places Ontology + prefix: place + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://purl.org/ontology/places#$1 +lov.plink: + authority: lov + description: A Multilingual and Multicultural Ontology Representing Family Relationships. + homepage: http://cedric.cnam.fr/isid/ontologies/PersonLink.owl + id: lov.plink + name: PersonLink Ontology + prefix: plink + source: lov.linkeddata.es + subjects: [] + uri_format: http://cedric.cnam.fr/isid/ontologies/PersonLink.owl#$1 +lov.plo: + authority: lov + description: An ontology for describing playlists, playlist entries and songs. + homepage: http://purl.org/net/po# + id: lov.plo + name: Playlist Ontology + prefix: plo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/po#$1 +lov.pmlp: + authority: lov + description: The provenance part of PML2 ontology. It is a fundamental component of PML2 ontology. + homepage: http://inference-web.org/2.0/pml-provenance.owl + id: lov.pmlp + name: PML2 provenance ontology + prefix: pmlp + source: lov.linkeddata.es + subjects: [] + uri_format: http://inference-web.org/2.0/pml-provenance.owl#$1 +lov.pmofn: + authority: lov + description: 'The FrameNet module of the PreMOn ontology extends the core module for representing concepts specific to FrameNet. The modeling is based on the [FrameNet II: Extended Theory and Practice](https://framenet2.icsi.berkeley.edu/docs/r1.5/book.pdf) book.' + homepage: http://premon.fbk.eu/ontology/fn + id: lov.pmofn + name: Predicate Model for Ontologies (PreMOn) - FrameNet ontology module + prefix: pmofn + source: lov.linkeddata.es + subjects: [] + uri_format: http://premon.fbk.eu/ontology/fn#$1 +lov.pmonb: + authority: lov + description: The NomBank module of the PreMOn ontology extends the core module for representing concepts specific to NomBank. The modelling is based on the NomBank Specifications. + homepage: http://premon.fbk.eu/ontology/nb + id: lov.pmonb + name: Predicate Model for Ontologies (PreMOn) - NomBank ontology module + prefix: pmonb + source: lov.linkeddata.es + subjects: [] + uri_format: http://premon.fbk.eu/ontology/nb#$1 +lov.pmopb: + authority: lov + description: The PropBank module of the PreMOn ontology extends the core module for representing concepts specific to PropBank. + homepage: http://premon.fbk.eu/ontology/pb + id: lov.pmopb + name: Predicate Model for Ontologies (PreMOn) - PropBank ontology module + prefix: pmopb + source: lov.linkeddata.es + subjects: [] + uri_format: http://premon.fbk.eu/ontology/pb#$1 +lov.pmovn: + authority: lov + description: The VerbNet module of the PreMOn ontology extends the core module with classes and properties specific to the VerbNet predicate model. The modelling is based on the VerbNet Annotation Guidelines. + homepage: http://premon.fbk.eu/ontology/vn + id: lov.pmovn + name: Predicate Model for Ontologies (PreMOn) - VerbNet ontology module + prefix: pmovn + source: lov.linkeddata.es + subjects: [] + uri_format: http://premon.fbk.eu/ontology/vn#$1 +lov.pna: + authority: lov + description: Press.net Asset Ontology describes news assets (text, images, video, data, etc), the relationships between them and how assets can be classified and semantically annotated. + homepage: http://data.press.net/ontology/asset/ + id: lov.pna + name: Press.net Asset Ontology + prefix: pna + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.press.net/ontology/asset/$1 +lov.pnc: + authority: lov + description: The Press.net Classification Ontology allows assets to be holistically classified using a controlled vocabulary or taxonomy. + homepage: http://data.press.net/ontology/classification/ + id: lov.pnc + name: Press.net Classification Ontology + prefix: pnc + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://data.press.net/ontology/classification/$1 +lov.pne: + authority: lov + description: Press.net Event Ontology models news-worthy events and their relationship to news assets and stuff (simple entities) in the world. + homepage: http://data.press.net/ontology/event/ + id: lov.pne + name: Press.net Event Ontology + prefix: pne + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.press.net/ontology/event/$1 +lov.pni: + authority: lov + description: The Identifier Ontology models non-RDF based Identifiers for resources. It is used to maintain a mapping between RDF resources identifiers and their equivalent IDs in an alternate, non-RDF based domain. + homepage: http://data.press.net/ontology/identifier/ + id: lov.pni + name: SNaP Identifier Ontology + prefix: pni + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.press.net/ontology/identifier/$1 +lov.pns: + authority: lov + description: 'Press.net Stuff Ontology models real world entities. There are two kinds of stuff: tangibles and intangibles. Tangible stuff includes persons, locations and organizations. Intangibles are abstract concepts such as smoking, feminism or love.' + homepage: http://data.press.net/ontology/stuff/ + id: lov.pns + name: Press.net Stuff Ontology + prefix: pns + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.press.net/ontology/stuff/$1 +lov.pnt: + authority: lov + description: Press.net Tag Ontology defines relationships for semantically annotating taggable things (for example news assets) with domain entities (stuff) and events. + homepage: http://data.press.net/ontology/tag/ + id: lov.pnt + name: Press.net Tag Ontology + prefix: pnt + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.press.net/ontology/tag/$1 +lov.po: + authority: lov + description: This ontology aims at providing a simple vocabulary for describing programmes. It covers brands, series (seasons), episodes, broadcast events, broadcast services, etc. + homepage: http://purl.org/ontology/po/ + id: lov.po + name: Programmes ontology + prefix: po + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/po/$1 +lov.poder: + authority: lov + description: A vocabulary to express information about people and their relations with Organizations, Companies, etc. + homepage: http://dev.poderopedia.com/vocab/schema + id: lov.poder + name: Poder Vocabulary + prefix: poder + source: lov.linkeddata.es + subjects: [] + uri_format: http://dev.poderopedia.com/vocab/$1 +lov.poso: + authority: lov + description: This ontology provides the terminologies used for positioning systems. + homepage: http://purl.org/poso/ + id: lov.poso + name: Positioning System Ontology + prefix: poso + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - mathematics + uri_format: http://purl.org/poso/$1 +lov.posocm: + authority: lov + description: This ontology provides the terminologies used for positioning systems. + homepage: http://purl.org/poso/common/ + id: lov.posocm + name: Positioning System Ontology Common Technologies, Algorithms and Systems + prefix: posocm + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://purl.org/poso/common/$1 +lov.postcode: + authority: lov + description: An ontology describing the postcode geography in Great Britain. + homepage: http://data.ordnancesurvey.co.uk/ontology/postcode/ + id: lov.postcode + name: Postcode Ontology + prefix: postcode + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://data.ordnancesurvey.co.uk/ontology/postcode/$1 +lov.poste: + authority: lov + description: Vocabulaire décrivant la répartition des points de contact du réseau postal en France métropolitaine, Guadeloupe, Guyane, La Réunion, Martinique, Mayotte, Monaco, Monte-Carlo et Saint-Pierre et Miquelon + homepage: http://data.lirmm.fr/ontologies/poste + id: lov.poste + name: Ontologie de la Poste + prefix: poste + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.lirmm.fr/ontologies/poste#$1 +lov.ppo: + authority: lov + description: An ontology to create privacy preferences for Linked Data + homepage: http://vocab.deri.ie/ppo + id: lov.ppo + name: Privacy Preference Ontology + prefix: ppo + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://vocab.deri.ie/ppo#$1 +lov.pproc: + authority: lov + description: The PPROC ontology defines the necessary concepts to describe public procurement process and the contracts of public sector (public e-procurement). The ontology has been designed with the main purpose of publishing data about public contracts. + homepage: http://contsem.unizar.es/def/sector-publico/pproc + id: lov.pproc + name: PPROC ontology + prefix: pproc + source: lov.linkeddata.es + subjects: + - law + uri_format: http://contsem.unizar.es/def/sector-publico/pproc#$1 +lov.pr: + authority: lov + description: A vocabulary for describing the ontology design pattern of property reification. + homepage: http://purl.org/ontology/prv/core# + id: lov.pr + name: Property Reification Vocabulary + prefix: pr + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/prv/core#$1 +lov.premis: + authority: lov + description: This ontology identifies the classes and properties used to describe preservation metadata in RDF. + homepage: http://www.loc.gov/premis/rdf/v1 + id: lov.premis + name: PREMIS Ontology + prefix: premis + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.loc.gov/premis/rdf/v1#$1 +lov.prissma: + authority: lov + description: PRISSMA (Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability) is a domain-independent vocabulary for displaying Web of Data resources in mobile environments. + homepage: http://ns.inria.fr/prissma/v2# + id: lov.prissma + name: Presentation of Resources for Interoperable Semantic and Shareable Mobile Adaptability + prefix: prissma + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://ns.inria.fr/prissma/v2#$1 +lov.pro: + authority: lov + description: PRO, the Publishing Roles Ontology, is an ontology for describing the role(s) in the publication process of a particular agent over a defined period of time. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies. + homepage: http://purl.org/spar/pro + id: lov.pro + name: The Publishing Roles Ontology + prefix: pro + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/pro/$1 +lov.prof: + authority: lov + description: >- + This vocabulary is for describing relationships between + standards/specifications, profiles of them and supporting artifacts such as + validating resources. + + + This model starts with [http://dublincore.org/2012/06/14/dcterms#Standard](dct:Standard) entities which can either be Base Specifications (a standard not profiling any other Standard) or Profiles (Standards which do profile others). Base Specifications or Profiles can have Resource Descriptors associated with them that defines implementing rules for the it. Resource Descriptors must indicate the role they play (to guide, to validate etc.) and the formalism they adhere to (dct:format) to allow for content negotiation. A vocabulary of Resource Roles are provided alongside this vocabulary but that list is extensible. + homepage: http://www.w3.org/ns/dx/prof + id: lov.prof + name: Profiles Vocabulary + prefix: prof + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/dx/prof/$1 +lov.prog: + authority: lov + description: This Vocabulary provides the means to create a document which describes a large event or other connected series of events. The primary purpose is to help humans comprehend the programme, not describe absolute truth. A single event (or even series) may have multiple programmes. + homepage: http://purl.org/prog/ + id: lov.prog + name: The Event Programme Vocabulary + prefix: prog + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/prog/$1 +lov.prov: + authority: lov + description: The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web. + homepage: http://www.w3.org/ns/prov# + id: lov.prov + name: W3C PROVenance Interchange + prefix: prov + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/prov#$1 +lov.provoc: + authority: lov + description: 'ProVoc (Product Vocabulary) is a vocabulary that can be used to represent information and manipulate them through the Web. This ontology reflects: 1) The basic hierarchy of a company: Group (Company), Divisions of a Group, Brand names attached to a Division or a Group, and 2) The production of a company: products, ranges of products (attached to a Brand), the composition of a product, packages of products...' + homepage: http://ns.inria.fr/provoc + id: lov.provoc + name: Product Vocabulary + prefix: provoc + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/provoc#$1 +lov.prv: + authority: lov + description: The Provenance Vocabulary Core Ontology provides the main classes and properties required to describe provenance of data on the Web. + homepage: http://purl.org/net/provenance/ns# + id: lov.prv + name: Provenance Vocabulary Core Ontology + prefix: prv + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/provenance/ns#$1 +lov.prvt: + authority: lov + description: Extends the Provenance Vocabulary by defining subclasses of the types of provenance elements introduced in the core ontology. + homepage: http://purl.org/net/provenance/types# + id: lov.prvt + name: Provenance Vocabulary types + prefix: prvt + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/provenance/types#$1 +lov.psh: + authority: lov + description: An OWL vocabulary to include and exploit probabilistic information in SHACL validation reports + homepage: http://ns.inria.fr/probabilistic-shacl/ + id: lov.psh + name: Probabilistic SHACL Validation + prefix: psh + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.inria.fr/probabilistic-shacl/$1 +lov.pso: + authority: lov + description: an ontology for describing the status held by a bibliographic document or other publication entity at each of the various stages in the publishing process. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies + homepage: http://purl.org/spar/pso + id: lov.pso + name: The Publishing Status Ontology + prefix: pso + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/pso/$1 +lov.ptop: + authority: lov + description: The PROTON Top module represents the most general classes + homepage: http://www.ontotext.com/proton/protontop + id: lov.ptop + name: PROTON (Proto Ontology), Top Module + prefix: ptop + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontotext.com/proton/protontop#$1 +lov.pubsub: + authority: lov + description: The eccenca Publish-Subscribe Vocabulary defines concepts and relations to create statements about publishers, subscribers and their subscriptions in a Publish-Subscribe environment based on the PubSubHubbub Core 0.4 specification. + homepage: https://vocab.eccenca.com/pubsub/ + id: lov.pubsub + name: Eccenca Publish-Subscribe Vocabulary + prefix: pubsub + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://vocab.eccenca.com/pubsub/$1 +lov.puv: + authority: lov + description: A simple ontology which implements the Parameter Usage Vocabulary semantic model, as described at https://github.com/nvs-vocabs/P01 + homepage: https://w3id.org/env/puv + id: lov.puv + name: Parameter Usage Vocabulary ontology + prefix: puv + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://w3id.org/env/puv#$1 +lov.pwo: + authority: lov + description: An ontology for describing the workflow associated with the publication of a document. + homepage: http://purl.org/spar/pwo + id: lov.pwo + name: The Publishing Workflow Ontology + prefix: pwo + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/spar/pwo/$1 +lov.qb: + authority: lov + description: This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. + homepage: http://purl.org/linked-data/cube + id: lov.qb + name: The data cube vocabulary + prefix: qb + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/linked-data/cube#$1 +lov.qb4o: + authority: lov + description: This vocabulary allows to publish and operate with OLAP cubes in RDF + homepage: http://purl.org/qb4olap/cubes + id: lov.qb4o + name: Vocabulary for publishing OLAP data cubes + prefix: qb4o + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/qb4olap/cubes#$1 +lov.qu: + authority: lov + description: >- + This ontology is partially based on the SysML QUDV (Quantities, Units, + Dimensions and Values) proposed by a working group of the SysML 1.2 Revision + Task Force (RTF), working in close coordination with the OMG MARTE + specification group. + + In order to generalize its potential usage and alignment with other standardization efforts concerning quantities and units, the QU ontology has been further developed as a complement to the Agriculture Meteorology example showcasing the ontology developed by the W3C Semantic Sensor Networks incubator group (SSN-XG). + homepage: http://purl.oclc.org/NET/ssnx/qu/qu + id: lov.qu + name: Quantity Kinds and Units + prefix: qu + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.oclc.org/NET/ssnx/qu/qu#$1 +lov.qudt: + authority: lov + description: The QUDT, or 'Quantity, Unit, Dimension and Type' collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. + homepage: http://qudt.org/schema/qudt + id: lov.qudt + name: Quantities, Units, Dimensions and Types + prefix: qudt + source: lov.linkeddata.es + subjects: [] + uri_format: http://qudt.org/schema/qudt/$1 +lov.r-arco: + authority: lov + description: The ArCo module is the root of the network ArCo - Architecture of Knowledge. It imports all the other modules and models top-level distinctions from the cultural heritage domain. + homepage: https://w3id.org/arco/ontology/arco + id: lov.r-arco + name: ArCo Ontology (ArCo network) + prefix: r-arco + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: https://w3id.org/arco/ontology/arco/$1 +lov.r4r: + authority: lov + description: >- + R4R is a light-weight ontology for representing general relationships of + resource for publication and reusing. It asserts that a certain reusing + context occurred and determined by its two basic relations, namely, + isPackagedWith and isCitedBy. The isPackagedWith relation declares the + resource is ready to be reused by incorporating License and Provenance + information. The Cites relation is an exceptional to isCitedBy which occurs + only two related objects cite each other at the same time. Five resource + objects including article, data, code, provenance and license are major + class concepts to represent in this ontology. + + + The namespace for all R4R terms is http://guava.iis.sinica.edu.tw/r4r/ + homepage: http://guava.iis.sinica.edu.tw/r4r + id: lov.r4r + name: Relations for Reusing (R4R) Ontology + prefix: r4r + source: lov.linkeddata.es + subjects: [] + uri_format: http://guava.iis.sinica.edu.tw/r4r/$1 +lov.radion: + authority: lov + description: RADion, and the higher level vocabularies that build upon it, are intended as a model that facilitates federation and co-operation. It is not the primary intention that repository owners redesign or convert their current systems and data to conform to RADion, but rather that it acts as a common layer among repositories that want to exchange data. + homepage: http://www.w3.org/ns/radion# + id: lov.radion + name: Repository Asset Distribution + prefix: radion + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/radion#$1 +lov.rains: + authority: lov + description: An ontology to model accountability of AI systems which use machine learning. + homepage: https://w3id.org/rains + id: lov.rains + name: The RAInS Ontology + prefix: rains + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/rains#$1 +lov.rami: + authority: lov + description: A vocabulary which represents the Reference Architecture Model for Industry 4.0 (RAMI), including the concept of the Administration Shell I4.0 Component. + homepage: https://w3id.org/i40/rami/ + id: lov.rami + name: rami - Reference Architecture Model + prefix: rami + source: lov.linkeddata.es + subjects: [] + uri_format: http://iais.fraunhofer.de/vocabs/rami#$1 +lov.raul: + authority: lov + description: 'A vocabulary to describe Web form widgets. Strongly aligned with the meta model of HTML Web forms. A RESTful service that can render HTML Web forms from RaUL models can be found at: http://w3c.org.au/raul' + homepage: http://vocab.deri.ie/raul + id: lov.raul + name: RAUL Vocabulary + prefix: raul + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/NET/raul#$1 +lov.rb: + authority: lov + description: Ontology for describing datasets and profiles in the RiverBench benchmark suite. + homepage: https://w3id.org/riverbench/schema/metadata + id: lov.rb + name: RiverBench metadata ontology + prefix: rb + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: https://w3id.org/riverbench/schema/metadata#$1 +lov.rbdoc: + authority: lov + description: Ontology with metadata needed to generate documentation of datasets, distributions, profiles, etc. in RiverBench + homepage: https://w3id.org/riverbench/schema/documentation + id: lov.rbdoc + name: RiverBench documentation ontology + prefix: rbdoc + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: https://w3id.org/riverbench/schema/documentation#$1 +lov.rdaa: + authority: lov + description: The Agent properties element set consists of properties representing the attributes and relationships of the RDA Agent, Person, Family, and Corporate Body entities. Each property in the element set has a domain of the class representing one of these entities. + homepage: http://rdaregistry.info/Elements/a + id: lov.rdaa + name: RDA Agent properties + prefix: rdaa + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdaregistry.info/Elements/a/$1 +lov.rdac: + authority: lov + description: The Classes element set consists of classes representing the RDA entities, including Work, Expression, Manifestation, Item, Person, Family, Corporate Body, and Agent. + homepage: http://rdaregistry.info/Elements/c + id: lov.rdac + name: RDA Classes + prefix: rdac + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdaregistry.info/Elements/c/$1 +lov.rdae: + authority: lov + description: The Expression properties element set consists of properties representing the attributes and relationships of the RDA Expression entity. Each property in the element set has a domain of the class representing this entity. + homepage: http://rdaregistry.info/Elements/e + id: lov.rdae + name: RDA Expression properties + prefix: rdae + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdaregistry.info/Elements/e/$1 +lov.rdafrbr: + authority: lov + description: Defines the core RDA classes, including FRBR levels Work, Expression, Manifestation and Item. + homepage: http://rdvocab.info/uri/schema/FRBRentitiesRDA + id: lov.rdafrbr + name: FRBR Entities for RDA + prefix: rdafrbr + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdvocab.info/uri/schema/FRBRentitiesRDA/$1 +lov.rdag1: + authority: lov + description: This is the provisional registration of the RDA Group 1 Element Vocabulary, managed by the DCMI/RDA Task Group. + homepage: http://rdvocab.info/Elements + id: lov.rdag1 + name: RDA Group 1 Elements + prefix: rdag1 + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdvocab.info/Elements/$1 +lov.rdag2: + authority: lov + description: The second group of metadata elements defined by RDA + homepage: http://rdvocab.info/ElementsGr2 + id: lov.rdag2 + name: RDA Group 2 Elements + prefix: rdag2 + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdvocab.info/ElementsGr2/$1 +lov.rdag3: + authority: lov + description: This group of RDA elements defines preferred and variant names for concepts, places and events + homepage: http://rdvocab.info/ElementsGr3 + id: lov.rdag3 + name: RDA Group 3 Elements + prefix: rdag3 + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdvocab.info/ElementsGr3/$1 +lov.rdai: + authority: lov + description: The Item properties element set consists of properties representing the attributes and relationships of the RDA Item entity. + homepage: http://rdaregistry.info/Elements/i + id: lov.rdai + name: RDA Item properties + prefix: rdai + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdaregistry.info/Elements/i/$1 +lov.rdam: + authority: lov + description: The Manifestation properties element set consists of properties representing the attributes and relationships of the RDA Manifestation entity. + homepage: http://rdaregistry.info/Elements/m + id: lov.rdam + name: RDA Manifestation properties + prefix: rdam + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdaregistry.info/Elements/m/$1 +lov.rdarel: + authority: lov + description: A vocabulary defining a large variety of specific relationships between the various levels of the FRBR pile. + homepage: http://rdvocab.info/RDARelationshipsWEMI + id: lov.rdarel + name: RDA Relationships for Works, Expressions, Manifestations, Items + prefix: rdarel + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdvocab.info/RDARelationshipsWEMI/$1 +lov.rdarel2: + authority: lov + description: RDA Relationships for Persons, Corporate Bodies, Families + homepage: http://metadataregistry.org/uri/schema/RDARelationshipsGR2 + id: lov.rdarel2 + name: RDA Relationships GR2 + prefix: rdarel2 + source: lov.linkeddata.es + subjects: [] + uri_format: http://metadataregistry.org/uri/schema/RDARelationshipsGR2/$1 +lov.rdarole: + authority: lov + description: Defines possible roles linking agents to FRBR objects (works, expressions, manifestations, items) + homepage: http://rdvocab.info/roles + id: lov.rdarole + name: RDA Roles + prefix: rdarole + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdvocab.info/roles/$1 +lov.rdau: + authority: lov + description: The Unconstrained properties element set consists of properties representing the attributes and relationships of the all RDA entities. Each property in the element set has semantics which are independent of the FRBR model and has no specified domain or range. + homepage: http://rdaregistry.info/Elements/u + id: lov.rdau + name: RDA Unconstrained properties + prefix: rdau + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdaregistry.info/Elements/u/$1 +lov.rdaw: + authority: lov + description: The Work properties element set consists of properties representing the attributes and relationships of the RDA Work entity. + homepage: http://rdaregistry.info/Elements/w + id: lov.rdaw + name: RDA Work properties + prefix: rdaw + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://rdaregistry.info/Elements/w/$1 +lov.rdf: + authority: lov + description: This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts. + homepage: http://www.w3.org/1999/02/22-rdf-syntax-ns# + id: lov.rdf + name: The RDF Concepts Vocabulary + prefix: rdf + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/1999/02/22-rdf-syntax-ns#$1 +lov.rdfa: + authority: lov + description: This document describes the RDFa Vocabulary for Term and Prefix Assignment. The Vocabulary is used to modify RDFa 1.1 processing behavior + homepage: http://www.w3.org/ns/rdfa# + id: lov.rdfa + name: RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting + prefix: rdfa + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/rdfa#$1 +lov.rdfg: + authority: lov + description: Properties allowing statement of intensional equivalence between RDF graphs + homepage: http://www.w3.org/2004/03/trix/rdfg-1/ + id: lov.rdfg + name: Graph + prefix: rdfg + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2004/03/trix/rdfg-1/$1 +lov.rdfp: + authority: lov + description: >- + ## RDF Presentation and RDF Presentation Negotiation + + + An RDF graph can be presented in several ways, using different media types. Examples of RDF media types include `application/rdf+xml`, `text/turtle`, `application/json+ld`. + + + Today, most of the content consumed/produced/published, on the Web is not presented in RDF. + + + In the Web of Things, HTTP servers and clients would rather exchange lightweight documents, potentially binary. + + Currently, most existing RDF Presentations generically apply to any RDF graph, at the cost of being heavy text-based documents. + + Yet, lightweight HTTP servers/clients could be better satisfied with consuming/producing/publishing lightweight documents, may its structure be application-specific. + homepage: https://w3id.org/rdfp/ + id: lov.rdfp + name: The RDF Presentation ontology + prefix: rdfp + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/rdfp/$1 +lov.rdfs: + authority: lov + description: RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. + homepage: http://www.w3.org/2000/01/rdf-schema# + id: lov.rdfs + name: The RDF Schema vocabulary + prefix: rdfs + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2000/01/rdf-schema#$1 +lov.rdft: + authority: lov + description: >- + This is a vocabulary document and is used to define classes and properties + used in + RDF 1.1 Test Cases and associated test manifests. + The URI of the vocabulary is http://www.w3.org/ns/rdftest# (abbreviated by rdft: in this document). + Turtle and an JSON-LD versions of the vocabulary are also available. + The vocabulary is published by W3C. + homepage: http://www.w3.org/ns/rdftest + id: lov.rdft + name: The RDF 1.1 Test Vocabulary + prefix: rdft + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/rdftest#$1 +lov.react: + authority: lov + description: >- + The REACT ontology aims to represent all the necessary knowledge to support + the achievement of island energy independence through renewable energy + generation and storage, a demand response platform, and promoting user + engagement in a local energy community. + + + The REACT ontology has been developed as part of the REACT project which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 824395. + homepage: https://w3id.org/react + id: lov.react + name: The REACT Ontology + prefix: react + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://w3id.org/react#$1 +lov.rec: + authority: lov + description: The Recommendation Ontology specification provides basic concepts and properties for describing recommendations on/ for the Semantic Web. + homepage: http://purl.org/ontology/rec/core# + id: lov.rec + name: Recommendation Ontology + prefix: rec + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/rec/core#$1 +lov.rec54: + authority: lov + description: This is (the start of) an event-based model of the W3C process; e.g. RECdd is the class of Recommendation Director's Decisions; i.e. messages to w3c-ac-members announcing a new W3C Recommendation. + homepage: http://www.w3.org/2001/02pd/rec54# + id: lov.rec54 + name: Model of the W3C Process + prefix: rec54 + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2001/02pd/rec54#$1 +lov.reco: + authority: lov + description: The RECO ontology defines the vocabulary for representing preferences-as-constraints and preferences-as-ratings as RDF graphs. This lightweight vocabulary provides domain-independent means to describe user profiles in a coherent and context-aware way. RECO has been designed as an extension of both Friend-Of-A-Friend (FOAF) and Who Am I! (WAI) ontologies. + homepage: http://purl.org/reco# + id: lov.reco + name: RECommendations Ontology + prefix: reco + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/reco#$1 +lov.reegle: + authority: lov + description: Vocabulary used to describe clean energy actors, projects and technologies + homepage: http://reegle.info/schema + id: lov.reegle + name: Renewable Energy and Energy Efficiency + prefix: reegle + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://reegle.info/schema#$1 +lov.rel: + authority: lov + description: A vocabulary for describing relationships between people + homepage: http://purl.org/vocab/relationship/ + id: lov.rel + name: Relationship + prefix: rel + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocab/relationship/$1 +lov.remetca: + authority: lov + description: Ontology for poetry description + homepage: http://www.purl.org/net/remetca# + id: lov.remetca + name: ReMetCa Ontology + prefix: remetca + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://www.purl.org/net/remetca#$1 +lov.rev: + authority: lov + description: Vocabulary for expressing reviews and ratings + homepage: http://purl.org/stuff/rev# + id: lov.rev + name: Review Vocabulary + prefix: rev + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/stuff/rev#$1 +lov.rico: + authority: lov + description: >- + RiC-O (Records in Contexts-Ontology) is an OWL ontology for describing + archival record resources. As the second part of Records in Contexts standard, + it is a formal representation of Records in Contexts Conceptual Model (RiC-CM). + The current official version is v0.2; it is + compliant with RiC-CM v0.2 full draft, that will be published in February or + March 2021, and that is slightly different from RiC-CM + v0.2 preview, that was published in December 2019. + RiC-O provides a generic vocabulary and formal rules for creating RDF + datasets (or generating them from existing archival metadata) that describe in a + consistent way any kind of archival record resource. It can support publishing + RDF datasets as Linked Data, querying them using SPARQL, and making inferences + using the logic of the ontology. + homepage: https://www.ica.org/standards/RiC/ontology + id: lov.rico + name: International Council on Archives Records in Contexts Ontology (ICA RiC-O) + prefix: rico + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: https://www.ica.org/standards/RiC/ontology#$1 +lov.rlog: + authority: lov + description: This is a helper ontology for NIF 2.0 to be able to log errors and warning messages. + homepage: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog# + id: lov.rlog + name: RDF Logging Ontology + prefix: rlog + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#$1 +lov.ro: + authority: lov + description: This ontology shows how AO and ORE ontologies can be used together to define a ResearchObject. This ontology is further customized by the wf4ever ontology. + homepage: http://purl.org/wf4ever/ro + id: lov.ro + name: The Research Object Ontology + prefix: ro + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/wf4ever/ro#$1 +lov.roh: + authority: lov + description: An ontology to address the Research Management of the CRUE's Spanish University System (Sistema Universitario Español) by applying an encompassing model not only capable of addressing the universities of the CRUE but also more belonging to the European Union. + homepage: http://w3id.org/roh + id: lov.roh + name: The ASIO ontology + prefix: roh + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://w3id.org/roh#$1 +lov.rooms: + authority: lov + description: A simple vocabulary for describing the rooms in a building. + homepage: http://vocab.deri.ie/rooms + id: lov.rooms + name: Buildings and Rooms Vocabulary + prefix: rooms + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://vocab.deri.ie/rooms#$1 +lov.rov: + authority: lov + description: Le vocabulaire des organisations enregistrées est un profil de l'ontologie des organisations pour décrire les organisations ayant acquis un statut légal au travers d'un processus d'inscription formel, typiquement dans un registre national ou régional. + homepage: http://www.w3.org/ns/regorg + id: lov.rov + name: Registered Organization Vocabulary + prefix: rov + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/regorg#$1 +lov.rr: + authority: lov + description: A vocabulary which can be used to specify a mapping of relational data to RDF. + homepage: http://www.w3.org/ns/r2rml# + id: lov.rr + name: RDB to RDF Mapping Language Schema + prefix: rr + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/r2rml#$1 +lov.rsctx: + authority: lov + description: This ontology represent context which may be interesting in providing recommendations to users. + homepage: http://softeng.polito.it/rsctx + id: lov.rsctx + name: Recommender System Context + prefix: rsctx + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://softeng.polito.it/rsctx#$1 +lov.rss: + authority: lov + description: RDF Schema declaration for Rich Site Summary (RSS) 1.0 + homepage: http://purl.org/rss/1.0 + id: lov.rss + name: Vocabulary for Rich Site Summary (RSS) 1.0 + prefix: rss + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/rss/1.0/$1 +lov.rto: + authority: lov + description: The Rail Topology Ontology models foundational rail topology concepts.. + homepage: https://w3id.org/rail/topo# + id: lov.rto + name: Rail Topology Ontology + prefix: rto + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/rail/topo#$1 +lov.ru: + authority: lov + description: Draft for a recommendation for metadata on Representational Units (RU) which appear in ontologies. It is so far harmonized for implementation through owl annotation properties. + homepage: http://purl.org/imbi/ru-meta.owl + id: lov.ru + name: Representational Units Metadata Ontology + prefix: ru + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/imbi/ru-meta.owl#$1 +lov.ruto: + authority: lov + description: The Databugger ontology describes concepts used in Databugger, a test driven data-debugging framework that can run automatically generated (based on a schema) and manually generated test cases against an endpoint. + homepage: http://rdfunit.aksw.org/ns/core# + id: lov.ruto + name: Test-Driven Data Debugging Ontology + prefix: ruto + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdfunit.aksw.org/ns/core#$1 +lov.s4ac: + authority: lov + description: A lightweight vocabulary to create fine-grained access control policies for Linked Data. + homepage: http://ns.inria.fr/s4ac/v2 + id: lov.s4ac + name: Social Semantic SPARQL Security For Access Control Ontology + prefix: s4ac + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://ns.inria.fr/s4ac/v2#$1 +lov.s4agri: + authority: lov + description: This ontology extends the SAREF ontology for the Agricultural domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Agricultural domain. + homepage: https://saref.etsi.org/saref4agri/ + id: lov.s4agri + name: SAREF extension for Agriculture + prefix: s4agri + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + - computer and information sciences + uri_format: https://saref.etsi.org/saref4agri/$1 +lov.s4bldg: + authority: lov + description: This ontology extends the SAREF ontology for the building domain by defining building devices and how they are located in a building. This extension is based on the ISO 16739:2013 Industry Foundation Classes (IFC) standard for data sharing in the construction and facility management industries. The descriptions of the classes and properties extracted from IFC have been taken from the IFC documentation. + homepage: https://saref.etsi.org/saref4bldg/ + id: lov.s4bldg + name: SAREF extension for building devices + prefix: s4bldg + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://saref.etsi.org/saref4bldg/$1 +lov.s4city: + authority: lov + description: This ontology extends the SAREF ontology for the Smart City domain. This work has been developed in the context of the STF 534 (https://portal.etsi.org/STF/STFs/STFHomePages/STF534.aspx), which was established with the goal to create three SAREF extensions, one of them for the Smart City domain. + homepage: https://saref.etsi.org/saref4city/ + id: lov.s4city + name: SAREF extension for Smart City + prefix: s4city + source: lov.linkeddata.es + subjects: + - political sciences + - computer and information sciences + uri_format: https://saref.etsi.org/saref4city/$1 +lov.s4ehaw: + authority: lov + description: >- + The objective of SAREF4EHAW is to extend SAREF ontology for the + eHealth/Ageing-well (EHAW) vertical. Clause 4.1 of the present document + shortly introduces a high level view of the envisioned SAREF4EHAW semantic + model and modular ontology, with the retained concepts (i.e. classes) and + their relations. + + SAREF4EHAW extension has been specified and formalised by investigating EHAW domain related resources, as reported in ETSI TR 103 509, such as: potential stakeholders, standardization initiatives, alliances/associations, European projects, EC directives, existing ontologies, and data repositories. Therefore, SAREF4EHAW modular ontology shall both: + - Allow the implementation of a limited set of typical EHAW related use cases already identified in ETSI TR 103 509, i.e. + - Use case 1 ?elderly at home monitoring and support?, + - Use case 2 ?monitoring and support of healthy lifestyles for citizens?, + - Use case 3 ?Early Warning System (EWS) and Cardiovascular Accidents detection?. + - Fulfil the eHealth Ageing Well related requirements provided in ETSI TR 103 509, mainly the ontological ones that were mostly taken as input for the ontology specification. + + SAREF4EHAW mainly reuses the following existing ontologies: SAREF, ETSI SmartBAN reference model, SAREF 4 Environment extension and W3C SSN System module. The following figure presents the high level view of SAREF4EHAW ontology. + + ![SAREF4SYST overview](diagrams/SAREF4EHAW_Model.jpg) + + For semantic interoperability handling purposes, an ontology based solution, combined with sensing-as-a-service and WoT strategies, is retained for SAREF4EHAW. Therefore, an upper level ontology, at service level, shall also behas been fully modelled (Service class and sub-classes depicted in the previous figure). + + For embedded semantic analytics purposes, SAREF4EHAW shall behas been designed using the modularity principle (see ETSI TR 103 509) and can thus be mainly described by the following self-contained knowledge sub-ontologies (or modules): HealthActor, Ban, HealthDevice, Function (measured data related concepts included) and Service. + homepage: https://saref.etsi.org/saref4ehaw/ + id: lov.s4ehaw + name: 'SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain' + prefix: s4ehaw + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://saref.etsi.org/saref4ehaw/$1 +lov.s4ener: + authority: lov + description: This is the extension of SAREF for the EEBus and Energy@Home project. The documentation of SAREF4EE is available at http://ontology.tno.nl/SAREF4EE_Documentation_v0.1.pdf. SAREF4EE represents 1) The configuration information exchanged in the use case 'Remote Network Management' according to the EEBus Technical Report, Protocol Specification- Remote Network Management, version 1.0.0.2, 2015-09-19; 2) The scheduling information about power sequences exchanged in the use cases Appliance scheduling through CEM and remote start' and 'Automatic cycle rescheduling', according to the message structures described in General Message Structures, version 0.1.1, 2015-10-07; 3) The monitor and control information exchanged in the use case 'Communicate appliance status and info on manually planned cycles', according to the monitoring and control part of the Energy@Home Data Model, version 1.0; and 4) the event-based data exchanged in the use case 'Demand Response', according to General Message Structures, version 0.1.1, 2015-10-07. + homepage: https://saref.etsi.org/saref4ener/ + id: lov.s4ener + name: 'SAREF4EE: the EEbus/Energy@home extension of SAREF' + prefix: s4ener + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://saref.etsi.org/saref4ener/$1 +lov.s4envi: + authority: lov + description: This ontology extends the SAREF ontology for the environment domain, specifically for the light pollution domain, including concepts like photometers, light, etc. + homepage: https://saref.etsi.org/saref4envi/ + id: lov.s4envi + name: SAREF extension for environment + prefix: s4envi + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://saref.etsi.org/saref4envi/$1 +lov.s4inma: + authority: lov + description: SAREF4INMA is an extension of SAREF for the industry and manufacturing domain. SAREF4INMA focuses on extending SAREF for the industry and manufacturing domain to solve the lack of interoperability between various types of production equipment that produce items in a factory and, once outside the factory, between different organizations in the value chain to uniquely track back the produced items to the corresponding production equipment, batches, material and precise time in which they were manufactured. SAREF4INMA is specified and published by ETSI in the TS 103 410-5 associated to this ontology file. SAREF4INMA was created to be aligned with related initiatives in the smart industry and manufacturing domain in terms of modelling and standardization, such as the Reference Architecture Model for Industry 4.0 (RAMI), which combines several standards used by the various national initiatives in Europe that support digitalization in manufacturing. The full list of use cases, standards and requirements that guided the creation of SAREF4INMA are described in the associated ETSI TR 103 507. + homepage: https://saref.etsi.org/saref4inma/ + id: lov.s4inma + name: 'SAREF4INMA: an extension of SAREF for the industry and manufacturing domain' + prefix: s4inma + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://saref.etsi.org/saref4inma/$1 +lov.s4syst: + authority: lov + description: >- + The present document is the technical specification of SAREF4SYST, a generic + extension of [ETSI TS 103 264 + SAREF](https://www.etsi.org/deliver/etsi_ts/103200_103299/103264/02.01.01_60/ts_103264v020101p.pdf) + that defines an ontology pattern which can be instantiated for different + domains. SAREF4SYST defines Systems, Connections between systems, and + Connection Points at which systems may be connected. These core concepts can + be used generically to define the topology of features of interest, and can + be specialized for multiple domains. The topology of features of interest is + highly important in many use cases. If a room holds a lighting device, and + if it is adjacent with an open window to a room whose luminosity is low, + then by turning on the lighting device in the former room one may expect + that the luminosity in the latter room will rise. + + + The SAREF4SYST ontology pattern can be instantiated for different domains. For example to describe zones inside a building (systems), that share a frontier (connections). Properties of systems are typically state variables (e.g. agent population, temperature), whereas properties of connections are typically flows (e.g. heat flow). + + + SAREF4SYST has two main aims: on the one hand, to extend SAREF with the capability or representing general topology of systems and how they are connected or interact and, on the other hand, to exemplify how ontology patterns may help to ensure an homogeneous structure of the overall SAREF ontology and speed up the development of extensions. + + + SAREF4SYST consists both of a core ontology, and guidelines to create ontologies following the SAREF4SYST ontology pattern. The core ontology is a lightweight OWL-DL ontology that defines 3 classes and 9 object properties. + + + Use cases for ontology patterns are described extensively in [ETSI TR 103 549 Clauses 4.2 and 4.3](https://www.etsi.org/deliver/etsi_tr/103500_103599/103549/01.01.01_60/tr_103549v010101p.pdf). + + + For the Smart Energy domain: + + + - Electric power systems can exchange electricity with other electric power systems. The electric energy can flow both ways in some cases (from the Public Grid to a Prosumer), or in only one way (from the Public Grid to a Load). Electric power systems can be made up of different sub-systems. Generic sub-types of electric power systems include producers, consumers, storage systems, transmission systems. + + - Electric power systems may be connected one to another through electrical connection points. An Electric power system may have multiple connection points (Multiple Winding Transformer generally have one single primary winding with two or more secondary windings). Generic sub-types of electrical connection points include plugs, sockets, direct-current, single-phase, three-phase, connection points. + + - An Electrical connection may exist between two Electric power systems at two of their respective connection points. Generic sub-types of electrical connections include Single-phase Buses, Three-phase Buses. A single-phase electric power system can be connected using different configurations at a three-phase bus (RN, SN, TN types). + + + For the Smart Building domain: + + + - Buildings, Storeys, Spaces, are different sub-types of Zones. Zones can contain sub-zones. Zones can be adjacent or intersect with other zones. + + - Two zones may share one or more connections. For example some fresh air may be created inside a storey if it has two controllable openings to the exterior at different cardinal points. + + + A graphical overview of the SAREF4SYST ontology is provided in Figure 1. In such figure: + + + - Rectangles are used to denote Classes. The label of the rectangle is the identifier of the Class. + + - Plain arrows are used to represent Object Properties between Classes. The label of the arrow is the identifier of the Object Property. The origin of the arrow is the domain Class of the property, and the target of the arrow is the range Class of the property. + + - Dashed arrows with identifiers between stereotype signs (i.e. "`<< >>`") refer to OWL axioms that are applied to some property. Four pairs of properties are inverse one of the other; the property `s4syst:connectedTo` is symmetric, and properties `s4syst:hasSubSystem` and `s4syst:hasSubSystem` are transitive. + + - A symbol =1 near the target of an arrow denotes that the associated property is functional. A symbol ? denotes a local existential restriction. + + + + ![SAREF4SYST overview](diagrams/overview.png) + homepage: https://saref.etsi.org/saref4syst/ + id: lov.s4syst + name: 'SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections' + prefix: s4syst + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://saref.etsi.org/saref4syst/$1 +lov.s4watr: + authority: lov + description: This ontology extends the SAREF ontology for the water domain. This work has been developed in the context of the STF 566, which was established with the goal to create three SAREF extensions, one of them for the water domain. + homepage: https://saref.etsi.org/saref4watr/ + id: lov.s4watr + name: SAREF extension for water + prefix: s4watr + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://saref.etsi.org/saref4watr/$1 +lov.s4wear: + authority: lov + description: SAREF4WEAR is an extension of SAREF for Wearables + homepage: https://saref.etsi.org/saref4wear/ + id: lov.s4wear + name: 'SAREF4WEAR: an extension of SAREF for Wearables' + prefix: s4wear + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://saref.etsi.org/saref4wear/$1 +lov.sam: + authority: lov + description: An OWL representation of the Sampling Features Schema described in clauses 8-10 of ISO 19156:2011 Geographic Information - Observations and Measurements. + homepage: http://def.seegrid.csiro.au/isotc211/iso19156/2011/sampling + id: lov.sam + name: The Sampling Features Schema Vocabulary + prefix: sam + source: lov.linkeddata.es + subjects: [] + uri_format: http://def.seegrid.csiro.au/isotc211/iso19156/2011/sampling#$1 +lov.samfl: + authority: lov + description: A simple OWL representation of the Sampling Features Schema described in clauses 9-11 of ISO 19156:2011 Geographic Information - Observations and Measurements + homepage: http://def.seegrid.csiro.au/ontology/om/sam-lite + id: lov.samfl + name: OWL for Sampling Features + prefix: samfl + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://def.seegrid.csiro.au/ontology/om/sam-lite#$1 +lov.san: + authority: lov + description: >- + This ontology is intended to describe Semantic Actuator Networks, as a + counterpoint to SSN definition of Semantic Sensor Networks. An actuator is a + physical device having an effect on the world (see Actuator for more + information). + + + It is worth noticing that some concepts are imported from SSN, but not SSN as a whole. This is a design choice intended to separate as much as possible the definition on actuator from the definition of sensor, which are completely different concept that can be used independantly from each other. + + + This ontology is used as a ontological module in IoT-O ontology. + homepage: http://www.irit.fr/recherches/MELODI/ontologies/SAN + id: lov.san + name: SAN (Semantic Actuator Network) + prefix: SAN + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.irit.fr/recherches/MELODI/ontologies/SAN#$1 +lov.san-lod: + authority: lov + description: SAN Ontology + homepage: http://dati.san.beniculturali.it/SAN/ + id: lov.san-lod + name: SAN Ontologia + prefix: san-lod + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://dati.san.beniculturali.it/SAN/$1 +lov.sao: + authority: lov + description: The SALT Annotation Ontology represents the connection layer between the rhetorical and argumentation and the document structure and content + homepage: http://salt.semanticauthoring.org/ontologies/sao + id: lov.sao + name: SALT Annotation Ontology + prefix: sao + source: lov.linkeddata.es + subjects: [] + uri_format: http://salt.semanticauthoring.org/ontologies/sao#$1 +lov.saont: + authority: lov + description: An ontology to model accountability of generic systems. + homepage: https://w3id.org/sao + id: lov.saont + name: The System Accountability Ontology + prefix: saont + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/sao#$1 +lov.saref: + authority: lov + description: The Smart Appliances REFerence (SAREF) ontology is a shared model of consensus that facilitates the matching of existing assets (standards/protocols/datamodels/etc.) in the smart appliances domain. The SAREF ontology provides building blocks that allow separation and recombination of different parts of the ontology depending on specific needs. + homepage: https://saref.etsi.org/core/ + id: lov.saref + name: 'SAREF: the Smart Appliances REFerence ontology' + prefix: saref + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://saref.etsi.org/core/$1 +lov.saws: + authority: lov + description: Ontology for the Sharing Ancient Wisdoms (SAWS) project, to represent the information and knowledge available in medieval gnomologia (collections of wise sayings). SAWS concentrates mainly on Ancient Greek and Arabic manuscripts containing wisdom literature. All class descriptions are provided by domain experts and the ontology has been developed through collaboration between these experts and ontology developers. + homepage: http://purl.org/saws/ontology + id: lov.saws + name: Sharing Ancient Wisdoms Ontology + prefix: saws + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://purl.org/saws/ontology#$1 +lov.sbeo: + authority: lov + description: >- + Smart Building Evacuation Ontology (SBEO) is an ontology that couples the + information about any building with its occupants such that it can be used + in many useful ways. For example, indoor localization of people, detection + of any hazard, a recommendation of normal routes such as shopping or stadium + seating routes, or safe and feasible emergency evacuation routes or both of + them all together. + + + The core SBEO covers the concepts related to the geometry of building, devices and components of the building, route graphs correspondent to the building topology, users' characteristics and preferences, situational awareness of both building (hazard detection, status of routes in terms of availability and occupancy) and users (tracking, management of groups, status in terms of fitness), and emergency evacuation. + homepage: https://w3id.org/sbeo + id: lov.sbeo + name: 'SBEO: Smart Building Evacuation Ontology' + prefix: sbeo + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://w3id.org/sbeo#$1 +lov.schema: + authority: lov + description: Search engines including Bing, Google, Yahoo! and Yandex rely on schema.org markup to improve the display of search results, making it easier for people to find the right web pages. + homepage: http://schema.org/ + id: lov.schema + name: Schema.org vocabulary + prefix: schema + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://schema.org/$1 +lov.scip: + authority: lov + description: A vocabulary for description of scientific people, focused on bio sciences + homepage: http://lod.taxonconcept.org/ontology/sci_people.owl + id: lov.scip + name: Scientific People Ontology + prefix: scip + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://lod.taxonconcept.org/ontology/sci_people.owl#$1 +lov.scoro: + authority: lov + description: SCoRO, the Scholarly Contributions and Roles Ontology, is an ontology for use by authors and publishers for describing the contributions that may be made and the roles that may be held by a person with respect to a journal article or other publication, and by research administrators and others for describing contributions and roles with respect to other aspects of scholarly research. + homepage: http://purl.org/spar/scoro/ + id: lov.scoro + name: Scholarly Contributions and Roles Ontology + prefix: scoro + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://purl.org/spar/scoro/$1 +lov.scot: + authority: lov + description: SCOT is an ontology for describing the structure and the semantics for tagging data across heterogenous users, sources, and applications. + homepage: http://rdfs.org/scot/ns# + id: lov.scot + name: Social Semantic Cloud of Tags + prefix: scot + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdfs.org/scot/ns#$1 +lov.scovo: + authority: lov + description: A vocabulary for representing statistical data on the Web. Note :The SCOVO vocabulary is deprecated. We strongly advise to use the Data Cube Vocabulary instead. + homepage: http://vocab.deri.ie/scovo + id: lov.scovo + name: The Statistical Core Vocabulary + prefix: scovo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/NET/scovo#$1 +lov.scsv: + authority: lov + description: Mapping vocabulary for CSV files that use Schema.org terms in the header. + homepage: http://vocab.deri.ie/scsv + id: lov.scsv + name: Schema.org CSV + prefix: scsv + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/NET/schema-org-csv#$1 +lov.sd: + authority: lov + description: Un vocabulaire pour décrire des services SPARQL publiés via le protocole SPARQL 1.1 pour RDF. Ces descriptions fournissent un mécanisme par lequel un client ou un utilisateur final peuvent obtenir des informations sur le service SPARQL, telles que les extensions de fonctions supportées ou les détails à propos des jeux de données disponibles. + homepage: http://www.w3.org/ns/sparql-service-description + id: lov.sd + name: SPARQL 1.1 Service Description + prefix: sd + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/sparql-service-description#$1 +lov.sdm: + authority: lov + description: A small vocabulary for representing SPARQL endpoint metadata on the web + homepage: https://w3id.org/vocab/sdm + id: lov.sdm + name: SPARQL endpoint metadata + prefix: sdm + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/vocab/sdm#$1 +lov.sdmx: + authority: lov + description: This vocabulary extends the data cube vocabulary to support publication of statistical data in RDF, using an information model based on SDMX + homepage: http://purl.org/linked-data/sdmx + id: lov.sdmx + name: SDMX-RDF vocabulary + prefix: sdmx + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/linked-data/sdmx#$1 +lov.sdmx-code: + authority: lov + description: Defines subclasses and instances of codes used in SDMX, such as currencies, decimals, frequencies ... + homepage: http://purl.org/linked-data/sdmx/2009/code + id: lov.sdmx-code + name: SDMX Code + prefix: sdmx-code + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/linked-data/sdmx/2009/code#$1 +lov.sdmx-dimension: + authority: lov + description: Defines dimensions for the statistical "cubes" defined by SDMX + homepage: http://purl.org/linked-data/sdmx/2009/dimension + id: lov.sdmx-dimension + name: SDMX Dimension + prefix: sdmx-dimension + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/linked-data/sdmx/2009/dimension#$1 +lov.sdo: + authority: lov + description: The SALT Document Ontology captures the linear structure of the publication, in addition to the identification and revisioning information of the publication's content. + homepage: http://salt.semanticauthoring.org/ontologies/sdo + id: lov.sdo + name: SALT Document Ontology + prefix: sdo + source: lov.linkeddata.es + subjects: + - other humanities + uri_format: http://salt.semanticauthoring.org/ontologies/sdo#$1 +lov.sealit: + authority: lov + description: The SeaLiT Ontology is a formal ontology intended to facilitate the integration, mediation and interchange of heterogeneous information related to maritime history. It aims at providing the semantic definitions needed to transform disparate, localised information sources of maritime history into a coherent global resource. It also serves as a common language for domain experts and IT developers to formulate requirements and to agree on system functionalities with respect to the correct handling of historical information. The ontology uses and extends the CIDOC Conceptual Reference Model (ISO 21127:2014), in particular version 7.1.1, as a general ontology of human activity, things and events happening in space and time. + homepage: http://www.sealitproject.eu/ontology/ + id: lov.sealit + name: SeaLiT Ontology + prefix: sealit + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.sealitproject.eu/ontology/$1 +lov.search: + authority: lov + description: A vocabulary for ranked search results, for use in the Sindice API. + homepage: http://vocab.deri.ie/search + id: lov.search + name: Sindice Search Vocabulary + prefix: search + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://sindice.com/vocab/search#$1 +lov.seas: + authority: lov + description: This vocabulary is version v0.1 of the ITEA2 Smart Energy Aware Systems project vocabulary. It enables the description of electricity measurements of a site using the Data Cube W3C vocabulary. + homepage: https://w3id.org/seas/ + id: lov.seas + name: SEAS ontology + prefix: seas + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/seas/$1 +lov.seas-eval: + authority: lov + description: >- + The Evaluation ontology describes evaluation of + [`seas:Property`ies](https://w3id.org/seas/Property). There may be: + + + - direct evaluations, or + + - qualified evaluations. + homepage: https://w3id.org/seas/EvaluationOntology + id: lov.seas-eval + name: The SEAS Evaluation ontology + prefix: seas-eval + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/seas/$1 +lov.seas-op: + authority: lov + description: The SEAS Operating Ontology defines evaluations of operating features of interest. + homepage: https://w3id.org/seas/OperatingOntology + id: lov.seas-op + name: The SEAS Failable System ontology + prefix: seas-op + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/seas/$1 +lov.seas-qudt: + authority: lov + description: This ontology defines proposed alignemnts with the QUDT ontology. + homepage: https://w3id.org/seas/QUDTAlignment + id: lov.seas-qudt + name: QUDT Alignment. + prefix: seas-qudt + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/seas/$1 +lov.seas-stats: + authority: lov + description: This ontology defines common evaluation interpretation concepts for statistics. + homepage: https://w3id.org/seas/StatisticsOntology + id: lov.seas-stats + name: The SEAS Statistics ontology. + prefix: seas-stats + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/seas/$1 +lov.seas-sys: + authority: lov + description: >- + The System Ontology defines Systems, Connections between systems, and + Connection Points at which systems may be connected. This ontology is then + specialized for multiple domains. For example: + + + - In electric energy: + - power systems consume, produce, store, and exchange electricity; + - power connections are where electricity flows between systems; + - power connection points are plugs, sockets, or power busses. + - In the electricity market: + - players and markets are systems; + - connections are contracts or transactions between two players, or between a player and a market; + - connection points include offers and bids. + homepage: https://w3id.org/seas/SystemOntology + id: lov.seas-sys + name: The SEAS System ontology + prefix: seas-sys + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/seas/$1 +lov.seasb: + authority: lov + description: This ontology defines batteries and their state of charge ratio property. + homepage: https://w3id.org/seas/BatteryOntology + id: lov.seasb + name: The SEAS Battery ontology. + prefix: seasb + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://w3id.org/seas/$1 +lov.seasbo: + authority: lov + description: >- + The SEAS Building ontology describes a taxonomy of buildings, building + spaces, and rooms. + + + Some categorizations are based on the energy efficiency related to their insulation etc., although the actual values for classes depend the country specific regulations and geographical locations. + + + Other categorizations are based on occupancy and activities. There is no single accepted categorization available. This taxonomy uses some types selected from: + + + - International building occupancy based categories (USA) + + - The Classification of Types of Constructions (EU) + + - Finnish building categorization VTJ2000 (Finland) + + - Wikipedia category page for Rooms: https://en.wikipedia.org/wiki/Category:Rooms + homepage: https://w3id.org/seas/BuildingOntology + id: lov.seasbo + name: The SEAS Building Ontology + prefix: seasbo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://w3id.org/seas/$1 +lov.seasd: + authority: lov + description: The SEAS Device ontology defines `seas:Device` as physical system that are designed to execute one or more procedures that involve the physical world. + homepage: https://w3id.org/seas/DeviceOntology + id: lov.seasd + name: The SEAS Device ontology + prefix: seasd + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://w3id.org/seas/$1 +lov.seasfo: + authority: lov + description: The SEAS Forecasting ontology extends the [Procedure Execution ontology (PEP)](https://w3id.org/pep/) + homepage: https://w3id.org/seas/ForecastingOntology + id: lov.seasfo + name: The SEAS Forecasting ontology + prefix: seasfo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://w3id.org/seas/$1 +lov.seast: + authority: lov + description: >- + This ontology defines: + + - a set of subclasses of `seas:Evaluation` to better interpret evaluations of quantifiable properties. + + - a set of sub properties of `seas:hasProperty` to qualify time-related properties. + homepage: https://w3id.org/seas/TimeOntology + id: lov.seast + name: The SEAS Time Ontology. + prefix: seast + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://w3id.org/seas/$1 +lov.seasto: + authority: lov + description: >- + The Seas Trading Ontology defines concepts and relations to describe + ownership, trading, bilateral contracts and market licenses: + + + - players own systems and trade commodities, which have a price; + + - bilateral electricity contracts are connections between electricity traders at which they exchange + + electricity; + + - electricity markets are connections between electricity traders at which they exchange electricity, + + using a market license; + + - electricity markets can be cleared, and balanced; + + - evaluations can have a traded volume validity context + homepage: https://w3id.org/seas/TradingOntology + id: lov.seasto + name: The SEAS Trading ontology + prefix: seasto + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: https://w3id.org/seas/$1 +lov.security: + authority: lov + description: A security ontology to annotate resources with security-related information + homepage: http://securitytoolbox.appspot.com/securityMain + id: lov.security + name: Security Ontology + prefix: security + source: lov.linkeddata.es + subjects: [] + uri_format: http://securitytoolbox.appspot.com/securityMain#$1 +lov.sem: + authority: lov + description: 'The SEM Ontology defines entities that make up the context of an event: Events, Actors, Places, Times.' + homepage: http://semanticweb.cs.vu.nl/2009/11/sem/ + id: lov.sem + name: The SEM Ontology + prefix: sem + source: lov.linkeddata.es + subjects: [] + uri_format: http://semanticweb.cs.vu.nl/2009/11/sem/$1 +lov.semio: + authority: lov + description: A vocabulary to describe signs in a semiotic approach + homepage: http://www.lingvoj.org/semio.rdf + id: lov.semio + name: Semio, an ontology of signs + prefix: semio + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.lingvoj.org/semio#$1 +lov.semiotics: + authority: lov + description: >- + A content ontology pattern that encodes a basic semiotic theory, by reusing + the situation pattern. The basic classes are: Expression, Meaning, Reference + (the semiotic triangle), LinguisticAct (for the pragmatics), and Agent. + + A linguistic act is said to be context for expressions, with their meanings and references, and agents involved. + + Based on this pattern, several specific linguistic acts, such as 'tagging', 'translating', 'defining', 'formalizing', etc. can be defined, so constituting a formal vocabulary for a pragmatic web. + homepage: http://www.ontologydesignpatterns.org/cp/owl/semiotics.owl + id: lov.semiotics + name: A content ontology pattern that encodes a basic semiotic theory, by reusing the situation pattern. + prefix: semiotics + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.ontologydesignpatterns.org/cp/owl/semiotics.owl#$1 +lov.semsur: + authority: lov + description: SemSur, the Semantic Survey Ontology, is a core ontology for describing individual research problems, approaches, implementations and evaluations in a structured, comparable way. + homepage: http://purl.org/SemSur/ + id: lov.semsur + name: The Semantic Survey Ontology (semsur) + prefix: semsur + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/SemSur/$1 +lov.seo: + authority: lov + description: The vocabulary allows for the description of data about scientific events such as conferences, symposiums and workshops. + homepage: https://w3id.org/seo + id: lov.seo + name: The Scientific Events Ontology + prefix: seo + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: https://w3id.org/seo#$1 +lov.seq: + authority: lov + description: Intended to represent sequence schemas. It defines the notion of transitive and intransitive precedence and their inverses. It can then be used between tasks, processes, time intervals, spatially locate objects, situations, etc. + homepage: http://www.ontologydesignpatterns.org/cp/owl/sequence.owl + id: lov.seq + name: Sequence Pattern + prefix: seq + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/cp/owl/sequence.owl#$1 +lov.service: + authority: lov + description: A micro-ontology that defines the general concept of a service. + homepage: http://purl.org/ontology/service + id: lov.service + name: The Service Ontology + prefix: service + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/service#$1 +lov.sf: + authority: lov + description: A specification of GeoSPARQL for simple features geometries (points, lines, polygons ...) + homepage: http://www.opengis.net/ont/sf + id: lov.sf + name: Simplified Features Geometry + prefix: sf + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://www.opengis.net/ont/sf#$1 +lov.sh: + authority: lov + description: This vocabulary defines terms used in SHACL, the W3C Shapes Constraint Language. + homepage: http://www.w3.org/ns/shacl# + id: lov.sh + name: W3C Shapes Constraint Language (SHACL) Vocabulary + prefix: sh + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/shacl#$1 +lov.shoah: + authority: lov + description: The ontology describing the Shoah domain, proposed here in beta version, aims to formally describe concepts and relationships that characterize the process of persecution and deportation of Jews in Italy between 1943 and 1945. + homepage: http://dati.cdec.it/lod/shoah/ + id: lov.shoah + name: Shoah Vocabulary Specification + prefix: shoah + source: lov.linkeddata.es + subjects: [] + uri_format: http://dati.cdec.it/lod/shoah/$1 +lov.shw: + authority: lov + description: An ontology defining weather-related concepts and properties being relevant to smart home systems that provide predictive control. + homepage: http://paul.staroch.name/thesis/SmartHomeWeather.owl# + id: lov.shw + name: Smart Home Weather + prefix: shw + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: http://paul.staroch.name/thesis/SmartHomeWeather.owl#$1 +lov.sim: + authority: lov + description: An ontology to describe associations between things. Although this ontology was designed with music similarity in mind, it can readily be applied to other domains. + homepage: http://purl.org/ontology/similarity/ + id: lov.sim + name: The Similarity Ontology + prefix: sim + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/similarity/$1 +lov.simu: + authority: lov + description: This ontology was designed to conceptualize symbolic meanings following Baudrillard's Simulacra and Simulation theory. Symbols, their meaning, the context in which the symbolic meaning (or simulation) exists and the source of the simulation are linked to a N-ary Simulation Class. + homepage: https://www.w3id.org/simulation/ontology/ + id: lov.simu + name: Simulation Ontology + prefix: simu + source: lov.linkeddata.es + subjects: + - generic + uri_format: https://www.w3id.org/simulation/ontology/$1 +lov.sio: + authority: lov + description: The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. + homepage: http://semanticscience.org/ontology/sio.owl + id: lov.sio + name: Semanticscience Integrated Ontology + prefix: sio + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://semanticscience.org/resource/$1 +lov.sioc: + authority: lov + description: SIOC is an ontology for describing the information in online communities. + homepage: http://rdfs.org/sioc/ns# + id: lov.sioc + name: Semantically-Interlinked Online Communities + prefix: sioc + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdfs.org/sioc/ns#$1 +lov.situ: + authority: lov + description: A pattern to represent contexts or situations, and the things that are contextualized. + homepage: http://www.ontologydesignpatterns.org/cp/owl/situation.owl + id: lov.situ + name: Situation Pattern + prefix: situ + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/cp/owl/situation.owl#$1 +lov.skos: + authority: lov + description: The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. + homepage: http://www.w3.org/2004/02/skos/core + id: lov.skos + name: Simple Knowledge Organization System + prefix: skos + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2004/02/skos/core#$1 +lov.skosxl: + authority: lov + description: SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities. + homepage: http://www.w3.org/2008/05/skos-xl + id: lov.skosxl + name: SKOS eXtension for Labels + prefix: skosxl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2008/05/skos-xl#$1 +lov.smg: + authority: lov + description: A Profile of the IEC Common Information Model for Smart Grids, developed by the Cerise-SG project. + homepage: http://ns.cerise-project.nl/energy/def/cim-smartgrid + id: lov.smg + name: CERISE CIM Profile for Smart Grids + prefix: smg + source: lov.linkeddata.es + subjects: [] + uri_format: http://ns.cerise-project.nl/energy/def/cim-smartgrid#$1 +lov.snarm: + authority: lov + description: This ontology is designed for representing access rights within a simple network of associated users/groups + homepage: http://rdf.myexperiment.org/ontologies/snarm/ + id: lov.snarm + name: Simple Network Access Rights Management Ontology + prefix: snarm + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://rdf.myexperiment.org/ontologies/snarm/$1 +lov.solid: + authority: lov + description: Solid terms + homepage: http://www.w3.org/ns/solid/terms + id: lov.solid + name: Solid terms + prefix: solid + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://www.w3.org/ns/solid/terms#$1 +lov.sor: + authority: lov + description: The Social Relationships ONtology (SORON) attempts to describe the different types of social relationships in society (both objective and subjective). Current version focuses on inter-personal 1:1 relationships (except family relationships). Other types of relationships may be covered in later versions. It complements FOAF and RELATIONSHIP ontologies. + homepage: http://purl.org/net/soron + id: lov.sor + name: 'SORON: Social Relationships ONtology' + prefix: sor + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/soron/$1 +lov.sosa: + authority: lov + description: This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group. + homepage: http://www.w3.org/ns/sosa/ + id: lov.sosa + name: Sensor, Observation, Sample, and Actuator (SOSA) Ontology + prefix: sosa + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: http://www.w3.org/ns/sosa/$1 +lov.sp: + authority: lov + description: An RDF Schema to syntactically represent SPARQL queries (including SPARQL UPDATE) as RDF triples. + homepage: http://spinrdf.org/sp + id: lov.sp + name: SPIN SPARQL Syntax + prefix: sp + source: lov.linkeddata.es + subjects: [] + uri_format: http://spinrdf.org/sp#$1 +lov.spatial: + authority: lov + description: A vocabulary for describing topological relations between features + homepage: http://geovocab.org/spatial + id: lov.spatial + name: NeoGeo Spatial Ontology + prefix: spatial + source: lov.linkeddata.es + subjects: + - mathematics + uri_format: http://geovocab.org/spatial#$1 +lov.spcm: + authority: lov + description: La planificación y monitorización de la ejecución de proyectos software puede llevarse a cabo con diferentes herramientas, desde sistemas basados en gestión de tareas, hasta herramientas especializadas en diagramas de Gantt o incluso mediante simples hojas de cálculo. Este vocabulario contempla los elementos típicos a la hora de controlar los proyectos de desarrollo o mantenimiento de software. + homepage: http://spi-fm.uca.es/spdef/models/deployment/spcm/1.0 + id: lov.spcm + name: Software Process Control Model + prefix: spcm + source: lov.linkeddata.es + subjects: [] + uri_format: http://spi-fm.uca.es/spdef/models/deployment/spcm/1.0#$1 +lov.spfood: + authority: lov + description: Defines concepts and properties specific for the SmartProducts Philips use case (cooking domain). + homepage: http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl + id: lov.spfood + name: SmartProducts Food Domain Model + prefix: spfood + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://kmi.open.ac.uk/projects/smartproducts/ontologies/food.owl#$1 +lov.spin: + authority: lov + description: An RDF Schema that can be used to attach constraints and rules to RDFS classes, and to encapsulate reusable SPARQL queries into functions and templates. + homepage: http://spinrdf.org/spin + id: lov.spin + name: SPIN Inferencing Vocabulary + prefix: spin + source: lov.linkeddata.es + subjects: [] + uri_format: http://spinrdf.org/spin#$1 +lov.sport: + authority: lov + description: A simple ontology for representing competitive sports events. + homepage: http://www.bbc.co.uk/ontologies/sport + id: lov.sport + name: BBC Sport Ontology + prefix: sport + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.bbc.co.uk/ontologies/sport/$1 +lov.spt: + authority: lov + description: TheSPITFIRE Ontology (spt) is based on the alignment among Dolce+DnS Ultralite(dul), the W3C Semantic Sensor Network ontology (ssn) and the Event Model-F ontology (event). + homepage: http://spitfire-project.eu/ontology/ns + id: lov.spt + name: SPITFIRE Ontology + prefix: spt + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://spitfire-project.eu/ontology/ns/$1 +lov.spvqa: + authority: lov + description: The ontology is aimed at the support of research groups in the field of Business Modeling and Knowledge Engineering (BMaKE) in their collaborative work for qualitatively analyzing scholarly papers as well as sharing the results of that analyses and judgements. + homepage: https://bmake.th-brandenburg.de/spv + id: lov.spvqa + name: Scholarly Papers Vocabulary with Focus on Qualtitative Analysis + prefix: spvqa + source: lov.linkeddata.es + subjects: [] + uri_format: https://bmake.th-brandenburg.de/spv#$1 +lov.sql: + authority: lov + description: The SQL AST Vocabulary allows SQL code abstract syntax trees to be published in RDF. + homepage: http://ns.inria.fr/ast/sql# + id: lov.sql + name: SQL Abstract Syntax Trees Vocabulary + prefix: sql + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://ns.inria.fr/ast/sql#$1 +lov.ssn: + authority: lov + description: This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports. + homepage: http://www.w3.org/ns/ssn/ + id: lov.ssn + name: Semantic Sensor Network Ontology + prefix: ssn + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3.org/ns/ssn/$1 +lov.ssno: + authority: lov + description: This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports. + homepage: http://www.w3.org/ns/ssn/ + id: lov.ssno + name: Semantic Sensor Network Ontology + prefix: ssno + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3.org/ns/ssn/$1 +lov.ssso: + authority: lov + description: An event-based RDF ontology for typical status in fulfillment of a service + homepage: http://purl.org/ontology/ssso + id: lov.ssso + name: Simple Service Status Ontology + prefix: ssso + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/ssso#$1 +lov.st: + authority: lov + description: This ontology provides the predicates necessary to describe an arrival of a transit vehicle and its departure at a certain Stop. + homepage: http://semweb.mmlab.be/ns/stoptimes#Ontology + id: lov.st + name: The Stop Times ontology + prefix: st + source: lov.linkeddata.es + subjects: [] + uri_format: http://semweb.mmlab.be/ns/stoptimes#$1 +lov.stac: + authority: lov + description: 'A vocabulary to describe main security and cryptographic concepts: attacks, security mechanisms, OSI model, security protocols, security tools in numerous technologies: Web applications, network management, Sensor networks, Cellular (2G, 3G, 4G) and Wireless (Wifi), etc.' + homepage: http://securitytoolbox.appspot.com/stac + id: lov.stac + name: 'Security Toolbox : Attacks and Countermeasures' + prefix: stac + source: lov.linkeddata.es + subjects: [] + uri_format: http://securitytoolbox.appspot.com/stac#$1 +lov.step: + authority: lov + description: A lightweight ontology for representing semantic trajectories and contextual elements in terms of features of interests and episodes. + homepage: http://purl.org/net/step + id: lov.step + name: Semantic Trajectory Episodes + prefix: step + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://purl.org/net/step#$1 +lov.sto: + authority: lov + description: A vocabulary to describe the relation between standards in use on the Industry 4.0, and related concepts + homepage: https://w3id.org/i40/sto# + id: lov.sto + name: i40 Standards Lanscape Vocabulary + prefix: sto + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/i40/sto#$1 +lov.stories: + authority: lov + description: The Stories ontology was developed in collaboration with the BBC, with an aim to creating an ontology for narrative representation that could be applied across a diverse set of cases. These included accounts of events in Northern Ireland, the storylines of Doctor Who episodes, and key events of the Battle of Britain. + homepage: http://purl.org/ontology/stories/ + id: lov.stories + name: Stories Ontology + prefix: stories + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/stories/$1 +lov.summa: + authority: lov + description: The SUMMA Vocabulary enables to request and represent summarized RDf resources. It should be used in context to the SUMMA API definition. + homepage: http://purl.org/voc/summa/ + id: lov.summa + name: SUMMA Vocabulary + prefix: summa + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/voc/summa/$1 +lov.sur: + authority: lov + description: Ontology for surveys based on the Coney data model. + homepage: https://www.w3id.org/survey-ontology + id: lov.sur + name: The Survey Ontology + prefix: sur + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/survey-ontology#$1 +lov.sw-quality: + authority: lov + description: Quality, architecture, and process are considered the keystones of software engineering. ISO defines them in three separate standards. However, their interaction has been poorly studied, so far. The SQuAP model (Software Quality, Architecture, Process) describes twenty-eight main factors that impact on software quality in banking systems, and each factor is described as a relation among some characteristics from the three ISO standards. Hence, SQuAP makes such relations emerge rigorously, although informally. SQaAP-Ont is an OWL ontology that formalises those relations in order to represent and reason via Linked Data about software engineering in a three-dimensional model consisting of quality, architecture, and process characteristics. + homepage: https://w3id.org/squap/ + id: lov.sw-quality + name: SQuAP Ontology + prefix: sw-quality + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/squap/SoftwareQuality/$1 +lov.swc: + authority: lov + description: The Semantic Web Conference ontology (SWC) is an ontology for describing academic conferences + homepage: http://data.semanticweb.org/ns/swc/ontology + id: lov.swc + name: Semantic Web Conference Ontology + prefix: swc + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://data.semanticweb.org/ns/swc/ontology#$1 +lov.swemls: + authority: lov + description: An ontology to describe a Semantic-Web Machine Learning System (SWeMLS) + homepage: https://w3id.org/semsys/ns/swemls + id: lov.swemls + name: Semantic-Web Machine Learning System (SWeMLS) Ontology + prefix: swemls + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/semsys/ns/swemls#$1 +lov.swp: + authority: lov + description: This vocabulary allows to attach an authority to a named graph + homepage: http://www.w3.org/2004/03/trix/swp-1 + id: lov.swp + name: Graph Authority + prefix: swp + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2004/03/trix/swp-1/$1 +lov.swpm: + authority: lov + description: During the modeling of software processes, work products are traditionally treated as atomic units, with names but no structure, and they are generated or changed during the course of the projects. In fact, the language SPEM does not offer mechanisms to detail the structure of work products, allowing only identify whether it is an artifact, a deliverable or an outcome of the project. The typical work products in the software processes are often documents or source code and they are managed from specialized or generic tools. For example, software modeling tools such as Rational Rose, or version control systems such as Git are examples of specialized tools that provide support to the management of certain types of work products. However, other generic tools such as content management systems, document management systems and collaborative editing systems or wikis can also be used to manage evidences of the processes. The design of models for certain types of work products has been an approach used in model-driven web methodologies. However, it is common the need for adapting and customizing well-known methodologies for their application in concrete situations and in specific organizations, a.k.a. process tailoring. Therefore, a vocabulary to define flexible work products in terms of structure and type of its artifacts is proposed here. + homepage: http://spi-fm.uca.es/spdef/models/deployment/swpm/1.0 + id: lov.swpm + name: Software Work Product Model + prefix: swpm + source: lov.linkeddata.es + subjects: [] + uri_format: http://spi-fm.uca.es/spdef/models/deployment/swpm/1.0#$1 +lov.swpo: + authority: lov + description: The aim of the Semantic Web Portal Ontology is to serve as the conceptual backbone for community portals driven by Semantic Web technologies. + homepage: http://sw-portal.deri.org/ontologies/swportal + id: lov.swpo + name: Semantic Web Portal Ontology + prefix: swpo + source: lov.linkeddata.es + subjects: [] + uri_format: http://sw-portal.deri.org/ontologies/swportal#$1 +lov.swrc: + authority: lov + description: An ontology for modeling entities of research communities such as persons, organisations, publications (bibliographic metadata) and their relationship + homepage: http://swrc.ontoware.org/ontology-07 + id: lov.swrc + name: Semantic Web for Research Communities + prefix: swrc + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://swrc.ontoware.org/ontology#$1 +lov.swrl: + authority: lov + description: OWL definition of the RDF Concrete Syntax for the Semantic Web Rule Language + homepage: http://www.w3.org/2003/11/swrl + id: lov.swrl + name: Semantic Web Rule Language + prefix: swrl + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2003/11/swrl#$1 +lov.synsem: + authority: lov + description: A model for the representation of lexical information relative to ontologies. Syntax and semantics module. + homepage: http://www.w3.org/ns/lemon/synsem + id: lov.synsem + name: Lexicon Model for Ontologies - Synsem + prefix: synsem + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/lemon/synsem#$1 +lov.tac: + authority: lov + description: The TripleAccessControl Ontology is an extension to WebAccessControl Ontology to describe access control rules for RDF triples. + homepage: http://ns.bergnet.org/tac/0.1/triple-access-control + id: lov.tac + name: TripleAccessControl Ontology + prefix: tac + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://ns.bergnet.org/tac/0.1/triple-access-control#$1 +lov.tag: + authority: lov + description: An ontology that let users define relationships between Tag objects and URIs of Semantic Web resources + homepage: http://www.holygoat.co.uk/owl/redwood/0.1/tags/ + id: lov.tag + name: Tag ontology + prefix: tag + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.holygoat.co.uk/owl/redwood/0.1/tags/$1 +lov.tao: + authority: lov + description: TAO is a light-weight vocabulary to describe asserted user’s subjective trust values. + homepage: http://vocab.deri.ie/tao + id: lov.tao + name: Trust Assertion Ontology + prefix: tao + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.deri.ie/tao#$1 +lov.tax: + authority: lov + description: EUdaphobase Taxonomy Ontology for the European Soil-Biology Data Warehouse for Soil Protection + homepage: https://w3id.org/EUTaxO + id: lov.tax + name: EUTaxO - EUdaphobase Taxonomy Ontology + prefix: tax + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: https://w3id.org/EUTaxO#$1 +lov.taxon: + authority: lov + description: This is the initial vocabulary for mapping the various taxon classes on the Linked Open Data Cloud + homepage: http://purl.org/biodiversity/taxon/ + id: lov.taxon + name: TaxonMap Ontology + prefix: taxon + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://purl.org/biodiversity/taxon/$1 +lov.taxref-ld: + authority: lov + description: Representation of the TAXREF taxonomic register as linked data. This resource is at the same time an ontology of classes depicting the taxa and a thesaurus (SKOS concept scheme) of the scientific names attached to the taxa. + homepage: http://taxref.mnhn.fr/lod/taxref-ld + id: lov.taxref-ld + name: TAXREF-LD Ontology + prefix: taxref-ld + source: lov.linkeddata.es + subjects: + - biological sciences + - earth and related environmental sciences + uri_format: http://taxref.mnhn.fr/lod/$1 +lov.tb: + authority: lov + description: An ontology to describe people and requests for timebanks. This includes the poeple's skills, limitations, and environment. + homepage: https://w3id.org/timebank + id: lov.tb + name: Timebank Ontology + prefix: tb + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/timebank#$1 +lov.td: + authority: lov + description: This ontology aims to model the Web of Things domain according to the W3C Interest Group (http://w3c.github.io/wot/) + homepage: https://www.w3.org/2019/wot/td + id: lov.td + name: Thing Description Ontology + prefix: td + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://www.w3.org/2019/wot/td#$1 +lov.tddfa: + authority: lov + description: Module for Action (and Frame) modelling inside domain. + homepage: https://w3id.org/todo/tododfa + id: lov.tddfa + name: 'TODODFA: Frame-Action Module for Task-Oriented Dialogue management Ontology (TODO)' + prefix: tddfa + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/todo/tododfa#$1 +lov.tddial: + authority: lov + description: Module for dialogue process and system output management. + homepage: https://w3id.org/todo/tododial + id: lov.tddial + name: 'TODODial: Dialogue Module for Task-Oriented Dialogue management Ontology (TODO)' + prefix: tddial + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/todo/tododial#$1 +lov.tddm: + authority: lov + description: Module for dialogue process and system output management. + homepage: https://w3id.org/todo/tododm + id: lov.tddm + name: 'TODODM: Dialogue Management Module for Task-Oriented Dialogue management Ontology (TODO)' + prefix: tddm + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/todo/tododm#$1 +lov.tddom: + authority: lov + description: Module for domain modelling. + homepage: https://w3id.org/todo/tododom + id: lov.tddom + name: 'TODODom: Domain Module for Task-Oriented Dialogue management Ontology (TODO)' + prefix: tddom + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/todo/tododom#$1 +lov.tddt: + authority: lov + description: Module for dialogue tracing. + homepage: https://w3id.org/todo/tododt + id: lov.tddt + name: 'TODODT: Dialogue Tracing Module for Task-Oriented Dialogue management Ontology (TODO)' + prefix: tddt + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/todo/tododt#$1 +lov.tddw: + authority: lov + description: Module for scenario modelling (world elements) of domain. + homepage: https://w3id.org/todo/tododw + id: lov.tddw + name: 'TODODW: World Module for Task-Oriented Dialogue management Ontology (TODO)' + prefix: tddw + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/todo/tododw#$1 +lov.te: + authority: lov + description: An entry sub-ontology of time (OWL-Time). + homepage: http://www.w3.org/2006/time-entry + id: lov.te + name: Time Entry + prefix: te + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2006/time-entry#$1 +lov.teach: + authority: lov + description: TEACH, the Teaching Core Vocabulary, is a lightweight vocabulary providing terms to enable teachers to relate things in their courses together. The Teaching Core Vocabulary is based on practical requirements set by providing seminar and course descriptions as Linked Data. + homepage: http://linkedscience.org/teach/ns# + id: lov.teach + name: Teaching Core Vocabulary Specification + prefix: teach + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://linkedscience.org/teach/ns#$1 +lov.tempo: + authority: lov + description: >- + In a typical (uni)temporal data model every resource's appearance (and + disappearance) is being tracked. + + Numerous systems accomplish unitemporal tracking, either externally by e.g. using git to record the insertion or deletion of a resource, or internally by e.g. using prov:generatedAtTime and prov:invalidatedAtTime. + + This axis of time is known as *system time*, and none of TempO's concern because for one there is readily available support, and moreover because unitemporal tracking is used for principally true statements, i.e. those that have always been (considered) true or will always be (considered) true. + + + TempO addresses bitemporal and tritemporal setups: Resources which are (known or believed to be) valid and efficacious for some time. + + A second time axis orthogonal to system time is introduced, that is a resource can be valid even though it is currently not in the system, or, conversely, can be already or still invalid by the time it enters the system. + + + Efficacy, sometimes called decision time, is yet another concept orthogonal to validity, i.e. a resource that is no longer or not yet valid can be efficacious. + + The converse, a valid but inefficacious resource in the system, is *usually* not encountered but TempO does not impose restrictions on the shape of the time area. + + + In general the necessity for tracking both validity and efficacy arises in areas where concepts are assigned a code or label that is subject to reuse following invalidation. + + Tracking efficacy and validity concurrently then allows for fine-grained control over how much future knowledge or how much past knowledge we tolerate in a datset. + + + Example: + + -------- + + Czechoslovakia was founded in 1918 but became part of Germany, Hungary and Poland in 1938. + + It was reestablished in 1945 but split into two sovereign states in 1993. + + The ISO 3166 country code for Czechoslovakia used to be 'CS', assigned in 1974, published in February 1978, and invalidated with the country's split. + + In 2003 ISO 3166 reassigned the country code 'CS' to Serbia and Montenegro. + + The facts were assembled in 2018 and written down as follows: + + cc:CSHH + a cc:ISO3166-CountryCode ; + rdfs:label "CS" ; + cc:refersTo "Czechoslovakia" ; + prov:generatedAtTime "2018-02-29T04:00:00Z"^^xsd:dateTime . + tempo:validFrom "1978-02"^^xsd:gYearMonth ; + tempo:validTill "1993-01-01"^^xsd:date ; + tempo:efficaciousFrom "1918"^^xsd:gYear , "1945"^^xsd:gYear ; + tempo:efficaciousTill "1938"^^xsd:gYear , "2003"^^xsd:gYear . + + The use of the country code 'CS' in a statement from 1988 can be resolved to cc:CSHH, as of today, free from ambiguity; it was valid back then after all and we know that today. + + The same query in 2017 (point-in-time query) would have yielded no results because the information hadn't been in the system back then. + + Point-in-time queries, however, are not TempO's major concern so only as-of-today queries are assumed from now on. + + + Following the country's split it is highly likely that news reports from, say, 1994 highlighting the then-recent past would still have used 'CS' to refer to cc:CSHH. + + According to the resource this is possible, a query for 'CS' in 1994 would bring up cc:CSHH as it is efficacious but marked as invalidated. + + + On the other end of history, the use of the code 'CS' in, say, 1976 is plausible. The code was decided on but not yet formally published. + + A query for 'CS' as used in 1976 would bring up cc:CSHH, marked as anachronistic. + + Going back further, a statement from, say 1942, using the code 'CS' must clearly refer to something else. + + A query for 'CS' as used in 1976 would yield not yield any results. + + + -- + + + The ontology IRI http://purl.org/tempo/ always resolve to the latest version of TempO. Particular versionIRIs such as http://purl.org/tempo/0.1/ can be used by clients to force the import of a particular version. + + + The goal of TempO is to allow for temporal constraints with control over how much future or past is permissible directly on the published resource, and as such, TempO does not restrict domain/ranges. + homepage: http://purl.org/tempo + id: lov.tempo + name: TempO - Temporal Ontology + prefix: tempo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/tempo/$1 +lov.test: + authority: lov + description: This ontology aims at defining the Quality Assurance Framework by collecting the test development experience of W3C Working Groups and summarizing the work done about tests and metadata. + homepage: http://www.w3.org/2006/03/test-description + id: lov.test + name: Test Metadata + prefix: test + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2006/03/test-description#$1 +lov.tfo: + authority: lov + description: This document describes functions which transform HTTP representations, i.e., the actual literal payloads of HTTP messages. + homepage: https://privatealpha.com/ontology/transformation/1# + id: lov.tfo + name: Transformation Functions Ontology + prefix: tfo + source: lov.linkeddata.es + subjects: [] + uri_format: https://privatealpha.com/ontology/transformation/1#$1 +lov.theatre: + authority: lov + description: An ontology for organising theatrical data. + homepage: http://purl.org/theatre# + id: lov.theatre + name: Theatre Ontology + prefix: theatre + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/theatre#$1 +lov.thors: + authority: lov + description: An OWL representation of the model for Temporal Ordinal Reference Systems defined in GeoSciML v3. + homepage: http://resource.geosciml.org/ontology/timescale/thors + id: lov.thors + name: The Temporal Ordinal Reference Systems + prefix: thors + source: lov.linkeddata.es + subjects: [] + uri_format: http://resource.geosciml.org/ontology/timescale/thors#$1 +lov.ti: + authority: lov + description: This pattern is extracted from DOLCE-UltraLite by partial clone of elements and expansion. Two datatype properties have been added which allow to express the boundaries of the time interval. + homepage: http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl + id: lov.ti + name: The Time Interval Pattern + prefix: ti + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#$1 +lov.time: + authority: lov + description: This vocabulary defines temporal entities such as time intervals, their properties and relationships. + homepage: http://www.w3.org/2006/time + id: lov.time + name: Time Ontology + prefix: time + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2006/time#$1 +lov.tio: + authority: lov + description: A vocabulary for describing tickets for events, transportation, or points of interest for e-commerce. + homepage: http://purl.org/tio/ns# + id: lov.tio + name: The Tickets Ontology + prefix: tio + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/tio/ns#$1 +lov.tis: + authority: lov + description: A generic pattern usable for all situations that require a temporal indexing. + homepage: http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl + id: lov.tis + name: Time Indexed Situation + prefix: tis + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ontologydesignpatterns.org/cp/owl/timeindexedsituation.owl$1 +lov.tisc: + authority: lov + description: TISC, the Open Time and Space Core Vocabulary, is a lightweight spatiotemporal vocabulary aiming to provide spatial and temporal terms such as "happensAt", "locatedAt", "rightOf" to enable practitioners to relate their data to time and space. + homepage: http://www.observedchange.com/tisc/ns# + id: lov.tisc + name: Open Time and Space Core Vocabulary + prefix: tisc + source: lov.linkeddata.es + subjects: [] + uri_format: http://observedchange.com/tisc/ns#$1 +lov.tl: + authority: lov + description: Extends owl-time ontology with support for several timelines, acting as a backbone to adress time interval/instants. Mainly designed with a multimedia use-case in mind. + homepage: http://purl.org/NET/c4dm/timeline.owl + id: lov.tl + name: The Timeline Ontology + prefix: tl + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/NET/c4dm/timeline.owl#$1 +lov.tm: + authority: lov + description: An OWL representation of part of the model for Temporal objects and reference systems from ISO 19108:2002 Geographic Information - Temporal Schema + homepage: http://def.seegrid.csiro.au/isotc211/iso19108/2002/temporal + id: lov.tm + name: A vocabulary for temporal objects in Geographic Information + prefix: tm + source: lov.linkeddata.es + subjects: [] + uri_format: http://def.seegrid.csiro.au/isotc211/iso19108/2002/temporal#$1 +lov.tmo: + authority: lov + description: The Translational Medicine Ontology (TMO) is a high-level, patient-centric ontology that extends existing domain ontologies to integrate data across aspects of drug discovery and clinical practice. The ontology has been developed by participants in the World Wide Web Consortium's Semantic Web for Health Care and Life Sciences Interest Group + homepage: http://www.w3.org/2001/sw/hcls/ns/transmed/ + id: lov.tmo + name: Translational Medicine Ontology + prefix: tmo + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: http://www.w3.org/2001/sw/hcls/ns/transmed/$1 +lov.toco: + authority: lov + description: A ontology developed for telecommunciation network systems with hybrid technologies, e.g., WiFi, LiFi, LTE, 2G/3G, optical, etc. + homepage: http://purl.org/toco/ + id: lov.toco + name: Toucan Ontology + prefix: toco + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/toco/$1 +lov.todo: + authority: lov + description: With the aim of enhancing natural communication between workers in industrial environments and the systems to be used by them, TODO (Task-Oriented Dialogue management Ontology) has been developed to be the core of task-oriented dialogue systems. TODO is a core ontology that provides task-oriented dialogue systems with the necessary means to be capable of naturally interacting with workers (both at understanding and at ommunication levels) and that can be easily adapted to different industrial scenarios, reducing adaptation time and costs. Moreover, it allows to store and reproduce the dialogue process to be able to learn from new interactions. + homepage: https://w3id.org/todo + id: lov.todo + name: 'TODO: Task-Oriented Dialogue management Ontology' + prefix: todo + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/todo#$1 +lov.topo: + authority: lov + description: "Ontologie décrivant les éléments du territoire et ses infrastructures. Elle repend l'essentiel du vocabulaire de la BDTOPO(IGN) et vise à couvrir l'ensemble des entités topographiques et administratives du territoire national. Les thèmes couverts sont: le réseau routier, le réseau ferroviaire, le réseau de transport d'énergie, le réseau hydrographique, les bâtiments, la végétation arborée, l'orographie, les communes, les points d'activité ou d'intérêt." + homepage: http://data.ign.fr/def/topo + id: lov.topo + name: Ontologie des éléments du territoire et de ses infrastructures de l'IGN + prefix: topo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://data.ign.fr/def/topo#$1 +lov.tp: + authority: lov + description: 'A vocabulary to describe touristic places: accommodations, points of interest, restaurants and attractions.' + homepage: http://tour-pedia.org/download/tp.owl + id: lov.tp + name: Tourpedia Ontology + prefix: tp + source: lov.linkeddata.es + subjects: [] + uri_format: http://tour-pedia.org/download/tp.owl#$1 +lov.traffic: + authority: lov + description: An ontology that describes the management of the traffic in a straight road with two lanes, both in the same direction. + homepage: http://www.sensormeasurement.appspot.com/ont/transport/traffic + id: lov.traffic + name: Road Traffic Management + prefix: traffic + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.sensormeasurement.appspot.com/ont/transport/traffic#$1 +lov.trait: + authority: lov + description: OntoMedia (Ontology for Media) has been designed to describe the traits of entities. + homepage: http://contextus.net/ontology/ontomedia/ext/common/trait# + id: lov.trait + name: OntoMedia Trait Representation + prefix: trait + source: lov.linkeddata.es + subjects: [] + uri_format: http://contextus.net/ontology/ontomedia/ext/common/trait#$1 +lov.transit: + authority: lov + description: A vocabulary for describing transit systems and routes + homepage: http://vocab.org/transit/terms/ + id: lov.transit + name: TRANSIT + prefix: transit + source: lov.linkeddata.es + subjects: [] + uri_format: http://vocab.org/transit/terms/$1 +lov.trao: + authority: lov + description: Transport Administration Ontology (TAO) for describing data from Swedish Transport Administration Web site. + homepage: http://linkeddata.finki.ukim.mk/lod/ontology/tao# + id: lov.trao + name: Transport Administration Ontology + prefix: trao + source: lov.linkeddata.es + subjects: [] + uri_format: http://linkeddata.finki.ukim.mk/lod/ontology/tao#$1 +lov.tree: + authority: lov + description: A hypermedia specification for fragmenting collections. + homepage: https://w3id.org/tree + id: lov.tree + name: TREE + prefix: tree + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/tree#$1 +lov.tresiot: + authority: lov + description: This ontology models trust recommendation concepts in SIoT to bridge the gap between abstract trust concepts and real-world device concepts. + homepage: https://liidr.org/trust-recommendation-in-social-internet-of-things/ + id: lov.tresiot + name: Ontology for Trust Recommendation in Social Internet of Things + prefix: tresiot + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://liidr.org/trust-recommendation-in-social-internet-of-things/$1 +lov.tsioc: + authority: lov + description: Extends the SIOC Core Ontology (Semantically-Interlinked Online Communities) by defining subclasses and subproperties of SIOC terms. + homepage: http://rdfs.org/sioc/types# + id: lov.tsioc + name: SIOC Types Ontology Module + prefix: tsioc + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdfs.org/sioc/types#$1 +lov.tsn: + authority: lov + description: This RDF ontology allows describing any Territorial Statistical Nomenclature (TSN) (i.e., partition of the territory) used as a support to socio-economic data (statistical data that describe territory in terms of population, unemployement rate, transport access, etc.). + homepage: http://purl.org/net/tsn# + id: lov.tsn + name: Territorial Statistical Nomenclature Ontology + prefix: tsn + source: lov.linkeddata.es + subjects: + - political sciences + - earth and related environmental sciences + - mathematics + uri_format: http://purl.org/net/tsn#$1 +lov.tsnc: + authority: lov + description: The TSN-Change ontology aims at describing changes that occured from one version of a Territorial Statistical Nomenclature (TSN) (i.e., partition of the territory) and its subsequent (e.g., change in territorial units boundaries to reflect an administrative reorganisation). + homepage: http://purl.org/net/tsnchange# + id: lov.tsnc + name: Territorial Statistical Nomenclature Change Ontology + prefix: tsnc + source: lov.linkeddata.es + subjects: + - political sciences + - earth and related environmental sciences + - mathematics + uri_format: http://purl.org/net/tsnchange#$1 +lov.turismo: + authority: lov + description: 'Esta ontología se ha construido dentro del proyecto financiado por el Ayuntamiento de Zaragoza: "Un visitante, una ruta", una aplicación informática para el cálculo de rutas turísticas en la ciudad de Zaragoza en base al perfil y contexto del usuario.' + homepage: http://idi.fundacionctic.org/cruzar/turismo + id: lov.turismo + name: Ontología de Turismo para el Ayuntamiento de Zaragoza + prefix: turismo + source: lov.linkeddata.es + subjects: [] + uri_format: http://idi.fundacionctic.org/cruzar/turismo#$1 +lov.tvc: + authority: lov + description: A pattern for the description of scenarios that involve entities having some value during a particular time and within a particular context. + homepage: http://www.essepuntato.it/2012/04/tvc + id: lov.tvc + name: The Time-indexed Value in Context + prefix: tvc + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.essepuntato.it/2012/04/tvc/$1 +lov.txn: + authority: lov + description: This ontology and the related TaxonConcept data set mints identifiers that are tied to a specific species concept which can have several names and classifications. + homepage: http://lod.taxonconcept.org/ontology/txn.owl + id: lov.txn + name: TaxonConcept Ontology + prefix: txn + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://lod.taxonconcept.org/ontology/txn.owl#$1 +lov.tzont: + authority: lov + description: A vocabulary to describe time zones and their geographical coverage. + homepage: http://www.w3.org/2006/timezone + id: lov.tzont + name: Time Zone Ontology + prefix: tzont + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2006/timezone#$1 +lov.uby: + authority: lov + description: >- + OLiA Annotation Model for Uby Parts of Speech (Gurevych et al, 2012) + + extracted from the Uby DTD (http://purl.org/olia/ubyCat.owl, version of Nov 21th, 2012). + + + References + + Iryna Gurevych, Judith Eckle-Kohler, Silvana Hartmann, Michael Matuschek, Christian M. Meyer and Christian Wirth, 2012, Uby - A Large-Scale Unified Lexical-Semantic Resource, Proceedings of the 13th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2012), Avignon, France. + + + The DTD is made available under a Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0) license which is available at http://creativecommons.org/licenses/by-sa/3.0/ + + You are free to share (copy, distribute and transmit) the work, to develop your own extensions (adapt, remix) of the work, and to make commercial use of the work. + homepage: http://purl.org/olia/ubyCat.owl + id: lov.uby + name: ubyCat.owl + prefix: uby + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/olia/ubyCat.owl#$1 +lov.uco: + authority: lov + description: Vocabulaire Web pour décrire les caractéristiques des voitures d'occasion pour le commerce électronique. + homepage: http://purl.org/uco/ns# + id: lov.uco + name: Used Cars Ontology + prefix: uco + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/uco/ns#$1 +lov.ucum: + authority: lov + description: |- + The instances of this ontology have been automatically + generated from the UCUM (The Unified Code for Units of Measure). + See http://aurora.rg.iupui.edu/UCUM/ for more details + on UCUM. The members of the MyMobileWeb consortium + explicitly acknowledge the copyright of the data from + the UCUM ontology. + homepage: http://purl.oclc.org/NET/muo/ucum/ + id: lov.ucum + name: Units of measurement ontology + prefix: ucum + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://purl.oclc.org/NET/muo/ucum/$1 +lov.ui: + authority: lov + description: An ontology suitable for describing forms, sequences in widgets + homepage: http://www.w3.org/ns/ui + id: lov.ui + name: A user interface ontology + prefix: ui + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/ui#$1 +lov.uiot: + authority: lov + description: Core module of the suite of ontologies for urban IoT devices. + homepage: http://www.w3id.org/urban-iot/core + id: lov.uiot + name: Urban IoT Ontologies - Core Module + prefix: uiot + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3id.org/urban-iot/core#$1 +lov.uiote: + authority: lov + description: Electric Mobility module of the suite of ontologies for urban IoT devices. + homepage: http://www.w3id.org/urban-iot/electric + id: lov.uiote + name: Ontologie per gli Apparati IoT Urbani - Modulo Electric Mobility + prefix: uiote + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3id.org/urban-iot/electric#$1 +lov.uiots: + authority: lov + description: Modulo Sharing Mobility delle ontologie per gli apparati IoT urbani. + homepage: http://www.w3id.org/urban-iot/sharing + id: lov.uiots + name: Ontologie per gli Apparati IoT Urbani - Modulo Sharing Mobility + prefix: uiots + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3id.org/urban-iot/sharing#$1 +lov.umbel: + authority: lov + description: UMBEL provides a general vocabulary of classes and predicates for describing domain ontologies, with the specific aim of promoting interoperability with external datasets and domains. + homepage: http://umbel.org/umbel + id: lov.umbel + name: Upper Mapping and Binding Exchange Layer + prefix: umbel + source: lov.linkeddata.es + subjects: + - generic + uri_format: http://umbel.org/umbel#$1 +lov.uneskos: + authority: lov + description: An RDF vocabulary for extending some SKOS and ISO-THES functions in order to improve the linked data consumption of SKOS datasets + homepage: http://purl.org/umu/uneskos + id: lov.uneskos + name: UNESKOS Vocabulary + prefix: uneskos + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/umu/uneskos#$1 +lov.uniprot: + authority: lov + description: Properties and classes used for protein annotation + homepage: http://purl.uniprot.org/core/ + id: lov.uniprot + name: Uniprot Core Ontology + prefix: uniprot + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://purl.uniprot.org/core/$1 +lov.uri4uri: + authority: lov + description: This vocabulary describes the entities which may be derived from a URI and the relationships between them, such as Internet Domains, prototcols, file suffixes etc. It was initially issued as part of an April 1st gag, but has utility beyond the initial joke. + homepage: http://uri4uri.net/vocab + id: lov.uri4uri + name: URI Vocabulary + prefix: uri4uri + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://uri4uri.net/vocab#$1 +lov.usability: + authority: lov + description: Ontology 'Usability' created to describe and store information about interactions of user with a software user interface + homepage: https://w3id.org/usability + id: lov.usability + name: Usability + prefix: usability + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/usability#$1 +lov.va: + authority: lov + description: This vocabulary allows the semantic description of visual analytics applications. It is based on the RDF Data Cube Vocabulary and the Semanticscience Integrated Ontology. + homepage: http://code-research.eu/ontology/visual-analytics + id: lov.va + name: The Visual Analytics Vocabulary + prefix: va + source: lov.linkeddata.es + subjects: [] + uri_format: http://code-research.eu/ontology/visual-analytics#$1 +lov.vaem: + authority: lov + description: The purpose of VAEM is to provide, by import, a foundation for commonly needed resources when building an ontology. + homepage: http://www.linkedmodel.org/schema/vaem + id: lov.vaem + name: Vocabulary for Attaching Essential Metadata + prefix: vaem + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.linkedmodel.org/schema/vaem#$1 +lov.vag: + authority: lov + description: The Vagueness Ontology (VO) allows one to specify vagueness characterisations of the TBox entities of an ontology. + homepage: http://www.essepuntato.it/2013/10/vagueness + id: lov.vag + name: The Vagueness Ontology + prefix: vag + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.essepuntato.it/2013/10/vagueness/$1 +lov.vann: + authority: lov + description: A vocabulary for annotating descriptions of vocabularies with examples and usage notes. + homepage: http://purl.org/vocab/vann/ + id: lov.vann + name: 'VANN: A vocabulary for annotating vocabulary descriptions' + prefix: vann + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocab/vann/$1 +lov.vartrans: + authority: lov + description: A model for the representation of lexical information relative to ontologies. Variation and translation module. + homepage: http://www.w3.org/ns/lemon/vartrans + id: lov.vartrans + name: Lexicon Model for Ontologies - Vartrans + prefix: vartrans + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/ns/lemon/vartrans#$1 +lov.vcard: + authority: lov + description: This ontology models and represents vCards in RDF using current best practices + homepage: http://www.w3.org/2006/vcard/ns + id: lov.vcard + name: An Ontology for vCards + prefix: vcard + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2006/vcard/ns#$1 +lov.vdpp: + authority: lov + description: The Vocabulary of Dataset Publication Projects (VDPP) allows to represent the status of a dataset publication project. It is mainly based on the Provenance Vocabulary (PRV), the Dataset Provenance Vocabulary (VOIDP), the Vocabulary of Interlinked Datasets (VoID), and the Description of a Project (DOAP) vocabulary. + homepage: http://data.lirmm.fr/ontologies/vdpp + id: lov.vdpp + name: Vocabulary for Dataset Publication Projects + prefix: vdpp + source: lov.linkeddata.es + subjects: [] + uri_format: http://data.lirmm.fr/ontologies/vdpp#$1 +lov.veo: + authority: lov + description: An ontology for describing vehicles and their emissions. + homepage: http://linkeddata.finki.ukim.mk/lod/ontology/veo# + id: lov.veo + name: Vehicle Emissions Ontology + prefix: veo + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + uri_format: http://linkeddata.finki.ukim.mk/lod/ontology/veo#$1 +lov.vgo: + authority: lov + description: The Video Game Ontology is an ontology designed for describing video games and all the resources related to their game plays. + homepage: http://purl.org/net/VideoGameOntology + id: lov.vgo + name: The Video Game Ontology + prefix: vgo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/VideoGameOntology#$1 +lov.vin: + authority: lov + description: This ontology was used as example in the first OWL Recommendation (February 2004) + homepage: http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine + id: lov.vin + name: Wine Ontology + prefix: vin + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#$1 +lov.vir: + authority: lov + description: >- + This ontology, called VIR, is an extension of CIDOC-CRM created to sustain + propositions on the nature of visual elements and permit these descriptions + to be published on the Web. + + With the term visual element, we refer to those signs identified in the visual space as distinct and documentable units, and subject to an analytical interpretation. + + The scope of this ontology is to s to provide a framework to support the identification, annotation and interconnections between diverse visual elements and presents and assist their documentation and retrieval. Specifically, the model aims to clarify the identity and the relation of these visual signs, providing the necessary classes to characterise their constituent elements, reference, symbolic content and source of interpretation. + + VIR expands on key entities and properties from CIDOC-CRM, introducing new classes and relationships responding to the visual and art historical community, specifically building up on the iconographical tradition. The result is a model which differentiates between interpretation and element identified, providing a clear distinction between denotation and signification of an element. As a consequence of such distinction, the ontology allows for the definition of diverse denotative criteria for the same representation, which could change based on traditions and perspective. Visual objects can be, in fact, polysemic and ambiguous, and it is not so easy to pin down a denotative or connotative meaning because they are very much context-dependent. + homepage: http://w3id.org/vir# + id: lov.vir + name: VIR - Visual Representation ontology + prefix: vir + source: lov.linkeddata.es + subjects: [] + uri_format: http://w3id.org/vir#$1 +lov.vivo: + authority: lov + description: An ontology of academic and research domain, developed in the framework of the VIVO project + homepage: http://vivoweb.org/ontology/core + id: lov.vivo + name: VIVO Core Ontology + prefix: vivo + source: lov.linkeddata.es + subjects: + - educational sciences + uri_format: http://vivoweb.org/ontology/core#$1 +lov.vmm: + authority: lov + description: In Software Engineering, as well as in other disciplines, it is common to use model-editing tools using a visual language. In particular, the editing tools allow you to design UML software models, so that let you manage much of the work products of a project. From the study of several UML tools, such as Enterprise Architect, Visual Paradigm for UML or Rational Rose, this vocabulary has been defined. This vocabulary represents the basic structure of these UML tools, but does not exclude others that allow you to use other visual languages for modeling software systems or other entities. + homepage: http://spi-fm.uca.es/spdef/models/genericTools/vmm/1.0 + id: lov.vmm + name: Visual Modeling tool Model + prefix: vmm + source: lov.linkeddata.es + subjects: [] + uri_format: http://spi-fm.uca.es/spdef/models/genericTools/vmm/1.0#$1 +lov.voaf: + authority: lov + description: A vocabulary to describe linked data vocabularies and their relations + homepage: http://purl.org/vocommons/voaf + id: lov.voaf + name: Vocabulary of a Friend + prefix: voaf + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vocommons/voaf#$1 +lov.voag: + authority: lov + description: VOAG is intended to specify licensing, attribution, provenance and governance of an ontology. + homepage: http://voag.linkedmodel.org/schema/voag + id: lov.voag + name: Vocabulary Of Attribution and Governance + prefix: voag + source: lov.linkeddata.es + subjects: [] + uri_format: http://voag.linkedmodel.org/voag#$1 +lov.vocals: + authority: lov + description: This ontology aims to model RDF streams, their metadata, and access endpoints for publishing and consuming these streams + homepage: http://w3id.org/rsp/vocals# + id: lov.vocals + name: 'VoCaLS: A Vocabulary and Catalog for Linked Streams' + prefix: vocals + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://w3id.org/rsp/vocals#$1 +lov.void: + authority: lov + description: The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. + homepage: http://vocab.deri.ie/void + id: lov.void + name: Vocabulary of Interlinked Datasets + prefix: void + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdfs.org/ns/void#$1 +lov.voidext: + authority: lov + description: The Extension of the Vocabulary of Interlinked Datasets (VoID) RDF Schema that includes the concept of virtual links. This extension enhances interoperability among heterogeneous and distributed RDF data sets by bridging them through explicitly defined virtual links. + homepage: http://purl.org/query/voidext + id: lov.voidext + name: Extended Vocabulary of Interlinked Datasets (VoIDext) + prefix: voidext + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/query/voidext#$1 +lov.voidwh: + authority: lov + description: An extension of W3C VoID that is able to represent these metrics for expressing the Connectivity Metrics of a Semantic Warehouse. + homepage: http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl + id: lov.voidwh + name: Void Warehouse Ontology + prefix: voidwh + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.ics.forth.gr/isl/VoIDWarehouse/VoID_Extension_Schema.owl$1 +lov.vra: + authority: lov + description: Le VRA Core est un ensemble de propriétés de métadonnées pour décrire les oeuvres d'art visuelles et les images qui les documentent. + homepage: http://simile.mit.edu/2003/10/ontologies/vraCore3# + id: lov.vra + name: RDFS Ontology for VRA + prefix: vra + source: lov.linkeddata.es + subjects: [] + uri_format: http://simile.mit.edu/2003/10/ontologies/vraCore3#$1 +lov.vrank: + authority: lov + description: The Vocabulary for Ranking (vRank) is an RDF Schema vocabulary for materializing ranking computations. + homepage: http://vocab.sti2.at/vrank + id: lov.vrank + name: Vocabulary for Ranking + prefix: vrank + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/voc/vrank#$1 +lov.vs: + authority: lov + description: An RDF vocabulary for relating SW vocabulary terms to their status. + homepage: http://www.w3.org/2003/06/sw-vocab-status/ns + id: lov.vs + name: SemWeb Vocab Status ontology + prefix: vs + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2003/06/sw-vocab-status/ns#$1 +lov.vsearch: + authority: lov + description: The vSearch vocabulary facilitates the querying and retrieval of vocabulary terms from a vocabularies directory. It can be used to map keywords with mapped result terms accompanied with a ranking value. + homepage: http://purl.org/vsearch/ + id: lov.vsearch + name: vSearch Vocabulary + prefix: vsearch + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vsearch/$1 +lov.vso: + authority: lov + description: The Vehicle Sales Ontology for Semantic Web-based E-Commerce + homepage: http://purl.org/vso/ns + id: lov.vso + name: Vehicle Sales Ontology + prefix: vso + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vso/ns#$1 +lov.vvo: + authority: lov + description: A vocabulary for describing Volkswagen-specific features of automobiles and their components + homepage: http://purl.org/vvo/ns# + id: lov.vvo + name: Volkswagen Vehicles Ontology + prefix: vvo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/vvo/ns#$1 +lov.w3c-ssn: + authority: lov + description: This ontology describes sensors and observations, and related concepts. It does not describe domain concepts, time, locations, etc. as these are intended to be included from other ontologies via OWL imports. + homepage: https://www.w3.org/ns/ssn + id: lov.w3c-ssn + name: Semantic Sensor Network Ontology + prefix: w3c-ssn + source: lov.linkeddata.es + subjects: + - earth and related environmental sciences + - computer and information sciences + uri_format: https://www.w3.org/ns/ssn/$1 +lov.wai: + authority: lov + description: WAI vocabulary aims to extend the FOAF specification through introducing the concepts of roles and profiles. In society, people are more than just persons, they can be musicians, presidents of government, firemen, football players or car drivers in a traffic jam. + homepage: http://purl.org/wai# + id: lov.wai + name: Roles and Profiles Ontology + prefix: wai + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/wai#$1 +lov.wdrs: + authority: lov + description: The Protocol for Web Description Resources (POWDER) allows metadata to be associated with groups of resources such as those found on a Web site. + homepage: http://www.w3.org/2007/05/powder-s + id: lov.wdrs + name: Protocol for Web Description Resources + prefix: wdrs + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3.org/2007/05/powder-s#$1 +lov.wf-invoc: + authority: lov + description: Wf-invoc is a simple profile of the P-plan ontology to describe how workflow steps are invoked within a workflow execution. + homepage: http://purl.org/net/wf-invocation + id: lov.wf-invoc + name: Workflow Invocation Ontology + prefix: wf-invoc + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/wf-invocation#$1 +lov.wfdesc: + authority: lov + description: This ontology ("wfdesc") describes an abstract workflow description structure, allowing the description of a scientific workflow as a direct acyclic graph, or a dataflow. This ontology is meant as an upper ontology for more specific workflow definitions, and as a way to express abstract workflows. The wfprov ontology shows how to link these descriptions to a provenance trace of a workflow execution. + homepage: http://purl.org/wf4ever/wfdesc + id: lov.wfdesc + name: The Wfdesc ontology + prefix: wfdesc + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/wf4ever/wfdesc#$1 +lov.wfm: + authority: lov + description: Ontology for describing Workflow Motifs. Workflow Motifs outline the kinds of data-intensive activities that are observed in workflows (data-operation motifs) and the different manners in which activities are implemented within workflows (workflow-oriented motifs). + homepage: http://purl.org/net/wf-motifs + id: lov.wfm + name: The Workflow Motif Ontology + prefix: wfm + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/net/wf-motifs#$1 +lov.wfprov: + authority: lov + description: The wfprov ontology shows how to express minimal provenance information about the execution of a workflow described using the wfdesc ontology. + homepage: http://purl.org/wf4ever/wfprov + id: lov.wfprov + name: The Wfprov Ontology + prefix: wfprov + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/wf4ever/wfprov#$1 +lov.whisky: + authority: lov + description: A small vocabulary for describing whisky varieties + homepage: http://vocab.org/whisky/terms + id: lov.whisky + name: Whisky Ontology + prefix: whisky + source: lov.linkeddata.es + subjects: + - agriculture, forestry, and fisheries + uri_format: http://vocab.org/whisky/terms/$1 +lov.whois: + authority: lov + description: A vocabulary to describe a person's profile and history + homepage: http://www.kanzaki.com/ns/whois + id: lov.whois + name: Who's who description vocabulary + prefix: whois + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.kanzaki.com/ns/whois#$1 +lov.wi: + authority: lov + description: The Weighted Interests Vocabulary specification provides basic concepts and properties for describing describing preferences (interests) within contexts, their temporal dynamics and their origin on/ for the Semantic Web. + homepage: http://purl.org/ontology/wi/core# + id: lov.wi + name: The Weighted Interests Vocabulary + prefix: wi + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/wi/core#$1 +lov.wikibase: + authority: lov + description: The system ontology of Wikibase + homepage: http://wikiba.se/ontology + id: lov.wikibase + name: Wikibase system ontology + prefix: wikibase + source: lov.linkeddata.es + subjects: [] + uri_format: http://wikiba.se/ontology#$1 +lov.wikim: + authority: lov + description: A partir del análisis de diversos sistemas, como MediaWiki, Confluence o DokuWiki, se ha diseñado este vocabulario. Téngase en cuenta que este modelo no describe completamente el modelo conceptual de todos los tipos de sistemas wiki, sino sólo de los elementos principales. + homepage: http://spi-fm.uca.es/spdef/models/genericTools/wikim/1.0 + id: lov.wikim + name: WIKI tool Model + prefix: wikim + source: lov.linkeddata.es + subjects: [] + uri_format: http://spi-fm.uca.es/spdef/models/genericTools/wikim/1.0#$1 +lov.wl: + authority: lov + description: WSMO-Lite is a lightweight approach to the semantic annotation of Web service descriptions, defined by the STI2 working group Conceptual Models for Services + homepage: http://www.wsmo.org/ns/wsmo-lite# + id: lov.wl + name: WSMO-Lite Ontology + prefix: wl + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.wsmo.org/ns/wsmo-lite#$1 +lov.wlo: + authority: lov + description: A simple vocabulary for describing biological species and related taxa. + homepage: http://purl.org/ontology/wo/ + id: lov.wlo + name: BBC Wildlife Ontology + prefix: wlo + source: lov.linkeddata.es + subjects: + - biological sciences + uri_format: http://purl.org/ontology/wo/$1 +lov.wo: + authority: lov + description: The Weighting Ontology specification provides a vocabulary for describing weightings and their referenced scales, on/ for the Semantic Web. + homepage: http://purl.org/ontology/wo/core# + id: lov.wo + name: Weighting Ontology + prefix: wo + source: lov.linkeddata.es + subjects: [] + uri_format: http://purl.org/ontology/wo/core#$1 +lov.wot: + authority: lov + description: Web Of Trust (wot) RDF vocabulary, described using W3C RDF Schema and the Web Ontology Language. + homepage: http://xmlns.com/wot/0.1/ + id: lov.wot + name: Web Of Trust + prefix: wot + source: lov.linkeddata.es + subjects: [] + uri_format: http://xmlns.com/wot/0.1/$1 +lov.wotsec: + authority: lov + description: Security mechanisms for the the Web of Thing + homepage: https://www.w3.org/2019/wot/security# + id: lov.wotsec + name: Security mechanisms for the Web of Things + prefix: wotsec + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: https://www.w3.org/2019/wot/security#$1 +lov.xapi: + authority: lov + description: This ontology contains a list of the classes and properties that can be used when for creating and publishing a controlled vocabulary dataset for xAPI communities of practice. + homepage: http://purl.org/xapi/ontology# + id: lov.xapi + name: xAPI Controlled Vocabulary Ontology + prefix: xapi + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://purl.org/xapi/ontology#$1 +lov.xbrll: + authority: lov + description: An attempt to publish XBRL standard following best practices on the Web. Not an official version from XBRL International and under development + homepage: https://w3id.org/vocab/xbrll + id: lov.xbrll + name: A lightweight XBRL vocabulary + prefix: xbrll + source: lov.linkeddata.es + subjects: [] + uri_format: https://w3id.org/vocab/xbrll#$1 +lov.xhv: + authority: lov + description: This is a vocabulary collection utilized by XHTML Family modules and document types using XHTML Modularization, including XHTML Role and XHTML + RDFa as defined in rdfa-syntax. + homepage: http://www.w3.org/1999/xhtml/vocab + id: lov.xhv + name: XHTML Vocabulary + prefix: xhv + source: lov.linkeddata.es + subjects: + - computer and information sciences + uri_format: http://www.w3.org/1999/xhtml/vocab#$1 +lov.xkos: + authority: lov + description: Extension de SKOS pour la représentation des nomenclatures + homepage: http://rdf-vocabulary.ddialliance.org/xkos + id: lov.xkos + name: XKOS + prefix: xkos + source: lov.linkeddata.es + subjects: [] + uri_format: http://rdf-vocabulary.ddialliance.org/xkos#$1 +lov.xsd: + authority: lov + description: The XML Schema representation + homepage: http://www.w3.org/2001/XMLSchema + id: lov.xsd + name: XML Schema + prefix: xsd + source: lov.linkeddata.es + subjects: [] + uri_format: http://www.w3.org/2001/XMLSchema#$1 +lov.yoga: + authority: lov + description: Yoga Ontology is the list of vocabularies that define the yogic practice. Where Yoga is the union of the mind and body. + homepage: https://yogaontology.org/ontology/ + id: lov.yoga + name: Yoga Ontology + prefix: yoga + source: lov.linkeddata.es + subjects: + - health sciences + uri_format: https://yogaontology.org/ontology/$1 +lov.zbwext: + authority: lov + description: Extensions to SKOS and other standard vocabularies used by the German National Library of Economics (ZBW) + homepage: http://zbw.eu/namespaces/zbw-extensions + id: lov.zbwext + name: ZBW Extensions + prefix: zbwext + source: lov.linkeddata.es + subjects: [] + uri_format: http://zbw.eu/namespaces/zbw-extensions/$1 diff --git a/fuji_server/data/linked_vocabs/mmisw_ontologies.json b/fuji_server/data/linked_vocabs/mmisw_ontologies.yaml similarity index 100% rename from fuji_server/data/linked_vocabs/mmisw_ontologies.json rename to fuji_server/data/linked_vocabs/mmisw_ontologies.yaml diff --git a/fuji_server/data/linked_vocabs/sdn_ontologies.json b/fuji_server/data/linked_vocabs/sdn_ontologies.json deleted file mode 100644 index 285b25cf..00000000 --- a/fuji_server/data/linked_vocabs/sdn_ontologies.json +++ /dev/null @@ -1,4160 +0,0 @@ -{ - "seadatanet.a01": { - "authority": "seadatanet", - "description": "Terms used at all hierarchical levels in the ICAN global thesaurus for coastal erosion. Terms used to populate drop-down lists in discovery portals.", - "homepage": "http://vocab.nerc.ac.uk/collection/A01/current/", - "id": "seadatanet.a01", - "name": "International Coastal Atlas Network Coastal Erosion Global Thesaurus", - "prefix": "a01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/A01/current/$1" - }, - "seadatanet.a02": { - "authority": "seadatanet", - "description": "Terms used at all hierarchical levels in the Oregon Coastal Atlas for coastal erosion layers, datasets and discovery.", - "homepage": "http://vocab.nerc.ac.uk/collection/A02/current/", - "id": "seadatanet.a02", - "name": "Oregon Coastal Atlas Coastal Erosion Thesaurus markup terms", - "prefix": "a02", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/A02/current/$1" - }, - "seadatanet.a03": { - "authority": "seadatanet", - "description": "Terms used at all hierarchical levels in the Oregon Coastal Atlas for categorisation and discovery, but not for layer or dataset markup.", - "homepage": "http://vocab.nerc.ac.uk/collection/A03/current/", - "id": "seadatanet.a03", - "name": "Oregon Coastal Atlas Coastal Erosion Thesaurus discovery terms", - "prefix": "a03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/A03/current/$1" - }, - "seadatanet.a04": { - "authority": "seadatanet", - "description": "A collection of terms used by the Irish Marine Data Atlas in association with the topic of coastal erosion", - "homepage": "http://vocab.nerc.ac.uk/collection/A04/current/", - "id": "seadatanet.a04", - "name": "MIDA Coastal Erosion Thesaurus", - "prefix": "a04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/A04/current/$1" - }, - "seadatanet.a05": { - "authority": "seadatanet", - "description": "Collection of terms used to group key measurements into a set of Essential Variables (EV) and their associated units as part of the AtlantOS Atlantic Ocean dataset", - "homepage": "http://vocab.nerc.ac.uk/collection/A05/current/", - "id": "seadatanet.a05", - "name": "AtlantOS Essential Variables", - "prefix": "a05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/A05/current/$1" - }, - "seadatanet.b02": { - "authority": "seadatanet", - "description": "Internationally registered materials used to assess the accuracy of analyses and for laboratory intercomparability studies with unique identifiers assigned by BODC.", - "homepage": "http://vocab.nerc.ac.uk/collection/B02/current/", - "id": "seadatanet.b02", - "name": "BODC-annotated certified reference materials", - "prefix": "b02", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B02/current/$1" - }, - "seadatanet.b03": { - "authority": "seadatanet", - "description": "Terms used to classify the type of reference material used by laboratories in the verification of analytical techniques in terms of consistency, accuracy and precision", - "homepage": "http://vocab.nerc.ac.uk/collection/B03/current/", - "id": "seadatanet.b03", - "name": "BODC-annotated reference material classifiers", - "prefix": "b03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B03/current/$1" - }, - "seadatanet.b04": { - "authority": "seadatanet", - "description": "Terms used to populate the title field in the BODC address book.", - "homepage": "http://vocab.nerc.ac.uk/collection/B04/current/", - "id": "seadatanet.b04", - "name": "BODC people titles", - "prefix": "b04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B04/current/$1" - }, - "seadatanet.b05": { - "authority": "seadatanet", - "description": "Terms used by BODC to describe roles that may be given to people within a governance structure.", - "homepage": "http://vocab.nerc.ac.uk/collection/B05/current/", - "id": "seadatanet.b05", - "name": "BODC governance roles", - "prefix": "b05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B05/current/$1" - }, - "seadatanet.b06": { - "authority": "seadatanet", - "description": "Terms describing automated integrity checks applied to data and metadata during BODC quality control.", - "homepage": "http://vocab.nerc.ac.uk/collection/B06/current/", - "id": "seadatanet.b06", - "name": "BODC data and metadata integrity checks", - "prefix": "b06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B06/current/$1" - }, - "seadatanet.b07": { - "authority": "seadatanet", - "description": "A catalogue of deployment methods of sampling net gears for the collection of mainly plankton, micronekton, and neuston organisms based on Wiebe P.H. et al. (2014)", - "homepage": "http://vocab.nerc.ac.uk/collection/B07/current/", - "id": "seadatanet.b07", - "name": "Sampling net gear deployment vocabulary", - "prefix": "b07", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B07/current/$1" - }, - "seadatanet.b09": { - "authority": "seadatanet", - "description": "Terms used to describe single and multiple nations who own datasets (and are part of the Celtic Seas Partnership) bounding the Celtic Seas Marine Region as designated by the Marine Strategy Framework Directive (MSFD)", - "homepage": "http://vocab.nerc.ac.uk/collection/B09/current/", - "id": "seadatanet.b09", - "name": "Celtic Seas Partnership data owner nations bordering MSFD Celtic Seas Marine Region", - "prefix": "b09", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B09/current/$1" - }, - "seadatanet.b11": { - "authority": "seadatanet", - "description": "Procedures or protocols that have been adopted by communities to ensure consistent and comparable methods are used when making observations from the environment. This also includes derivation and quality assurance practices.", - "homepage": "http://vocab.nerc.ac.uk/collection/B11/current/", - "id": "seadatanet.b11", - "name": "BODC Standard Operating Procedures and Protocols for environmental observations", - "prefix": "b11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B11/current/$1" - }, - "seadatanet.b12": { - "authority": "seadatanet", - "description": "Terms used by BODC to define measurement attributes described by numbers associated with data held in its repositories.", - "homepage": "http://vocab.nerc.ac.uk/collection/B12/current/", - "id": "seadatanet.b12", - "name": "BODC measurement numeric attribute types", - "prefix": "b12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B12/current/$1" - }, - "seadatanet.b20": { - "authority": "seadatanet", - "description": "Terms used by the Celtic Seas Partnership to categorise stakeholders according to the marine areas within which they operate.", - "homepage": "http://vocab.nerc.ac.uk/collection/B20/current/", - "id": "seadatanet.b20", - "name": "Celtic Seas Partnership stakeholder sectors", - "prefix": "b20", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B20/current/$1" - }, - "seadatanet.b21": { - "authority": "seadatanet", - "description": "Terms used by the Celtic Seas Partnership to broadly describe the spatial area of influence of a project, programme or initiative.", - "homepage": "http://vocab.nerc.ac.uk/collection/B21/current/", - "id": "seadatanet.b21", - "name": "Celtic Seas Partnership scale", - "prefix": "b21", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B21/current/$1" - }, - "seadatanet.b22": { - "authority": "seadatanet", - "description": "Terms used by the Celtic Seas Partnership to describe the transboundary nature of a project, programme or initiative.", - "homepage": "http://vocab.nerc.ac.uk/collection/B22/current/", - "id": "seadatanet.b22", - "name": "Celtic Seas Partnership governance mechanisms", - "prefix": "b22", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/B22/current/$1" - }, - "seadatanet.b39": { - "authority": "seadatanet", - "description": "Names of variables recorded into NetCDF files by the underway monitoring system on National Marine Facilities Sea Systems (NMF-SS) research vessels such as the RRS James Cook and RRS Discovery. 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"subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C17/current/$1" - }, - "seadatanet.c18": { - "authority": "seadatanet", - "description": "Country names published by ICES on behalf of IOC as part of their RNODC (formats) responsibility. 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], - "uri_format": "http://vocab.nerc.ac.uk/collection/C41/current/$1" - }, - "seadatanet.c43": { - "authority": "seadatanet", - "description": "Terms developed by BODC to classify the magnitude of a discharge of oil into the marine environment", - "homepage": "http://vocab.nerc.ac.uk/collection/C43/current/", - "id": "seadatanet.c43", - "name": "BODC oilspill quantity", - "prefix": "c43", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C43/current/$1" - }, - "seadatanet.c45": { - "authority": "seadatanet", - "description": "Concepts specified as descriptors of good environmental status as defined by the Marine Strategy Framework Directive as published in 2010/477/EU: Commission Decision of 1 September 2010 on criteria and methodological standards on good environmental status of marine waters (notified under document C(2010) 5956).", - "homepage": "http://vocab.nerc.ac.uk/collection/C45/current/", - "id": "seadatanet.c45", - "name": "Marine Strategy Framework Directive descriptors 2010/477/EU", - "prefix": "c45", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C45/current/$1" - }, - "seadatanet.c46": { - "authority": "seadatanet", - "description": "Concepts specified as criteria to be used to measure good environmental status as defined by the Marine Strategy Framework Directive as published in 2010/477/EU: Commission Decision of 1 September 2010 on criteria and methodological standards on good environmental status of marine waters (notified under document C(2010) 5956).", - "homepage": "http://vocab.nerc.ac.uk/collection/C46/current/", - "id": "seadatanet.c46", - "name": "Marine Strategy Framework Directive criteria 2010/477/EU", - "prefix": "c46", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C46/current/$1" - }, - "seadatanet.c47": { - "authority": "seadatanet", - "description": "Concepts specified as indicators to be used to measure good environmental status as defined by the Marine Strategy Framework Directive as published in 2010/477/EU: Commission Decision of 1 September 2010 on criteria and methodological standards on good environmental status of marine waters (notified under document C(2010) 5956).", - "homepage": "http://vocab.nerc.ac.uk/collection/C47/current/", - "id": "seadatanet.c47", - "name": "Marine Strategy Framework Directive indicators 2010/477/EU", - "prefix": "c47", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C47/current/$1" - }, - "seadatanet.c48": { - "authority": "seadatanet", - "description": "Documents produced by the Marine Environmental Data and Information Network specifying information content standards for the collection of specific types of marine data", - 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"id": "seadatanet.c62", - "name": "BODC administrative region names", - "prefix": "c62", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C62/current/$1" - }, - "seadatanet.c64": { - "authority": "seadatanet", - "description": "Terms used specify regions of the seas around the UK based on bio-geographical features rather than administrative boundaries", - "homepage": "http://vocab.nerc.ac.uk/collection/C64/current/", - "id": "seadatanet.c64", - "name": "United Kingdom Charting Progress 2 sea regions", - "prefix": "c64", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C64/current/$1" - }, - "seadatanet.c67": { - "authority": "seadatanet", - "description": "Terms used by BODC to describe groups of related parameters brought together to form a series from the sample schema. 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"source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C87/current/$1" - }, - "seadatanet.c88": { - "authority": "seadatanet", - "description": "Terms used by BODC to describe roles specifying access rights to assets, which include data objects, web pages, services and vocabulary lists.", - "homepage": "http://vocab.nerc.ac.uk/collection/C88/current/", - "id": "seadatanet.c88", - "name": "BODC asset access right roles", - "prefix": "c88", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C88/current/$1" - }, - "seadatanet.c89": { - "authority": "seadatanet", - "description": "Terms used by BODC for roles that describe the relationship between a person or organisation with a specific dataset.", - "homepage": "http://vocab.nerc.ac.uk/collection/C89/current/", - "id": "seadatanet.c89", - "name": "BODC dataset roles", - "prefix": "c89", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C89/current/$1" - }, - "seadatanet.c96": { - "authority": "seadatanet", - "description": "Entities in the BODC data model that may be associated with a spatial coverage in the real world", - "homepage": "http://vocab.nerc.ac.uk/collection/C96/current/", - "id": "seadatanet.c96", - "name": "BODC data model spatial objects", - "prefix": "c96", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C96/current/$1" - }, - "seadatanet.c98": { - "authority": "seadatanet", - "description": "Terms used to classify the lists held in the Vocabulary Server (formerly known as code tables) by the subject of their contents.", - "homepage": "http://vocab.nerc.ac.uk/collection/C98/current/", - "id": "seadatanet.c98", - "name": "Vocabulary Server list subject categories", - "prefix": "c98", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/C98/current/$1" - }, - "seadatanet.d01": { - "authority": "seadatanet", - "description": "A vocabulary of SKOS top concepts for use as entry points to a SKOS scheme defining the DCAT theme keywords for use in linked data representations of the SeaDataNet EDMED catalogue.", - "homepage": "http://vocab.nerc.ac.uk/collection/D01/current/", - "id": "seadatanet.d01", - "name": "DCAT Themes for Linked Data Representation of the SeaDataNet EDMED Catalogue", - "prefix": "d01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/D01/current/$1" - }, - "seadatanet.e01": { - "authority": "seadatanet", - "description": "Names of stations providing sea level data into the ESEAS network.", - 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}, - "seadatanet.el1": { - "authority": "seadatanet", - "description": "Terms used to identify actions performed on sampling and observation platforms. 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This vocabulary is the result of an harmonisation exercise between the Eurofleets Automatic Reporting System (EARS) ontology and the Rolling Deck to Repository (R2R) project, for research vessel event logs. 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"oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/F02/current/$1" - }, - "seadatanet.g01": { - "authority": "seadatanet", - "description": "Identification of when a given event occurred", - "homepage": "http://vocab.nerc.ac.uk/collection/G01/current/", - "id": "seadatanet.g01", - "name": "CI_DateTypeCode", - "prefix": "g01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G01/current/$1" - }, - "seadatanet.g02": { - "authority": "seadatanet", - "description": "Function performed by the resource", - "homepage": "http://vocab.nerc.ac.uk/collection/G02/current/", - "id": "seadatanet.g02", - "name": "CI_OnlineFunctionCode", - "prefix": "g02", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G02/current/$1" - }, - "seadatanet.g03": { - "authority": "seadatanet", - "description": "Mode in which the data are represented", - "homepage": "http://vocab.nerc.ac.uk/collection/G03/current/", - "id": "seadatanet.g03", - "name": "CI_PresentationFormCode", - "prefix": "g03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G03/current/$1" - }, - "seadatanet.g04": { - "authority": "seadatanet", - "description": "Function performed by the responsible party", - "homepage": "http://vocab.nerc.ac.uk/collection/G04/current/", - "id": "seadatanet.g04", - "name": "CI_RoleCode", - "prefix": "g04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G04/current/$1" - }, - "seadatanet.g05": { - "authority": "seadatanet", - "description": "Type or method for evaluating an identified data quality measure", - "homepage": "http://vocab.nerc.ac.uk/collection/G05/current/", - "id": "seadatanet.g05", - "name": "DQ_EvaluationMethodTypeCode", - "prefix": "g05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G05/current/$1" - }, - "seadatanet.g06": { - "authority": "seadatanet", - "description": "Justification for the correlation of two datasets", - "homepage": "http://vocab.nerc.ac.uk/collection/G06/current/", - "id": "seadatanet.g06", - "name": "DS_AssociationTypeCode", - "prefix": "g06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G06/current/$1" - }, - "seadatanet.g07": { - "authority": "seadatanet", - "description": "Type of aggregation activity in which datasets are related", - "homepage": "http://vocab.nerc.ac.uk/collection/G07/current/", - "id": "seadatanet.g07", - "name": "DS_InitiativeTypeCode", - "prefix": "g07", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G07/current/$1" - }, - "seadatanet.g08": { - "authority": "seadatanet", - "description": "Code indicating whether grid data are points or area", - "homepage": "http://vocab.nerc.ac.uk/collection/G08/current/", - "id": "seadatanet.g08", - "name": "MD_CellGeometryCode", - "prefix": "g08", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G08/current/$1" - }, - "seadatanet.g09": { - "authority": "seadatanet", - "description": "Name of the character coding standard used in the resource", - "homepage": "http://vocab.nerc.ac.uk/collection/G09/current/", - "id": "seadatanet.g09", - "name": "MD_CharacterSetCode", - "prefix": "g09", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G09/current/$1" - }, - "seadatanet.g10": { - "authority": "seadatanet", - "description": "Name of the handling restrictions on the dataset", - "homepage": "http://vocab.nerc.ac.uk/collection/G10/current/", - "id": "seadatanet.g10", - "name": "MD_ClassificationCode", - "prefix": "g10", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G10/current/$1" - }, - "seadatanet.g11": { - "authority": "seadatanet", - "description": "Specific type of information represented in the cell", - "homepage": "http://vocab.nerc.ac.uk/collection/G11/current/", - "id": "seadatanet.g11", - "name": "MD_CoverageContentTypeCode", - "prefix": "g11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G11/current/$1" - }, - "seadatanet.g12": { - "authority": "seadatanet", - "description": "Datatype of element or entity", - "homepage": "http://vocab.nerc.ac.uk/collection/G12/current/", - "id": "seadatanet.g12", - "name": "MD_DatatypeCode", - "prefix": "g12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G12/current/$1" - }, - "seadatanet.g13": { - "authority": "seadatanet", - "description": "Name of the dimension", - "homepage": "http://vocab.nerc.ac.uk/collection/G13/current/", - "id": "seadatanet.g13", - "name": "MD_DimensionNameTypeCode ", - "prefix": "g13", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G13/current/$1" - }, - "seadatanet.g14": { - "authority": "seadatanet", - "description": "Name of point or vector objects used to locate zero-, one-, two-, or three-dimensional spatial locations in the dataset", - "homepage": "http://vocab.nerc.ac.uk/collection/G14/current/", - "id": "seadatanet.g14", - "name": "MD_GeometricObjectTypeCode", - "prefix": "g14", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G14/current/$1" - }, - "seadatanet.g15": { - "authority": "seadatanet", - "description": "Code which indicates conditions which may affect the image", - "homepage": "http://vocab.nerc.ac.uk/collection/G15/current/", - "id": "seadatanet.g15", - "name": "MD_ImagingConditionCode ", - "prefix": "g15", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G15/current/$1" - }, - "seadatanet.g17": { - "authority": "seadatanet", - "description": "Frequency with which modifications and deletions are made to the data after they are first produced", - "homepage": "http://vocab.nerc.ac.uk/collection/G17/current/", - "id": "seadatanet.g17", - "name": "MD_MaintenanceFrequencyCode", - "prefix": "g17", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G17/current/$1" - }, - "seadatanet.g18": { - "authority": "seadatanet", - "description": "Method used to write to the medium", - "homepage": "http://vocab.nerc.ac.uk/collection/G18/current/", - "id": "seadatanet.g18", - "name": "MD_MediumFormatCode", - "prefix": "g18", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G18/current/$1" - }, - "seadatanet.g20": { - "authority": "seadatanet", - "description": "Obligation of the element or entity", - "homepage": "http://vocab.nerc.ac.uk/collection/G20/current/", - "id": "seadatanet.g20", - "name": "MD_ObligationCode", - "prefix": "g20", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G20/current/$1" - }, - "seadatanet.g21": { - "authority": "seadatanet", - "description": "Point in a pixel corresponding to the Earth location of the pixel", - "homepage": "http://vocab.nerc.ac.uk/collection/G21/current/", - "id": "seadatanet.g21", - "name": "MD_PixelOrientationCode", - "prefix": "g21", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/G21/current/$1" - }, - "seadatanet.g22": { - "authority": "seadatanet", - "description": "Status of the dataset or progress of a review", - "homepage": "http://vocab.nerc.ac.uk/collection/G22/current/", - "id": "seadatanet.g22", - 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Known in SEA-SEARCH as 'Library 2' or cdi_measurement_codes.", - "homepage": "http://vocab.nerc.ac.uk/collection/L02/current/", - "id": "seadatanet.l02", - "name": "SeaDataNet Geospatial Feature Types", - "prefix": "l02", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L02/current/$1" - }, - "seadatanet.l03": { - "authority": "seadatanet", - "description": "Terms used to express a classification of measurement periodicity in the SeaDataNet project.", - "homepage": "http://vocab.nerc.ac.uk/collection/L03/current/", - "id": "seadatanet.l03", - "name": "SeaDataNet Measurement Periodicity Categories", - "prefix": "l03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L03/current/$1" - }, - "seadatanet.l04": { - "authority": "seadatanet", - "description": "Terms used to group features or objects (sometimes called features of interest) in which measurements or observations may be made or of which samples may be collected.", - "homepage": "http://vocab.nerc.ac.uk/collection/L04/current/", - "id": "seadatanet.l04", - "name": "Matrix Categories", - "prefix": "l04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L04/current/$1" - }, - "seadatanet.l05": { - "authority": "seadatanet", - "description": "Terms used to classify groups of sensors, instruments, sources of algorithmically computed data (numerical models) or samplers (collectors of water, SPM, sediment, rock, air or biota samples).", - "homepage": "http://vocab.nerc.ac.uk/collection/L05/current/", - "id": "seadatanet.l05", - "name": "SeaDataNet device categories", - "prefix": "l05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L05/current/$1" - }, - "seadatanet.l06": { - "authority": "seadatanet", - "description": "2-level grouping term hierarchy used for vehicles, structures or organisms capable of bearing instruments or tools for the collection of physical, chemical, geological or biological samples or data.", - "homepage": "http://vocab.nerc.ac.uk/collection/L06/current/", - "id": "seadatanet.l06", - "name": "SeaVoX Platform Categories", - "prefix": "l06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L06/current/$1" - }, - "seadatanet.l07": { - "authority": "seadatanet", - "description": "Terms for mechanisms by which data objects described by SeaDataNet Central Data Index (CDI) records may be obtained before SeaDataNet is fully implemented.", - "homepage": "http://vocab.nerc.ac.uk/collection/L07/current/", - "id": "seadatanet.l07", - "name": "SeaDataNet data access mechanisms", - "prefix": "l07", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L07/current/$1" - }, - "seadatanet.l08": { - "authority": "seadatanet", - "description": "Terms used to represent and classify data access policies in operation in the SeaDataNet project.", - "homepage": "http://vocab.nerc.ac.uk/collection/L08/current/", - "id": "seadatanet.l08", - "name": "SeaDataNet Data Access Restriction Policies", - "prefix": "l08", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L08/current/$1" - }, - "seadatanet.l10": { - "authority": "seadatanet", - "description": "Co-ordinate reference systems used for positions (latitude/longitude or grid references) in SeaDataNet metadata. May include 3D co-ordinate systems, but not vertical elevation datums like OD Newlyn.", - "homepage": "http://vocab.nerc.ac.uk/collection/L10/current/", - "id": "seadatanet.l10", - "name": "SeaDataNet geographic co-ordinate reference frames", - "prefix": "l10", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L10/current/$1" - }, - "seadatanet.l11": { - "authority": "seadatanet", - "description": "Terms used to describe the zero point for vertical co-ordinate reference systems (datums).", - "homepage": "http://vocab.nerc.ac.uk/collection/L11/current/", - "id": "seadatanet.l11", - "name": "SeaDataNet depth measurement reference planes", - "prefix": "l11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L11/current/$1" - }, - "seadatanet.l12": { - "authority": "seadatanet", - "description": "Terms that are used to describe quality control procedures applied to data parameters.", - "homepage": "http://vocab.nerc.ac.uk/collection/L12/current/", - "id": "seadatanet.l12", - "name": "SeaDataNet parameter quality control procedures", - "prefix": "l12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L12/current/$1" - }, - "seadatanet.l13": { - "authority": "seadatanet", - "description": "Terms used to describe data coverage over the vertical (z) co-ordinate.", - "homepage": "http://vocab.nerc.ac.uk/collection/L13/current/", - "id": "seadatanet.l13", - "name": "SeaVoX Vertical Co-ordinate Coverages", - "prefix": "l13", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L13/current/$1" - }, - "seadatanet.l14": { - "authority": "seadatanet", - "description": "Terms used to describe the operational status of data collection activities within the SeaDataNet project.", - "homepage": "http://vocab.nerc.ac.uk/collection/L14/current/", - "id": "seadatanet.l14", - "name": "SeaDataNet Activity Operational Stati", - "prefix": "l14", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L14/current/$1" - }, - "seadatanet.l15": { - "authority": "seadatanet", - "description": "Terms used to by SeaDataNet to describe formally recognised standards for data acquisition and handling procedures.", - "homepage": "http://vocab.nerc.ac.uk/collection/L15/current/", - "id": "seadatanet.l15", - "name": "SeaDataNet quality management system accreditations", - "prefix": "l15", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L15/current/$1" - }, - "seadatanet.l18": { - "authority": "seadatanet", - "description": "Terms used as units in the quantification of what was collected or measured in a Cruise Summary Report (ROSCOP) record.", - "homepage": "http://vocab.nerc.ac.uk/collection/L18/current/", - "id": "seadatanet.l18", - "name": "SeaDataNet Cruise Summary Report quantification units", - "prefix": "l18", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L18/current/$1" - }, - "seadatanet.l19": { - "authority": "seadatanet", - "description": "Terms used in SeaDataNet metadata to describe the purpose of a keyword. An extension of the ISO19115 KeywordTypeCode codelist.", - "homepage": "http://vocab.nerc.ac.uk/collection/L19/current/", - "id": "seadatanet.l19", - "name": "SeaDataNet keyword types", - "prefix": "l19", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L19/current/$1" - }, - "seadatanet.l20": { - "authority": "seadatanet", - "description": "Flags used to provide additional information, usually referring to data quality, about data values in SeaDataNet data files.", - "homepage": "http://vocab.nerc.ac.uk/collection/L20/current/", - "id": "seadatanet.l20", - "name": "SeaDataNet measurand qualifier flags", - "prefix": "l20", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L20/current/$1" - }, - "seadatanet.l21": { - "authority": "seadatanet", - "description": "High-level classification of devices based on function and mode of deployment.", - "homepage": "http://vocab.nerc.ac.uk/collection/L21/current/", - "id": "seadatanet.l21", - "name": "SeaDataNet device category types", - "prefix": "l21", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L21/current/$1" - }, - "seadatanet.l22": { - "authority": "seadatanet", - "description": "Terms for distinct sampling or measuring devices that may be identified in the real world in terms of manufacturer and model number.", - "homepage": "http://vocab.nerc.ac.uk/collection/L22/current/", - "id": "seadatanet.l22", - "name": "SeaVoX Device Catalogue", - "prefix": "l22", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L22/current/$1" - }, - "seadatanet.l23": { - "authority": "seadatanet", - "description": "Types of metadata record in the SeaDataNet metadata catalogue repositories", - "homepage": "http://vocab.nerc.ac.uk/collection/L23/current/", - "id": "seadatanet.l23", - "name": "SeaDataNet metadata entities", - "prefix": "l23", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L23/current/$1" - }, - "seadatanet.l24": { - "authority": "seadatanet", - "description": "Formats used for data delivery by SeaDataNet.", - "homepage": "http://vocab.nerc.ac.uk/collection/L24/current/", - "id": "seadatanet.l24", - "name": "SeaDataNet data transport formats", - "prefix": "l24", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L24/current/$1" - }, - "seadatanet.l26": { - "authority": "seadatanet", - "description": "Units of measure (P06 subset) that may be used for sampling intervals in the EDIOS metadata schema. Required to prevent times with units of kilograms!", - "homepage": "http://vocab.nerc.ac.uk/collection/L26/current/", - "id": "seadatanet.l26", - "name": "EDIOS permitted sampling interval units", - "prefix": "l26", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L26/current/$1" - }, - "seadatanet.l27": { - "authority": "seadatanet", - "description": "A catalogue including standardised labels of encoding schemes used for data value qualifying information such as data quality ", - "homepage": "http://vocab.nerc.ac.uk/collection/L27/current/", - "id": "seadatanet.l27", - "name": "SeaVoX data quality control flagging conventions", - "prefix": "l27", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L27/current/$1" - }, - "seadatanet.l30": { - "authority": "seadatanet", - "description": "Organisations supplying or holding data concerned with the EU MEDATLAS project.", - "homepage": "http://vocab.nerc.ac.uk/collection/L30/current/", - "id": "seadatanet.l30", - "name": "MEDATLAS Data Centres", - "prefix": "l30", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L30/current/$1" - }, - "seadatanet.l31": { - "authority": "seadatanet", - "description": "Flags representing concepts used to specify quality of Geo-Seas data objects. These are a subset of SeaDataNet measurand qualifier flags.", - "homepage": "http://vocab.nerc.ac.uk/collection/L31/current/", - "id": "seadatanet.l31", - "name": "Geo-Seas data object quality flags", - "prefix": "l31", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L31/current/$1" - }, - "seadatanet.l33": { - "authority": "seadatanet", - "description": "Terms specified by WMO to label XBT data with the type of probe used and the algorithm used to compute depth.", - "homepage": "http://vocab.nerc.ac.uk/collection/L33/current/", - "id": "seadatanet.l33", - "name": "WMO C3 vocabulary of XBT data types", - "prefix": "l33", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L33/current/$1" - }, - "seadatanet.l34": { - "authority": "seadatanet", - "description": "Quality flags used for the primary level of the IODE Quality Flag Scheme for the Exchange of Oceanographic and Marine Meteorological Data, IODE Manuals and Guides 54, Vol. 3.", - "homepage": "http://vocab.nerc.ac.uk/collection/L34/current/", - "id": "seadatanet.l34", - "name": "IODE Primary Level quality flags", - "prefix": "l34", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L34/current/$1" - }, - "seadatanet.l35": { - "authority": "seadatanet", - "description": "A collection of terms which denote the manufacturers or developers of devices (includes manufacturer and/or developer collaborations).", - "homepage": "http://vocab.nerc.ac.uk/collection/L35/current/", - "id": "seadatanet.l35", - "name": "SenseOcean device developers and manufacturers", - "prefix": "l35", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/L35/current/$1" - }, - "seadatanet.m01": { - "authority": "seadatanet", - "description": "Terms describing what types of data formats exist in a data set so a human can identify if the data is likely to be of use and select a tool to interrogate that data.", - "homepage": "http://vocab.nerc.ac.uk/collection/M01/current/", - "id": "seadatanet.m01", - "name": "MEDIN data format categories", - "prefix": "m01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M01/current/$1" - }, - "seadatanet.m03": { - "authority": "seadatanet", - "description": "Terms used to describe different areas within an offshore renewable energy development.", - "homepage": "http://vocab.nerc.ac.uk/collection/M03/current/", - "id": "seadatanet.m03", - "name": "The Crown Estate Renewable Energy Development Areas", - "prefix": "m03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M03/current/$1" - }, - "seadatanet.m04": { - "authority": "seadatanet", - "description": "Terms used to describe different development phases of an offshore renewable energy development.", - "homepage": "http://vocab.nerc.ac.uk/collection/M04/current/", - "id": "seadatanet.m04", - "name": "The Crown Estate Renewable Energy Development Phases", - "prefix": "m04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M04/current/$1" - }, - "seadatanet.m05": { - "authority": "seadatanet", - "description": "Categories in a classification of the purpose and anticipated outcome of activities by governing bodies.", - "homepage": "http://vocab.nerc.ac.uk/collection/M05/current/", - "id": "seadatanet.m05", - "name": "MEDIN socio-economic governance objective categories", - "prefix": "m05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M05/current/$1" - }, - "seadatanet.m06": { - "authority": "seadatanet", - "description": "Categories in a classification of the purpose of activities in which the state of something at different times is determined.", - "homepage": "http://vocab.nerc.ac.uk/collection/M06/current/", - "id": "seadatanet.m06", - "name": "MEDIN monitoring activity categories", - "prefix": "m06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M06/current/$1" - }, - "seadatanet.m09": { - "authority": "seadatanet", - "description": "Terms used to classify techniques used to assess the socio-economic value of an ecosystem.", - "homepage": "http://vocab.nerc.ac.uk/collection/M09/current/", - "id": "seadatanet.m09", - "name": "MEDIN ecosystem valuation method types", - "prefix": "m09", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M09/current/$1" - }, - "seadatanet.m10": { - "authority": "seadatanet", - "description": "Terms used to describe techniques used to assess the socio-economic value of an ecosystem.", - "homepage": "http://vocab.nerc.ac.uk/collection/M10/current/", - "id": "seadatanet.m10", - "name": "MEDIN ecosystem valuation methods", - "prefix": "m10", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M10/current/$1" - }, - "seadatanet.m11": { - "authority": "seadatanet", - "description": "Terms used to classify the conditions and processes through which natural ecosystems sustain and fulfil human life.", - "homepage": "http://vocab.nerc.ac.uk/collection/M11/current/", - "id": "seadatanet.m11", - "name": "MEDIN ecosystem service types", - "prefix": "m11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M11/current/$1" - }, - "seadatanet.m12": { - "authority": "seadatanet", - "description": "Categories of activity carried out by humans which exert an impact on the marine environment, as defined by the Joint Nature Conservation Committee (JNCC) ", - "homepage": "http://vocab.nerc.ac.uk/collection/M12/current/", - "id": "seadatanet.m12", - "name": "JNCC categories of human activity in the marine environment", - "prefix": "m12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M12/current/$1" - }, - "seadatanet.m13": { - "authority": "seadatanet", - "description": "The standard list activities carried out by humans to manage the coastal environment, as defined by the Joint Nature Conservation Committee (JNCC)", - "homepage": "http://vocab.nerc.ac.uk/collection/M13/current/", - "id": "seadatanet.m13", - "name": "JNCC standard list of human activities in the marine environment", - "prefix": "m13", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M13/current/$1" - }, - "seadatanet.m14": { - "authority": "seadatanet", - "description": "List of defined pressures (stated by the Joint Nature Conservation Committee (JNCC) to be the mechanisms through which activities impact the marine environment) as specified by the Convention for the Protection of the Marine Environment for the North-East Atlantic (OSPAR) International Correspondence Group on Cumulative Effects (ICG-C) and distributed by the Joint Nature Conservation Committee ", - "homepage": "http://vocab.nerc.ac.uk/collection/M14/current/", - "id": "seadatanet.m14", - "name": "OSPAR list of defined pressures on the marine environment", - "prefix": "m14", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M14/current/$1" - }, - "seadatanet.m15": { - "authority": "seadatanet", - "description": "Themes under which defined pressures in M14 are categorised by the Convention for the Protection of the Marine Environment for the North-East Atlantic (OSPAR) International Correspondence Group on Cumulative Effects (ICG-C) and distributed by the Joint Nature Conservation Committee (JNCC) ", - "homepage": "http://vocab.nerc.ac.uk/collection/M15/current/", - "id": "seadatanet.m15", - "name": "OSPAR list of themes of defined pressures on the marine environment", - "prefix": "m15", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/M15/current/$1" - }, - "seadatanet.m16": { - "authority": "seadatanet", - "description": "Terms used to describe techniques used by marine engineers to investigate marine earth materials. 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The list is used to populate \nhttp://purl.org/spar/datacite/hasGeneralResourceType from the EDC's GEMINI profiles.", - "homepage": "http://vocab.nerc.ac.uk/collection/N06/current/", - "id": "seadatanet.n06", - "name": "NERC Environmental Data Centres DataCite General Resource Types", - "prefix": "n06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/N06/current/$1" - }, - "seadatanet.od1": { - "authority": "seadatanet", - "description": "Collection of terms used within the French Ocean Data and Services Cluster ODATIS for data discovery and product or dataset aggregation. Whenever applicable, Essential Variable terms are linked to the authoritative source of Essential Climate Ocean and Biodiversity Variable definitions maintained by the Global Observing System for Climate (GCOS), the Global Ocean Observing System (GOOS) and the Group on Earth Observations Biodiversity Observation Network (GEO BON).", - "homepage": "http://vocab.nerc.ac.uk/collection/OD1/current/", - "id": "seadatanet.od1", - "name": "ODATIS aggregation parameters and Essential Variable names", - "prefix": "od1", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/OD1/current/$1" - }, - "seadatanet.og1": { - "authority": "seadatanet", - "description": "Terms in this vocabulary are under the content governance of the OceanGliders Data Management Task Team (OGDMTT) on behalf of the OceanGliders community and Everyone's Gliding Observatories (EGO). Terms describe measured phenomena within the OG/EGO format.", - "homepage": "http://vocab.nerc.ac.uk/collection/OG1/current/", - "id": "seadatanet.og1", - "name": "OceanGliders Parameter Usage Vocabulary", - "prefix": "og1", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/OG1/current/$1" - }, - "seadatanet.p01": { - "authority": "seadatanet", - "description": "Terms built using the BODC parameter semantic model designed to describe individual measured phenomena. May be used to mark up sets of data such as a NetCDF array or spreadsheet column. Units must be specified when using a P01 code. The P06 unit that is linked to individual P01 in the NVS is the one used in BODC's systems but external users can use any appropriate units.", - "homepage": "http://vocab.nerc.ac.uk/collection/P01/current/", - "id": "seadatanet.p01", - "name": "BODC Parameter Usage Vocabulary", - "prefix": "p01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P01/current/$1" - }, - "seadatanet.p02": { - "authority": "seadatanet", - "description": "Terms describing fine-grained related groups of measurement phenomena designed to be used in dataset discovery interfaces.", - "homepage": "http://vocab.nerc.ac.uk/collection/P02/current/", - "id": "seadatanet.p02", - "name": "SeaDataNet Parameter Discovery Vocabulary", - "prefix": "p02", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P02/current/$1" - }, - "seadatanet.p03": { - "authority": "seadatanet", - "description": "Terms agreed within the EU SeaDataNet community to describe coarse-grained groupings of related measurement phenomena.", - "homepage": "http://vocab.nerc.ac.uk/collection/P03/current/", - "id": "seadatanet.p03", - "name": "SeaDataNet Agreed Parameter Groups", - "prefix": "p03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P03/current/$1" - }, - "seadatanet.p04": { - "authority": "seadatanet", - "description": "Concatenated category, topic, term and variable separated by '>'. From Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3.", - "homepage": "http://vocab.nerc.ac.uk/collection/P04/current/", - "id": "seadatanet.p04", - "name": "Global Change Master Directory Science Keywords V5", - "prefix": "p04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P04/current/$1" - }, - "seadatanet.p05": { - "authority": "seadatanet", - "description": "Terms defined by ISO describing data themes. Used to populate the mandatory ISO19115 topic category field.", - "homepage": "http://vocab.nerc.ac.uk/collection/P05/current/", - "id": "seadatanet.p05", - "name": "International Standards Organisation ISO19115 Topic Categories", - "prefix": "p05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P05/current/$1" - }, - "seadatanet.p06": { - "authority": "seadatanet", - "description": "Terms approved for use by BODC to describe the measurement units for data held in its repositories.", - "homepage": "http://vocab.nerc.ac.uk/collection/P06/current/", - "id": "seadatanet.p06", - "name": "BODC-approved data storage units", - "prefix": "p06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P06/current/$1" - }, - "seadatanet.p07": { - "authority": "seadatanet", - "description": "Terms used for definitive but not necessarily comprehensive descriptions of measured phenomena in the CF conventions (a content standard for data stored in NetCDF).", - "homepage": "http://vocab.nerc.ac.uk/collection/P07/current/", - "id": "seadatanet.p07", - "name": "Climate and Forecast Standard Names", - "prefix": "p07", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P07/current/$1" - }, - "seadatanet.p08": { - "authority": "seadatanet", - "description": "Terms used to classify SeaDataNet Agreed Parameter Groups to provide topic/theme level terms in a hierarchical parameter discovery interface.", - "homepage": "http://vocab.nerc.ac.uk/collection/P08/current/", - "id": "seadatanet.p08", - "name": "SeaDataNet Parameter Disciplines", - "prefix": "p08", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P08/current/$1" - }, - "seadatanet.p09": { - "authority": "seadatanet", - "description": "Terms under the content governance of SISMER used to describe measured phenomena within the MEDATLAS project.", - "homepage": "http://vocab.nerc.ac.uk/collection/P09/current/", - "id": "seadatanet.p09", - "name": "MEDATLAS Parameter Usage Vocabulary", - "prefix": "p09", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P09/current/$1" - }, - "seadatanet.p10": { - "authority": "seadatanet", - "description": "Terms used to describe sensors, instruments and other pieces of scientific equipment in the NASA Global Change Master Directory metadatabase.", - "homepage": "http://vocab.nerc.ac.uk/collection/P10/current/", - "id": "seadatanet.p10", - "name": "Global Change Master Directory Instrument Keywords", - "prefix": "p10", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P10/current/$1" - }, - "seadatanet.p11": { - "authority": "seadatanet", - "description": "Category level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3.", - "homepage": "http://vocab.nerc.ac.uk/collection/P11/current/", - "id": "seadatanet.p11", - "name": "Global Change Master Directory Science Keyword categories", - "prefix": "p11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P11/current/$1" - }, - "seadatanet.p12": { - "authority": "seadatanet", - "description": "Topic level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3.", - "homepage": "http://vocab.nerc.ac.uk/collection/P12/current/", - "id": "seadatanet.p12", - "name": "Global Change Master Directory Science Keyword topics", - "prefix": "p12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P12/current/$1" - }, - "seadatanet.p13": { - "authority": "seadatanet", - "description": "Term level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3.", - "homepage": "http://vocab.nerc.ac.uk/collection/P13/current/", - "id": "seadatanet.p13", - "name": "Global Change Master Directory Science Keyword terms", - "prefix": "p13", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P13/current/$1" - }, - "seadatanet.p14": { - "authority": "seadatanet", - "description": "Variable level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3.", - "homepage": "http://vocab.nerc.ac.uk/collection/P14/current/", - "id": "seadatanet.p14", - "name": "Global Change Master Directory Science Keyword variables", - "prefix": "p14", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P14/current/$1" - }, - "seadatanet.p15": { - "authority": "seadatanet", - "description": "Terms used to describe measured phenomena derivation algorithms in the CF conventions (a content standard for data stored in NetCDF), primarily targeted at statistical parameters.", - "homepage": "http://vocab.nerc.ac.uk/collection/P15/current/", - "id": "seadatanet.p15", - "name": "Climate and Forecast Cell Methods", - "prefix": "p15", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P15/current/$1" - }, - "seadatanet.p17": { - "authority": "seadatanet", - "description": "Research vessels deemed to be of interest to POGO. 'Of interest' is defined as active ocean-going research vessels greater than 60m in length", - "homepage": "http://vocab.nerc.ac.uk/collection/P17/current/", - "id": "seadatanet.p17", - "name": "Partnership for Observation of the Global Ocean ships of interest", - "prefix": "p17", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P17/current/$1" - }, - "seadatanet.p18": { - "authority": "seadatanet", - "description": "Chronostratigraphic unit terms from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3.", - "homepage": "http://vocab.nerc.ac.uk/collection/P18/current/", - "id": "seadatanet.p18", - "name": "Global Change Master Directory Chronostratigraphic Units", - "prefix": "p18", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P18/current/$1" - }, - "seadatanet.p19": { - "authority": "seadatanet", - "description": "Terms used to describe sensor-bearing platforms from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3.", - "homepage": "http://vocab.nerc.ac.uk/collection/P19/current/", - "id": "seadatanet.p19", - "name": "Global Change Master Directory platforms", - "prefix": "p19", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P19/current/$1" - }, - "seadatanet.p20": { - "authority": "seadatanet", - "description": "Terms used in NASA's GCMD to describe the function of related URLs embedded in DIF metadata records. Also used for NERC DataGrid service bindings.", - "homepage": "http://vocab.nerc.ac.uk/collection/P20/current/", - "id": "seadatanet.p20", - "name": "Global Change Master Directory URL content types", - "prefix": "p20", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P20/current/$1" - }, - "seadatanet.p21": { - "authority": "seadatanet", - "description": "Base terms (all hierarchical levels) interlinked by a relationship network to build the Marisaurus thesaurus.", - "homepage": "http://vocab.nerc.ac.uk/collection/P21/current/", - "id": "seadatanet.p21", - "name": "Marisaurus Thesaurus", - "prefix": "p21", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P21/current/$1" - }, - "seadatanet.p22": { - "authority": "seadatanet", - "description": "Groupings of spatial data according to Annex I, II and III of the INSPIRE Directive [DS-D2.5]", - "homepage": "http://vocab.nerc.ac.uk/collection/P22/current/", - "id": "seadatanet.p22", - "name": "GEMET - INSPIRE themes, version 1.0", - "prefix": "p22", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P22/current/$1" - }, - "seadatanet.p23": { - "authority": "seadatanet", - "description": "Coarse grained grouping terms designed by MEDIN to provide the top level for a parameter discovery thesaurus.", - "homepage": "http://vocab.nerc.ac.uk/collection/P23/current/", - "id": "seadatanet.p23", - "name": "MEDIN Parameter Discipline Keywords", - "prefix": "p23", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P23/current/$1" - }, - "seadatanet.p24": { - "authority": "seadatanet", - "description": "Classification concepts for units of measure based upon the fundamental SI quantities upon which they are based.", - "homepage": "http://vocab.nerc.ac.uk/collection/P24/current/", - "id": "seadatanet.p24", - "name": "Units of measure dimensions", - "prefix": "p24", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P24/current/$1" - }, - "seadatanet.p25": { - "authority": "seadatanet", - "description": "Terms used to describe phenomena within the NETMAR project at a granularity level suitable for labelling data aggregations or assessing whether the parameter is appropriate as an input to a given WPS.", - "homepage": "http://vocab.nerc.ac.uk/collection/P25/current/", - "id": "seadatanet.p25", - "name": "NETMAR aggregation parameters", - "prefix": "p25", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P25/current/$1" - }, - "seadatanet.p26": { - "authority": "seadatanet", - "description": "A collection of categories and sub-categories developed by ISO to classify services that display or process spatial data", - "homepage": "http://vocab.nerc.ac.uk/collection/P26/current/", - "id": "seadatanet.p26", - "name": "ISO19119 geographic services taxonomy", - "prefix": "p26", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P26/current/$1" - }, - "seadatanet.p27": { - "authority": "seadatanet", - "description": "Terms used to describe the environmental spatial location of an aliquot of a simulated oil spill by the METEO France MOTHY model.", - "homepage": "http://vocab.nerc.ac.uk/collection/P27/current/", - "id": "seadatanet.p27", - "name": "Oil spill spillet location", - "prefix": "p27", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P27/current/$1" - }, - "seadatanet.p28": { - "authority": "seadatanet", - "description": "Terms used to describe the operational stati of pollution cleanup sites in the Cedre cleanup site service.", - "homepage": "http://vocab.nerc.ac.uk/collection/P28/current/", - "id": "seadatanet.p28", - "name": "Cedre pollution site cleanup operational stati", - "prefix": "p28", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P28/current/$1" - }, - "seadatanet.p29": { - "authority": "seadatanet", - "description": "Terms used to describe the characteristics of regions of the Earth's Surface or their representation in a numerical simulation in the CF metadata conventions for data stored in NetCDF.", - "homepage": "http://vocab.nerc.ac.uk/collection/P29/current/", - "id": "seadatanet.p29", - "name": "Climate and Forecast Area Types", - "prefix": "p29", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P29/current/$1" - }, - "seadatanet.p30": { - "authority": "seadatanet", - "description": "Terms used to label regions of the Earth's Surface or their representation in a numerical simulation in the CF metadata conventions for data stored in NetCDF.", - "homepage": "http://vocab.nerc.ac.uk/collection/P30/current/", - "id": "seadatanet.p30", - "name": "Climate and Forecast Standardized Region Names", - "prefix": "p30", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P30/current/$1" - }, - "seadatanet.p31": { - "authority": "seadatanet", - "description": "Terms used to define the recognised metadata attributes for the description of CF-compliant data stored in NetCDF files.", - "homepage": "http://vocab.nerc.ac.uk/collection/P31/current/", - "id": "seadatanet.p31", - "name": "Climate and Forecast Attribute Names", - "prefix": "p31", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P31/current/$1" - }, - "seadatanet.p35": { - "authority": "seadatanet", - "description": "Labels used for aggregated parameters in the EMODNET chemistry lot", - "homepage": "http://vocab.nerc.ac.uk/collection/P35/current/", - "id": "seadatanet.p35", - "name": "EMODnet Chemistry aggregated parameter names", - "prefix": "p35", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P35/current/$1" - }, - "seadatanet.p36": { - "authority": "seadatanet", - "description": "Terms based on the EU MSFD used by the EMODNET chemistry lot to provide coarse granularity groupings of the chemical parameters it covers.", - "homepage": "http://vocab.nerc.ac.uk/collection/P36/current/", - "id": "seadatanet.p36", - "name": "EMODnet Chemistry chemical groups", - "prefix": "p36", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P36/current/$1" - }, - "seadatanet.p37": { - "authority": "seadatanet", - "description": "Terms used by the CF community to describe the calendar systems used for time co-ordinates in CF-compliant data files", - "homepage": "http://vocab.nerc.ac.uk/collection/P37/current/", - "id": "seadatanet.p37", - "name": "Climate and Forecast Calendars", - "prefix": "p37", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P37/current/$1" - }, - "seadatanet.p38": { - "authority": "seadatanet", - "description": "Terms used by the CF community to describe the data coverage over the vertical (z) co-ordinate. This is used to describe the Earth Realm in the CF Standard Name semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/P38/current/", - "id": "seadatanet.p38", - "name": "Climate and Forecast Vertical Co-ordinate Coverages", - "prefix": "p38", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P38/current/$1" - }, - "seadatanet.p64": { - "authority": "seadatanet", - "description": "Concatenated category, topic, term and variable separated by '>'. From Olsen L.M. et. al (2007) NASA/GCMD Earth Science Keywords Version 6.0.0.0", - "homepage": "http://vocab.nerc.ac.uk/collection/P64/current/", - "id": "seadatanet.p64", - "name": "Global Change Master Directory Science Keywords V6", - "prefix": "p64", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/P64/current/$1" - }, - "seadatanet.q01": { - "authority": "seadatanet", - "description": "Collection of terms used by the Ocean Biogeographic Information System to standardise attributes related to sampling instruments and methods.", - "homepage": "http://vocab.nerc.ac.uk/collection/Q01/current/", - "id": "seadatanet.q01", - "name": "OBIS sampling instruments and methods attributes", - "prefix": "q01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/Q01/current/$1" - }, - "seadatanet.r01": { - "authority": "seadatanet", - "description": "Terms describing the type of data contained in an Argo netCDF file. Argo netCDF variable DATA_TYPE is populated by R01 prefLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R01/current/", - "id": "seadatanet.r01", - "name": "Argo data type", - "prefix": "r01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R01/current/$1" - }, - "seadatanet.r03": { - "authority": "seadatanet", - "description": "Terms describing individual measured phenomena, used to mark up sets of data in Argo netCDF arrays. Argo netCDF variables PARAMETER and TRAJECTORY_PARAMETERS are populated by R03 altLabel; R03 altLabel is also used to name netCDF profile files parameter variables .", - "homepage": "http://vocab.nerc.ac.uk/collection/R03/current/", - "id": "seadatanet.r03", - "name": "Argo parameter codes", - "prefix": "r03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R03/current/$1" - }, - "seadatanet.r04": { - "authority": "seadatanet", - "description": "Codes for data centres and institutions handling or managing Argo data. Argo netCDF variable DATA_CENTRE is populated by R04 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R04/current/", - "id": "seadatanet.r04", - "name": "Argo data centres and institutions", - "prefix": "r04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R04/current/$1" - }, - "seadatanet.r05": { - "authority": "seadatanet", - "description": "Accuracy in latitude and longitude measurements received from the positioning system, grouped by location accuracy classes.", - "homepage": "http://vocab.nerc.ac.uk/collection/R05/current/", - "id": "seadatanet.r05", - "name": "Argo position accuracy", - "prefix": "r05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R05/current/$1" - }, - "seadatanet.r06": { - "authority": "seadatanet", - "description": "Processing stage of the data based on the concatenation of processing level and class indicators. Argo netCDF variable DATA_STATE_INDICATOR is populated by R06 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R06/current/", - "id": "seadatanet.r06", - "name": "Argo data state indicators", - "prefix": "r06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R06/current/$1" - }, - "seadatanet.r07": { - "authority": "seadatanet", - "description": "Coded history information for each action performed on each profile by a data centre. Argo netCDF variable HISTORY_ACTION is populated by R07 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R07/current/", - "id": "seadatanet.r07", - "name": "Argo history action codes", - "prefix": "r07", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R07/current/$1" - }, - "seadatanet.r08": { - "authority": "seadatanet", - "description": "Subset of instrument type codes from the World Meteorological Organization (WMO) Common Code Table C-3 (CCT C-3) 1770, named 'Instrument make and type for water temperature profile measurement with fall rate equation coefficients' and available here: https://library.wmo.int/doc_num.php?explnum_id=11283. Argo netCDF variable WMO_INST_TYPE is populated by R08 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R08/current/", - "id": "seadatanet.r08", - "name": "Argo instrument types", - "prefix": "r08", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R08/current/$1" - }, - "seadatanet.r09": { - "authority": "seadatanet", - "description": "List of float location measuring systems. Argo netCDF variable POSITIONING_SYSTEM is populated by R09 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R09/current/", - "id": "seadatanet.r09", - "name": "Argo positioning system", - "prefix": "r09", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R09/current/$1" - }, - "seadatanet.r10": { - "authority": "seadatanet", - "description": "List of telecommunication systems. Argo netCDF variable TRANS_SYSTEM is populated by R10 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R10/current/", - "id": "seadatanet.r10", - "name": "Argo transmission systems", - "prefix": "r10", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R10/current/$1" - }, - "seadatanet.r11": { - "authority": "seadatanet", - "description": "List of real-time quality-control tests and corresponding binary identifiers, used as reference to populate the Argo netCDF HISTORY_QCTEST variable.", - "homepage": "http://vocab.nerc.ac.uk/collection/R11/current/", - "id": "seadatanet.r11", - "name": "Argo real-time quality-control test identifiers", - "prefix": "r11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R11/current/$1" - }, - "seadatanet.r12": { - "authority": "seadatanet", - "description": "Data processing step codes for history record. Argo netCDF variable TRANS_SYSTEM is populated by R12 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R12/current/", - "id": "seadatanet.r12", - "name": "Argo history processing step codes", - "prefix": "r12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R12/current/$1" - }, - "seadatanet.r13": { - "authority": "seadatanet", - "description": "Ocean area codes assigned to each profile in the Metadata directory (index) file of the Argo Global Assembly Centre.", - "homepage": "http://vocab.nerc.ac.uk/collection/R13/current/", - "id": "seadatanet.r13", - "name": "Argo ocean area codes and boundary definitions", - "prefix": "r13", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R13/current/$1" - }, - "seadatanet.r14": { - "authority": "seadatanet", - "description": "List of technical parameters reported by a float at every cycle. Technical parameter names follow a naming convention to indicate what is being reported (category), where or when (descriptor), and in what units, delimited by an underscore. They are stored in the float 'tech.nc' file, under TECHNICAL_PARAMETER_NAME. Each technical parameter name has an associated value, stored in TECHNICAL_PARAMTER_VALUE. Argo netCDF variable TECHNICAL_PARAMETER_NAME is populated by R14 prefLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R14/current/", - "id": "seadatanet.r14", - "name": "Argo technical parameter names", - "prefix": "r14", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R14/current/$1" - }, - "seadatanet.r15": { - "authority": "seadatanet", - "description": "Measurement code IDs used in Argo Trajectory netCDF files. Argo netCDF variable MEASUREMENT_CODE is populated by R15 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R15/current/", - "id": "seadatanet.r15", - "name": "Argo trajectory measurement code identifiers", - "prefix": "r15", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R15/current/$1" - }, - "seadatanet.r16": { - "authority": "seadatanet", - "description": "Profile sampling schemes and sampling methods. Argo netCDF variable VERTICAL_SAMPLING_SCHEME is populated by R16 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R16/current/", - "id": "seadatanet.r16", - "name": "Argo vertical sampling schemes", - "prefix": "r16", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R16/current/$1" - }, - "seadatanet.r18": { - "authority": "seadatanet", - "description": "List of float configuration settings selected by the float Principal Investigator (PI). Configuration parameters may or may not be reported by the float, and do not constitute float measurements. Configuration parameters selected for a float are stored in the float 'meta.nc' file, under CONFIG_PARAMETER_NAME. Each configuration parameter name has an associated value, stored in CONFIG_PARAMETER_VALUE. Argo netCDF variable CONFIG_PARAMETER_NAME is populated by R18 prefLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R18/current/", - "id": "seadatanet.r18", - "name": "Argo configuration parameter names", - "prefix": "r18", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R18/current/$1" - }, - "seadatanet.r19": { - "authority": "seadatanet", - "description": "Flag scale for values in all Argo netCDF cycle timing variables. Argo netCDF cycle timing variables JULD__STATUS are populated by R19 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R19/current/", - "id": "seadatanet.r19", - "name": "Argo STATUS flags", - "prefix": "r19", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R19/current/$1" - }, - "seadatanet.r20": { - "authority": "seadatanet", - "description": "Codes to indicate the best estimate of whether the float touched the ground during a specific cycle. Argo netCDF variable GROUNDED in the Trajectory file is populated by R20 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R20/current/", - "id": "seadatanet.r20", - "name": "Argo GROUNDED flags", - "prefix": "r20", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R20/current/$1" - }, - "seadatanet.r21": { - "authority": "seadatanet", - "description": "Argo status flag on the Representative Park Pressure (RPP). Argo netCDF variable REPRESENTATIVE_PARK_PRESSURE_STATUS in the Trajectory file is populated by R21 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R21/current/", - "id": "seadatanet.r21", - "name": "Argo status flag on the Representative Park Pressure (RPP)", - "prefix": "r21", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R21/current/$1" - }, - "seadatanet.r22": { - "authority": "seadatanet", - "description": "List of platform family/category of Argo floats. Argo netCDF variable PLATFORM_FAMILY is populated by R22 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R22/current/", - "id": "seadatanet.r22", - "name": "Argo platform family", - "prefix": "r22", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R22/current/$1" - }, - "seadatanet.r23": { - "authority": "seadatanet", - "description": "List of Argo float types. Argo netCDF variable PLATFORM_TYPE is populated by R23 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R23/current/", - "id": "seadatanet.r23", - "name": "Argo platform type", - "prefix": "r23", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R23/current/$1" - }, - "seadatanet.r24": { - "authority": "seadatanet", - "description": "List of Argo float manufacturers. Argo netCDF variable PLATFORM_MAKER is populated by R24 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R24/current/", - "id": "seadatanet.r24", - "name": "Argo platform maker", - "prefix": "r24", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R24/current/$1" - }, - "seadatanet.r25": { - "authority": "seadatanet", - "description": "Terms describing sensor types mounted on Argo floats. Argo netCDF variable SENSOR is populated by R25 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R25/current/", - "id": "seadatanet.r25", - "name": "Argo sensor types", - "prefix": "r25", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R25/current/$1" - }, - "seadatanet.r26": { - "authority": "seadatanet", - "description": "Terms describing developers and manufacturers of sensors mounted on Argo floats. Argo netCDF variable SENSOR_MAKER is populated by R26 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R26/current/", - "id": "seadatanet.r26", - "name": "Argo sensor manufacturers", - "prefix": "r26", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R26/current/$1" - }, - "seadatanet.r27": { - "authority": "seadatanet", - "description": "Terms listing models of sensors mounted on Argo floats. Note: avoid using the manufacturer name and sensor firmware version in new entries when possible. Argo netCDF variable SENSOR_MODEL is populated by R27 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R27/current/", - "id": "seadatanet.r27", - "name": "Argo sensor models", - "prefix": "r27", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R27/current/$1" - }, - "seadatanet.r28": { - "authority": "seadatanet", - "description": "List of Argo floats controller board types and generations. Argo netCDF variables CONTROLLER_BOARD_TYPE_PRIMARY and, when needed, CONTROLLER_BOARD_TYPE_SECONDARY, are populated by R28 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R28/current/", - "id": "seadatanet.r28", - "name": "Argo controller board types and generations", - "prefix": "r28", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R28/current/$1" - }, - "seadatanet.r40": { - "authority": "seadatanet", - "description": "List of Principal Investigator (PI) names in charge of Argo floats. Argo netCDF variable PI_NAME is populated by R40 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/R40/current/", - "id": "seadatanet.r40", - "name": "Argo Principal Investigator (PI) names", - "prefix": "r40", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/R40/current/$1" - }, - "seadatanet.rd2": { - "authority": "seadatanet", - "description": "Quality flag scale for delayed-mode measurements. Argo netCDF variables _ADJUSTED_QC in 'D' mode are populated by RD2 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/RD2/current/", - "id": "seadatanet.rd2", - "name": "Argo delayed-mode quality control measurement flags", - "prefix": "rd2", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/RD2/current/$1" - }, - "seadatanet.rmc": { - "authority": "seadatanet", - "description": "Categories of trajectory measurement codes listed in NVS collection 'R15'", - "homepage": "http://vocab.nerc.ac.uk/collection/RMC/current/", - "id": "seadatanet.rmc", - "name": "Argo measurement code categories", - "prefix": "rmc", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/RMC/current/$1" - }, - "seadatanet.rp2": { - "authority": "seadatanet", - "description": "Quality control flag scale for whole profiles. Argo netCDF variables PROFILE__QC are populated by RP2 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/RP2/current/", - "id": "seadatanet.rp2", - "name": "Argo profile quality control flags", - "prefix": "rp2", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/RP2/current/$1" - }, - "seadatanet.rr2": { - "authority": "seadatanet", - "description": "Quality flag scale for real-time measurements. Argo netCDF variables _QC in 'R' mode and _ADJUSTED_QC in 'A' mode are populated by RR2 altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/RR2/current/", - "id": "seadatanet.rr2", - "name": "Argo real-time quality control measurement flags", - "prefix": "rr2", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/RR2/current/$1" - }, - "seadatanet.rtv": { - "authority": "seadatanet", - "description": "Timing variables representing stages of an Argo float profiling cycle, most of which are associated with a trajectory measurement code ID listed in NVS collection 'R15'. Argo netCDF cycle timing variable names JULD__STATUS are constructed by RTV altLabel.", - "homepage": "http://vocab.nerc.ac.uk/collection/RTV/current/", - "id": "seadatanet.rtv", - "name": "Argo float cycle timing variables", - "prefix": "rtv", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/RTV/current/$1" - }, - "seadatanet.s01": { - "authority": "seadatanet", - "description": "Terms used to describe the information entities that are combined in the BODC semantic model to produce a phenomenon description.", - "homepage": "http://vocab.nerc.ac.uk/collection/S01/current/", - "id": "seadatanet.s01", - "name": "BODC parameter semantic model component names", - "prefix": "s01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S01/current/$1" - }, - "seadatanet.s02": { - "authority": "seadatanet", - "description": "Terms used to describe the relationship between the 'where theme' and the 'what theme' in the BODC semantic model for measured phenomena descriptions.", - "homepage": "http://vocab.nerc.ac.uk/collection/S02/current/", - "id": "seadatanet.s02", - "name": "BODC parameter semantic model relationships between what theme and where theme", - "prefix": "s02", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S02/current/$1" - }, - "seadatanet.s03": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for a sample preparation entity (part of the how theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S03/current/", - "id": "seadatanet.s03", - "name": "BODC parameter semantic model sample preparation entity descriptions", - "prefix": "s03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S03/current/$1" - }, - "seadatanet.s04": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for an analytical method entity (part of the how theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S04/current/", - "id": "seadatanet.s04", - "name": "BODC parameter semantic model analytical method entity descriptions", - "prefix": "s04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S04/current/$1" - }, - "seadatanet.s05": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for data processing description (part of the how theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S05/current/", - "id": "seadatanet.s05", - "name": "BODC parameter semantic model data processing entity descriptions", - "prefix": "s05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S05/current/$1" - }, - "seadatanet.s06": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used to specify the property element of a parameter (part of the 'what' theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S06/current/", - "id": "seadatanet.s06", - "name": "BODC parameter semantic model parameter entity names", - "prefix": "s06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S06/current/$1" - }, - "seadatanet.s07": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for a parameter statistic (part of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S07/current/", - "id": "seadatanet.s07", - "name": "BODC parameter semantic model parameter statistic", - "prefix": "s07", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S07/current/$1" - }, - "seadatanet.s09": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for biological entity size (part of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S09/current/", - "id": "seadatanet.s09", - "name": "BODC parameter semantic model biological entity size terms", - "prefix": "s09", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S09/current/$1" - }, - "seadatanet.s10": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining terms used to refer to a biological entity sex category (part of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S10/current/", - "id": "seadatanet.s10", - "name": "BODC parameter semantic model biological entity sex category terms", - "prefix": "s10", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S10/current/$1" - }, - "seadatanet.s11": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used to specify the development or life cycle stage of a biological entity (part of the 'what' theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S11/current/", - "id": "seadatanet.s11", - "name": "BODC parameter semantic model biological entity development stage terms", - "prefix": "s11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S11/current/$1" - }, - "seadatanet.s12": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for biological entity (component of the what theme) plant or animal parts in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S12/current/", - "id": "seadatanet.s12", - "name": "BODC parameter semantic model biological entity subcomponent terms", - "prefix": "s12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S12/current/$1" - }, - "seadatanet.s13": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for ad-hoc qualification of a biological entity (component of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S13/current/", - "id": "seadatanet.s13", - "name": "BODC parameter semantic model biological entity subgroup terms", - "prefix": "s13", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S13/current/$1" - }, - "seadatanet.s14": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for morphology of a biological entity (component of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S14/current/", - "id": "seadatanet.s14", - "name": "BODC parameter semantic model biological entity morphology terms", - "prefix": "s14", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S14/current/$1" - }, - "seadatanet.s15": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for colour or optical appearance of a biological entity (component of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S15/current/", - "id": "seadatanet.s15", - "name": "BODC parameter semantic model biological entity colour terms", - "prefix": "s15", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S15/current/$1" - }, - "seadatanet.s18": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used for a physical entity (part of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S18/current/", - "id": "seadatanet.s18", - "name": "BODC parameter semantic model physical entity names", - "prefix": "s18", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S18/current/$1" - }, - "seadatanet.s19": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used to qualify a generic physical entity (part of the what theme) in the BODC parameter semantic model.", - "homepage": "http://vocab.nerc.ac.uk/collection/S19/current/", - "id": "seadatanet.s19", - "name": "BODC parameter semantic model physical entity subgroup names", - "prefix": "s19", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S19/current/$1" - }, - "seadatanet.s20": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used to describe the reference with respect to which a physical entity (part of the what theme) in the BODC parameter. semantic model is specified.", - "homepage": "http://vocab.nerc.ac.uk/collection/S20/current/", - "id": "seadatanet.s20", - "name": "BODC parameter semantic model physical entity datum names", - "prefix": "s20", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S20/current/$1" - }, - "seadatanet.s21": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used to describe the sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme.", - "homepage": "http://vocab.nerc.ac.uk/collection/S21/current/", - "id": "seadatanet.s21", - "name": "BODC parameter semantic model sphere names", - "prefix": "s21", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S21/current/$1" - }, - "seadatanet.s22": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms that may be used to describe subgroupings of the sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme.", - "homepage": "http://vocab.nerc.ac.uk/collection/S22/current/", - "id": "seadatanet.s22", - "name": "BODC parameter semantic model sphere subgroup names", - "prefix": "s22", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S22/current/$1" - }, - "seadatanet.s23": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the terms for phase (dissolved, particulate etc.) within a sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme.", - "homepage": "http://vocab.nerc.ac.uk/collection/S23/current/", - "id": "seadatanet.s23", - "name": "BODC semantic model sphere phase names", - "prefix": "s23", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S23/current/$1" - }, - "seadatanet.s24": { - "authority": "seadatanet", - "description": "Concepts describing physical or logical (i.e. categories) subdivisions of a phase (i.e. subcomponent) of a sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme.", - "homepage": "http://vocab.nerc.ac.uk/collection/S24/current/", - "id": "seadatanet.s24", - "name": "BODC semantic model sphere phase subgroup names", - "prefix": "s24", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S24/current/$1" - }, - "seadatanet.s25": { - "authority": "seadatanet", - "description": "Terms used to describe biological entities (organisms or parts thereof) in the BODC Parameter Usage Vocabulary", - "homepage": "http://vocab.nerc.ac.uk/collection/S25/current/", - "id": "seadatanet.s25", - "name": "BODC parameter semantic model biological entity names", - "prefix": "s25", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S25/current/$1" - }, - "seadatanet.s26": { - "authority": "seadatanet", - "description": "Terms used to describe the medium in which a measurement was made in the semantic model that underpins the BODC parameter discovery vocabulary", - "homepage": "http://vocab.nerc.ac.uk/collection/S26/current/", - "id": "seadatanet.s26", - "name": "BODC parameter semantic model matrices", - "prefix": "s26", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S26/current/$1" - }, - "seadatanet.s27": { - "authority": "seadatanet", - "description": "Terms for chemicals whose quantity in a matrix is determined to generate measurements in the BODC parameter usage vocabulary semantic model. Includes elements, compounds, isotopes and mixtures.", - "homepage": "http://vocab.nerc.ac.uk/collection/S27/current/", - "id": "seadatanet.s27", - "name": "BODC parameter semantic model chemical substances", - "prefix": "s27", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S27/current/$1" - }, - "seadatanet.s28": { - "authority": "seadatanet", - "description": "The six encoded modes of operation for a deployed Seaglider.", - "homepage": "http://vocab.nerc.ac.uk/collection/S28/current/", - "id": "seadatanet.s28", - "name": "Seaglider Guidance and Control Phase Settings", - "prefix": "s28", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S28/current/$1" - }, - "seadatanet.s29": { - "authority": "seadatanet", - "description": "Terms used to describe physical entities in the BODC Parameter Usage Vocabulary", - "homepage": "http://vocab.nerc.ac.uk/collection/S29/current/", - "id": "seadatanet.s29", - "name": "BODC parameter semantic model physical entity compound names", - "prefix": "s29", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S29/current/$1" - }, - "seadatanet.s30": { - "authority": "seadatanet", - "description": "Controlled vocabulary defining the relationship between two biological entities in the BODC parameter semantic model for biological parameters related to e.g. predator-prey interactions.", - "homepage": "http://vocab.nerc.ac.uk/collection/S30/current/", - "id": "seadatanet.s30", - "name": "BODC parameter semantic model relationships between biological entities", - "prefix": "s30", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/S30/current/$1" - }, - "seadatanet.t01": { - "authority": "seadatanet", - "description": "Standardised list of major research areas within the British Antarctic Survey for classifying materials and activities.", - "homepage": "http://vocab.nerc.ac.uk/collection/T01/current/", - "id": "seadatanet.t01", - "name": "British Antarctic Survey research topics", - "prefix": "t01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/T01/current/$1" - }, - "seadatanet.v12": { - "authority": "seadatanet", - "description": "Controlled vocabularies deemed to be of interest to the SeaDataNet project or users of its standards", - "homepage": "http://vocab.nerc.ac.uk/collection/V12/current/", - "id": "seadatanet.v12", - "name": "SeaDataNet Vocabularies", - "prefix": "v12", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/V12/current/$1" - }, - "seadatanet.v22": { - "authority": "seadatanet", - "description": "Concept collections used within ISO Code List representations for ISO19139 encoding of SeaDataNet CDIs and CSRs", - "homepage": "http://vocab.nerc.ac.uk/collection/V22/current/", - "id": "seadatanet.v22", - "name": "SeaDataNet CDI/CSR ISO Code List collections", - "prefix": "v22", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/V22/current/$1" - }, - "seadatanet.v23": { - "authority": "seadatanet", - "description": "Concept collections used within ISOTC211/19115 namespace of ISO Code List representations for ISO19139 encoding of SeaDataNet CDIs and CSRs", - "homepage": "http://vocab.nerc.ac.uk/collection/V23/current/", - "id": "seadatanet.v23", - "name": "SeaDataNet GMX and imported ISO Code List collections", - "prefix": "v23", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/V23/current/$1" - }, - "seadatanet.w01": { - "authority": "seadatanet", - "description": "Vocabulary in support of SeaDataNet's implementation of OGC Sensor Web Enablement. This is the top level vocabulary with many narrower concepts from other vocabularies.", - "homepage": "http://vocab.nerc.ac.uk/collection/W01/current/", - "id": "seadatanet.w01", - "name": "SeaDataNet Sensor Web Enablement and SensorML type vocabulary", - "prefix": "w01", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W01/current/$1" - }, - "seadatanet.w02": { - "authority": "seadatanet", - "description": "Vocabulary in support of SeaDataNet's (SDN) implementation of OGC Sensor Web Enablement (SWE). This is the lower level SDN SEW specific vocabulary.", - "homepage": "http://vocab.nerc.ac.uk/collection/W02/current/", - "id": "seadatanet.w02", - "name": "SeaDataNet Sensor Web Enablement and SensorML sub-type vocabulary", - "prefix": "w02", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W02/current/$1" - }, - "seadatanet.w03": { - "authority": "seadatanet", - "description": "Terms used to describe events or operations that have taken place during the life of an observation system (e.g. a sensor, a platform, an instrument, a network).", - "homepage": "http://vocab.nerc.ac.uk/collection/W03/current/", - "id": "seadatanet.w03", - "name": "SensorML History Event Types", - "prefix": "w03", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W03/current/$1" - }, - "seadatanet.w04": { - "authority": "seadatanet", - "description": "Terms used in SensorML to describe properties of an observation system that further qualify or quantify its output values.", - "homepage": "http://vocab.nerc.ac.uk/collection/W04/current/", - "id": "seadatanet.w04", - "name": "SensorML Capability Section Terms", - "prefix": "w04", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W04/current/$1" - }, - "seadatanet.w05": { - "authority": "seadatanet", - "description": "Terms used in SensorML to describe properties of an observation system that do not further qualify or quantify its output values.", - "homepage": "http://vocab.nerc.ac.uk/collection/W05/current/", - "id": "seadatanet.w05", - "name": "SensorML Characteristic Section Terms", - "prefix": "w05", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W05/current/$1" - }, - "seadatanet.w06": { - "authority": "seadatanet", - "description": "Terms used in SensorML to describe aspects of an observation system (e.g. the type of process, the type of sensor, or its intended applications).", - "homepage": "http://vocab.nerc.ac.uk/collection/W06/current/", - "id": "seadatanet.w06", - "name": "SensorML Classification Section Terms", - "prefix": "w06", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W06/current/$1" - }, - "seadatanet.w07": { - "authority": "seadatanet", - "description": "Terms used in SensorML to identify an observation system.", - "homepage": "http://vocab.nerc.ac.uk/collection/W07/current/", - "id": "seadatanet.w07", - "name": "SensorML Identification Section Terms", - "prefix": "w07", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W07/current/$1" - }, - "seadatanet.w08": { - "authority": "seadatanet", - "description": "Terms used in SensorML to describe the role and contact information for an observation system.", - "homepage": "http://vocab.nerc.ac.uk/collection/W08/current/", - "id": "seadatanet.w08", - "name": "SensorML Contact Section Terms", - "prefix": "w08", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W08/current/$1" - }, - "seadatanet.w09": { - "authority": "seadatanet", - "description": "Terms used in SWE Observations and Measurements that describe the measurements made by an observing system and the features involved in this process.", - "homepage": "http://vocab.nerc.ac.uk/collection/W09/current/", - "id": "seadatanet.w09", - "name": "Sensor Web Enablement Observations and Measurements Section Terms", - "prefix": "w09", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W09/current/$1" - }, - "seadatanet.w10": { - "authority": "seadatanet", - "description": "Terms used in SensorML to describe the software interactions with an observing system. The terms are typically used in the SensorML Outputs section.", - "homepage": "http://vocab.nerc.ac.uk/collection/W10/current/", - "id": "seadatanet.w10", - "name": "SensorML Output Section Data Interface Terms", - "prefix": "w10", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W10/current/$1" - }, - "seadatanet.w11": { - "authority": "seadatanet", - "description": "Terms used in SensorML to describe aspects of an Event.", - "homepage": "http://vocab.nerc.ac.uk/collection/W11/current/", - "id": "seadatanet.w11", - "name": "SensorML Event Classification Terms", - "prefix": "w11", - "source": "http://vocab.nerc.ac.uk", - "subjects": [ - "earth and related environmental sciences", - "oceanography" - ], - "uri_format": "http://vocab.nerc.ac.uk/collection/W11/current/$1" - } -} diff --git a/fuji_server/data/linked_vocabs/sdn_ontologies.yaml b/fuji_server/data/linked_vocabs/sdn_ontologies.yaml new file mode 100644 index 00000000..47010177 --- /dev/null +++ b/fuji_server/data/linked_vocabs/sdn_ontologies.yaml @@ -0,0 +1,3577 @@ +seadatanet.a01: + authority: seadatanet + description: Terms used at all hierarchical levels in the ICAN global thesaurus for coastal erosion. Terms used to populate drop-down lists in discovery portals. + homepage: http://vocab.nerc.ac.uk/collection/A01/current/ + id: seadatanet.a01 + name: International Coastal Atlas Network Coastal Erosion Global Thesaurus + prefix: a01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/A01/current/$1 +seadatanet.a02: + authority: seadatanet + description: Terms used at all hierarchical levels in the Oregon Coastal Atlas for coastal erosion layers, datasets and discovery. + homepage: http://vocab.nerc.ac.uk/collection/A02/current/ + id: seadatanet.a02 + name: Oregon Coastal Atlas Coastal Erosion Thesaurus markup terms + prefix: a02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/A02/current/$1 +seadatanet.a03: + authority: seadatanet + description: Terms used at all hierarchical levels in the Oregon Coastal Atlas for categorisation and discovery, but not for layer or dataset markup. + homepage: http://vocab.nerc.ac.uk/collection/A03/current/ + id: seadatanet.a03 + name: Oregon Coastal Atlas Coastal Erosion Thesaurus discovery terms + prefix: a03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/A03/current/$1 +seadatanet.a04: + authority: seadatanet + description: A collection of terms used by the Irish Marine Data Atlas in association with the topic of coastal erosion + homepage: http://vocab.nerc.ac.uk/collection/A04/current/ + id: seadatanet.a04 + name: MIDA Coastal Erosion Thesaurus + prefix: a04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/A04/current/$1 +seadatanet.a05: + authority: seadatanet + description: Collection of terms used to group key measurements into a set of Essential Variables (EV) and their associated units as part of the AtlantOS Atlantic Ocean dataset + homepage: http://vocab.nerc.ac.uk/collection/A05/current/ + id: seadatanet.a05 + name: AtlantOS Essential Variables + prefix: a05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/A05/current/$1 +seadatanet.b02: + authority: seadatanet + description: Internationally registered materials used to assess the accuracy of analyses and for laboratory intercomparability studies with unique identifiers assigned by BODC. + homepage: http://vocab.nerc.ac.uk/collection/B02/current/ + id: seadatanet.b02 + name: BODC-annotated certified reference materials + prefix: b02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B02/current/$1 +seadatanet.b03: + authority: seadatanet + description: Terms used to classify the type of reference material used by laboratories in the verification of analytical techniques in terms of consistency, accuracy and precision + homepage: http://vocab.nerc.ac.uk/collection/B03/current/ + id: seadatanet.b03 + name: BODC-annotated reference material classifiers + prefix: b03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B03/current/$1 +seadatanet.b04: + authority: seadatanet + description: Terms used to populate the title field in the BODC address book. + homepage: http://vocab.nerc.ac.uk/collection/B04/current/ + id: seadatanet.b04 + name: BODC people titles + prefix: b04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B04/current/$1 +seadatanet.b05: + authority: seadatanet + description: Terms used by BODC to describe roles that may be given to people within a governance structure. + homepage: http://vocab.nerc.ac.uk/collection/B05/current/ + id: seadatanet.b05 + name: BODC governance roles + prefix: b05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B05/current/$1 +seadatanet.b06: + authority: seadatanet + description: Terms describing automated integrity checks applied to data and metadata during BODC quality control. + homepage: http://vocab.nerc.ac.uk/collection/B06/current/ + id: seadatanet.b06 + name: BODC data and metadata integrity checks + prefix: b06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B06/current/$1 +seadatanet.b07: + authority: seadatanet + description: A catalogue of deployment methods of sampling net gears for the collection of mainly plankton, micronekton, and neuston organisms based on Wiebe P.H. et al. (2014) + homepage: http://vocab.nerc.ac.uk/collection/B07/current/ + id: seadatanet.b07 + name: Sampling net gear deployment vocabulary + prefix: b07 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B07/current/$1 +seadatanet.b09: + authority: seadatanet + description: Terms used to describe single and multiple nations who own datasets (and are part of the Celtic Seas Partnership) bounding the Celtic Seas Marine Region as designated by the Marine Strategy Framework Directive (MSFD) + homepage: http://vocab.nerc.ac.uk/collection/B09/current/ + id: seadatanet.b09 + name: Celtic Seas Partnership data owner nations bordering MSFD Celtic Seas Marine Region + prefix: b09 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B09/current/$1 +seadatanet.b11: + authority: seadatanet + description: Procedures or protocols that have been adopted by communities to ensure consistent and comparable methods are used when making observations from the environment. This also includes derivation and quality assurance practices. + homepage: http://vocab.nerc.ac.uk/collection/B11/current/ + id: seadatanet.b11 + name: BODC Standard Operating Procedures and Protocols for environmental observations + prefix: b11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B11/current/$1 +seadatanet.b12: + authority: seadatanet + description: Terms used by BODC to define measurement attributes described by numbers associated with data held in its repositories. + homepage: http://vocab.nerc.ac.uk/collection/B12/current/ + id: seadatanet.b12 + name: BODC measurement numeric attribute types + prefix: b12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B12/current/$1 +seadatanet.b20: + authority: seadatanet + description: Terms used by the Celtic Seas Partnership to categorise stakeholders according to the marine areas within which they operate. + homepage: http://vocab.nerc.ac.uk/collection/B20/current/ + id: seadatanet.b20 + name: Celtic Seas Partnership stakeholder sectors + prefix: b20 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B20/current/$1 +seadatanet.b21: + authority: seadatanet + description: Terms used by the Celtic Seas Partnership to broadly describe the spatial area of influence of a project, programme or initiative. + homepage: http://vocab.nerc.ac.uk/collection/B21/current/ + id: seadatanet.b21 + name: Celtic Seas Partnership scale + prefix: b21 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B21/current/$1 +seadatanet.b22: + authority: seadatanet + description: Terms used by the Celtic Seas Partnership to describe the transboundary nature of a project, programme or initiative. + homepage: http://vocab.nerc.ac.uk/collection/B22/current/ + id: seadatanet.b22 + name: Celtic Seas Partnership governance mechanisms + prefix: b22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B22/current/$1 +seadatanet.b39: + authority: seadatanet + description: Names of variables recorded into NetCDF files by the underway monitoring system on National Marine Facilities Sea Systems (NMF-SS) research vessels such as the RRS James Cook and RRS Discovery. Variables are from meteorological, hydrographic and navigational instruments. + homepage: http://vocab.nerc.ac.uk/collection/B39/current/ + id: seadatanet.b39 + name: NMF-SS Research Vessel underway variable NetCDF vocabulary + prefix: b39 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B39/current/$1 +seadatanet.b75: + authority: seadatanet + description: Up-to-date names and addresses for organisational entities referenced in BODC systems. + homepage: http://vocab.nerc.ac.uk/collection/B75/current/ + id: seadatanet.b75 + name: BODC Organisations + prefix: b75 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B75/current/$1 +seadatanet.b76: + authority: seadatanet + description: Terms used to describe designs or versions of platforms. + homepage: http://vocab.nerc.ac.uk/collection/B76/current/ + id: seadatanet.b76 + name: BODC Platform Models + prefix: b76 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/B76/current/$1 +seadatanet.bq1: + authority: seadatanet + description: Terms used by the EMODnet Bathymetry Lot to define the estimated horizontal accuracy of bathymetric data (QI_Horizontal). + homepage: http://vocab.nerc.ac.uk/collection/BQ1/current/ + id: seadatanet.bq1 + name: EMODnet Bathymetry Quality Indicators of horizontal accuracy (QI_Horizontal) + prefix: bq1 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/BQ1/current/$1 +seadatanet.bq2: + authority: seadatanet + description: Terms used by the EMODnet Bathymetry Lot to define the estimated vertical accuracy of bathymetric data (QI_Vertical). + homepage: http://vocab.nerc.ac.uk/collection/BQ2/current/ + id: seadatanet.bq2 + name: EMODnet Bathymetry Quality Indicators of vertical accuracy (QI_Vertical) + prefix: bq2 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/BQ2/current/$1 +seadatanet.bq3: + authority: seadatanet + description: Terms used by the EMODnet Bathymetry Lot to define the purpose of the bathymetry survey (QI_Purpose). + homepage: http://vocab.nerc.ac.uk/collection/BQ3/current/ + id: seadatanet.bq3 + name: EMODnet Bathymetry Quality Indicators of survey purpose (QI_Purpose) + prefix: bq3 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/BQ3/current/$1 +seadatanet.c00: + authority: seadatanet + description: Terms used to describe the provenance of a water depth included in BODC metadata + homepage: http://vocab.nerc.ac.uk/collection/C00/current/ + id: seadatanet.c00 + name: BODC Seafloor Depth Data Sources + prefix: c00 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C00/current/$1 +seadatanet.c10: + authority: seadatanet + description: Terms that describe groups of BODC series with common independent variable characteristics. + homepage: http://vocab.nerc.ac.uk/collection/C10/current/ + id: seadatanet.c10 + name: BODC series feature types + prefix: c10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C10/current/$1 +seadatanet.c16: + authority: seadatanet + description: Sea area terms from the IHB(1953) list plus additional terms added under SeaDataNet governance. + homepage: http://vocab.nerc.ac.uk/collection/C16/current/ + id: seadatanet.c16 + name: SeaDataNet sea areas + prefix: c16 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C16/current/$1 +seadatanet.c17: + authority: seadatanet + description: Identifiers and metadata for platform instances (combinations of names and physical entities such as hulls or airframes). + homepage: http://vocab.nerc.ac.uk/collection/C17/current/ + id: seadatanet.c17 + name: ICES Platform Codes + prefix: c17 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C17/current/$1 +seadatanet.c18: + authority: seadatanet + description: Country names published by ICES on behalf of IOC as part of their RNODC (formats) responsibility. Maintained until 2003. + homepage: http://vocab.nerc.ac.uk/collection/C18/current/ + id: seadatanet.c18 + name: Intergovernmental Oceanographic Commission countries + prefix: c18 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C18/current/$1 +seadatanet.c19: + authority: seadatanet + description: Terms specified by the SeaVoX vocabulary governance to describe coherent regions of the hydrosphere. Includes land masses enclosing freshwater bodies. + homepage: http://vocab.nerc.ac.uk/collection/C19/current/ + id: seadatanet.c19 + name: SeaVoX salt and fresh water body gazetteer + prefix: c19 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C19/current/$1 +seadatanet.c30: + authority: seadatanet + description: Bodies responsible for the intellectual control of vocabularies served by the NDG/SeaDataNet vocabulary server. + homepage: http://vocab.nerc.ac.uk/collection/C30/current/ + id: seadatanet.c30 + name: Active vocabulary content governance authorities + prefix: c30 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C30/current/$1 +seadatanet.c31: + authority: seadatanet + description: 'WMO ship type codes used to classify voluntary observing ships. Source: [WMO No.47 - International List of Selected, Supplementary and Auxiliary Ships](http://www.wmo.int/pages/prog/www/ois/pub47/pub47-home.htm).' + homepage: http://vocab.nerc.ac.uk/collection/C31/current/ + id: seadatanet.c31 + name: World Meteorological Organisation voluntary observing ship category + prefix: c31 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C31/current/$1 +seadatanet.c32: + authority: seadatanet + description: ISO country codes from ISO3166-1 and ISO3166-3 lists taken from www.iso.org on 16/08/2011 plus OGC terms for missing values and the ISO 3166 Maintenance Agency (ISO3166/MA) Exceptionally Reserved code for the European Union. + homepage: http://vocab.nerc.ac.uk/collection/C32/current/ + id: seadatanet.c32 + name: International Standards Organisation countries + prefix: c32 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C32/current/$1 +seadatanet.c33: + authority: seadatanet + description: Abbreviated terms used to specify categories of data production tools in the NERC DataGrid MOLES metadata schema. + homepage: http://vocab.nerc.ac.uk/collection/C33/current/ + id: seadatanet.c33 + name: NERC DataGrid data production tool category + prefix: c33 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C33/current/$1 +seadatanet.c34: + authority: seadatanet + description: Terms used to specify why an activity was undertaken. + homepage: http://vocab.nerc.ac.uk/collection/C34/current/ + id: seadatanet.c34 + name: Activity purpose categories + prefix: c34 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C34/current/$1 +seadatanet.c35: + authority: seadatanet + description: Medium-granularity (hierarchical level 3 of 5) terms describing the environment associated with an activity from a biological perspective. + homepage: http://vocab.nerc.ac.uk/collection/C35/current/ + id: seadatanet.c35 + name: European Nature Information System Level 3 Habitats + prefix: c35 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C35/current/$1 +seadatanet.c36: + authority: seadatanet + description: Legislative acts, agreements and treaties that have provided the impetus for monitoring activities to be undertaken. + homepage: http://vocab.nerc.ac.uk/collection/C36/current/ + id: seadatanet.c36 + name: Monitoring activity legislative drivers + prefix: c36 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C36/current/$1 +seadatanet.c37: + authority: seadatanet + description: Labels applied to areas of ten degrees latitude by ten degrees longitude in the Marsden Square system. + homepage: http://vocab.nerc.ac.uk/collection/C37/current/ + id: seadatanet.c37 + name: Ten-degree Marsden Squares + prefix: c37 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C37/current/$1 +seadatanet.c38: + authority: seadatanet + description: Names of a geographic location at which a cruise may begin or end. Used by SeaDataNet to populate Cruise Summary Report metadata. + homepage: http://vocab.nerc.ac.uk/collection/C38/current/ + id: seadatanet.c38 + name: SeaDataNet Ports Gazetteer + prefix: c38 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C38/current/$1 +seadatanet.c39: + authority: seadatanet + description: Codes and terms developed from the Douglas wind sea states to describe the general condition of the surface of a large water body. + homepage: http://vocab.nerc.ac.uk/collection/C39/current/ + id: seadatanet.c39 + name: World Meteorological Organisation sea states + prefix: c39 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C39/current/$1 +seadatanet.c40: + authority: seadatanet + description: Terms used to classify the accuracy and reliablity of pollution reports filed under the Bonn Agreement. + homepage: http://vocab.nerc.ac.uk/collection/C40/current/ + id: seadatanet.c40 + name: Bonn Agreement pollution report accuracy + prefix: c40 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C40/current/$1 +seadatanet.c41: + authority: seadatanet + description: Terms developed by BODC to provide a standard classification of pollution sources to be used in UK pollution reports filed under the Bonn Agreement. + homepage: http://vocab.nerc.ac.uk/collection/C41/current/ + id: seadatanet.c41 + name: BODC marine pollution sources + prefix: c41 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C41/current/$1 +seadatanet.c43: + authority: seadatanet + description: Terms developed by BODC to classify the magnitude of a discharge of oil into the marine environment + homepage: http://vocab.nerc.ac.uk/collection/C43/current/ + id: seadatanet.c43 + name: BODC oilspill quantity + prefix: c43 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C43/current/$1 +seadatanet.c45: + authority: seadatanet + description: 'Concepts specified as descriptors of good environmental status as defined by the Marine Strategy Framework Directive as published in 2010/477/EU: Commission Decision of 1 September 2010 on criteria and methodological standards on good environmental status of marine waters (notified under document C(2010) 5956).' + homepage: http://vocab.nerc.ac.uk/collection/C45/current/ + id: seadatanet.c45 + name: Marine Strategy Framework Directive descriptors 2010/477/EU + prefix: c45 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C45/current/$1 +seadatanet.c46: + authority: seadatanet + description: 'Concepts specified as criteria to be used to measure good environmental status as defined by the Marine Strategy Framework Directive as published in 2010/477/EU: Commission Decision of 1 September 2010 on criteria and methodological standards on good environmental status of marine waters (notified under document C(2010) 5956).' + homepage: http://vocab.nerc.ac.uk/collection/C46/current/ + id: seadatanet.c46 + name: Marine Strategy Framework Directive criteria 2010/477/EU + prefix: c46 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C46/current/$1 +seadatanet.c47: + authority: seadatanet + description: 'Concepts specified as indicators to be used to measure good environmental status as defined by the Marine Strategy Framework Directive as published in 2010/477/EU: Commission Decision of 1 September 2010 on criteria and methodological standards on good environmental status of marine waters (notified under document C(2010) 5956).' + homepage: http://vocab.nerc.ac.uk/collection/C47/current/ + id: seadatanet.c47 + name: Marine Strategy Framework Directive indicators 2010/477/EU + prefix: c47 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C47/current/$1 +seadatanet.c48: + authority: seadatanet + description: Documents produced by the Marine Environmental Data and Information Network specifying information content standards for the collection of specific types of marine data + homepage: http://vocab.nerc.ac.uk/collection/C48/current/ + id: seadatanet.c48 + name: MEDIN Data Guidelines + prefix: c48 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C48/current/$1 +seadatanet.c59: + authority: seadatanet + description: Generic terms used by BODC to describe the relationship between organisations and projects or data collection activities such as cruises + homepage: http://vocab.nerc.ac.uk/collection/C59/current/ + id: seadatanet.c59 + name: BODC organisation roles within activities and projects + prefix: c59 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C59/current/$1 +seadatanet.c60: + authority: seadatanet + description: Terms used in the NDG project to describe the relationship between subjects and objects in RDF triples, including vocabulary term mappings. + homepage: http://vocab.nerc.ac.uk/collection/C60/current/ + id: seadatanet.c60 + name: NERC DataGrid vocabulary term relationships + prefix: c60 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C60/current/$1 +seadatanet.c61: + authority: seadatanet + description: Labels used by BODC to populate 'city' or 'post town' metadata fields. + homepage: http://vocab.nerc.ac.uk/collection/C61/current/ + id: seadatanet.c61 + name: BODC post town names + prefix: c61 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C61/current/$1 +seadatanet.c62: + authority: seadatanet + description: Labels used by BODC to populate 'county' metadata fields. + homepage: http://vocab.nerc.ac.uk/collection/C62/current/ + id: seadatanet.c62 + name: BODC administrative region names + prefix: c62 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C62/current/$1 +seadatanet.c64: + authority: seadatanet + description: Terms used specify regions of the seas around the UK based on bio-geographical features rather than administrative boundaries + homepage: http://vocab.nerc.ac.uk/collection/C64/current/ + id: seadatanet.c64 + name: United Kingdom Charting Progress 2 sea regions + prefix: c64 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C64/current/$1 +seadatanet.c67: + authority: seadatanet + description: Terms used by BODC to describe groups of related parameters brought together to form a series from the sample schema. Each term maps to multiple BODC parameter sets. + homepage: http://vocab.nerc.ac.uk/collection/C67/current/ + id: seadatanet.c67 + name: BODC series parameter collection names + prefix: c67 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C67/current/$1 +seadatanet.c71: + authority: seadatanet + description: Terms used by BODC to classify the organisation entities with which it deals. + homepage: http://vocab.nerc.ac.uk/collection/C71/current/ + id: seadatanet.c71 + name: BODC organisation categories + prefix: c71 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C71/current/$1 +seadatanet.c72: + authority: seadatanet + description: Concepts that describe sediment corer deployment operational issues. + homepage: http://vocab.nerc.ac.uk/collection/C72/current/ + id: seadatanet.c72 + name: BODC core failure codes + prefix: c72 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C72/current/$1 +seadatanet.c75: + authority: seadatanet + description: Concepts used to populate 'organisation' fields in BODC metadata schemas. When used in conjunction with the C75PK group of functions (NMNOW, NMTHEN, NMALL)they provide access to past organisation names. For example, the C75 code 'ISB' translates to 'Proudman Oceanographic Laboratory' for a date in 1995, but to 'National Oceanography Centre, Liverpool' for a date in 2015. + homepage: http://vocab.nerc.ac.uk/collection/C75/current/ + id: seadatanet.c75 + name: BODC Organisation Histories + prefix: c75 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C75/current/$1 +seadatanet.c77: + authority: seadatanet + description: Terms used to describe shipboard activities (sometimes inaccurately described as parameters) by SeaDataNet in Cruise Summary Report (formerly known as ROSCOP) metadata. + homepage: http://vocab.nerc.ac.uk/collection/C77/current/ + id: seadatanet.c77 + name: SeaDataNet Cruise Summary Report data categories + prefix: c77 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C77/current/$1 +seadatanet.c86: + authority: seadatanet + description: SeaDataNet terms to describe roles associated with access rights to data, metadata and project information or the responsibilities for a contact within an activity, project or dataset. + homepage: http://vocab.nerc.ac.uk/collection/C86/current/ + id: seadatanet.c86 + name: SeaDataNet contact and security access roles + prefix: c86 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C86/current/$1 +seadatanet.c87: + authority: seadatanet + description: Terms used by BODC to describe roles associated with scientific projects. + homepage: http://vocab.nerc.ac.uk/collection/C87/current/ + id: seadatanet.c87 + name: BODC project roles + prefix: c87 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C87/current/$1 +seadatanet.c88: + authority: seadatanet + description: Terms used by BODC to describe roles specifying access rights to assets, which include data objects, web pages, services and vocabulary lists. + homepage: http://vocab.nerc.ac.uk/collection/C88/current/ + id: seadatanet.c88 + name: BODC asset access right roles + prefix: c88 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C88/current/$1 +seadatanet.c89: + authority: seadatanet + description: Terms used by BODC for roles that describe the relationship between a person or organisation with a specific dataset. + homepage: http://vocab.nerc.ac.uk/collection/C89/current/ + id: seadatanet.c89 + name: BODC dataset roles + prefix: c89 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C89/current/$1 +seadatanet.c96: + authority: seadatanet + description: Entities in the BODC data model that may be associated with a spatial coverage in the real world + homepage: http://vocab.nerc.ac.uk/collection/C96/current/ + id: seadatanet.c96 + name: BODC data model spatial objects + prefix: c96 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C96/current/$1 +seadatanet.c98: + authority: seadatanet + description: Terms used to classify the lists held in the Vocabulary Server (formerly known as code tables) by the subject of their contents. + homepage: http://vocab.nerc.ac.uk/collection/C98/current/ + id: seadatanet.c98 + name: Vocabulary Server list subject categories + prefix: c98 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/C98/current/$1 +seadatanet.d01: + authority: seadatanet + description: A vocabulary of SKOS top concepts for use as entry points to a SKOS scheme defining the DCAT theme keywords for use in linked data representations of the SeaDataNet EDMED catalogue. + homepage: http://vocab.nerc.ac.uk/collection/D01/current/ + id: seadatanet.d01 + name: DCAT Themes for Linked Data Representation of the SeaDataNet EDMED Catalogue + prefix: d01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/D01/current/$1 +seadatanet.e01: + authority: seadatanet + description: Names of stations providing sea level data into the ESEAS network. + homepage: http://vocab.nerc.ac.uk/collection/E01/current/ + id: seadatanet.e01 + name: ESEAS active tide gauge sites + prefix: e01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/E01/current/$1 +seadatanet.e02: + authority: seadatanet + description: >- + The standard states of processed data defined by the Earth Observing System + Data and Information Ssytem (EOSDIS) Data Panel, which are also consistent + with the Committee on Data Management, Archiving, + + and Computing (CODMAC) definitions. + homepage: http://vocab.nerc.ac.uk/collection/E02/current/ + id: seadatanet.e02 + name: Processing Levels for Earth Observing System Standard Data Products + prefix: e02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/E02/current/$1 +seadatanet.el1: + authority: seadatanet + description: Terms used to identify actions performed on sampling and observation platforms. This vocabulary is the result of an harmonisation exercise between the Eurofleets Automatic Reporting System (EARS) ontology and the Rolling Deck to Repository (R2R) project, for research vessel event logs. The terms it contains should be applicable to any sampling or observation platforms. + homepage: http://vocab.nerc.ac.uk/collection/EL1/current/ + id: seadatanet.el1 + name: SeaVoX Sampling and Observation Platform Event Actions + prefix: el1 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/EL1/current/$1 +seadatanet.el2: + authority: seadatanet + description: Terms used to identify processes performed on sampling and observation platforms. This vocabulary is the result of an harmonisation exercise between the Eurofleets Automatic Reporting System (EARS) ontology and the Rolling Deck to Repository (R2R) project, for research vessel event logs. The terms it contains should be applicable to any sampling or observation platforms. + homepage: http://vocab.nerc.ac.uk/collection/EL2/current/ + id: seadatanet.el2 + name: SeaVoX Sampling and Observation Platform Event Processes + prefix: el2 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/EL2/current/$1 +seadatanet.f02: + authority: seadatanet + description: Terms recommended by an international consortium of marine microbial flow cytometry experts to standardise the naming and definition of groups derived from flow cytometry analysis of marine samples. + homepage: http://vocab.nerc.ac.uk/collection/F02/current/ + id: seadatanet.f02 + name: Marine Microbial Flow Cytometry Standardised Group Names + prefix: f02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/F02/current/$1 +seadatanet.g01: + authority: seadatanet + description: Identification of when a given event occurred + homepage: http://vocab.nerc.ac.uk/collection/G01/current/ + id: seadatanet.g01 + name: CI_DateTypeCode + prefix: g01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G01/current/$1 +seadatanet.g02: + authority: seadatanet + description: Function performed by the resource + homepage: http://vocab.nerc.ac.uk/collection/G02/current/ + id: seadatanet.g02 + name: CI_OnlineFunctionCode + prefix: g02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G02/current/$1 +seadatanet.g03: + authority: seadatanet + description: Mode in which the data are represented + homepage: http://vocab.nerc.ac.uk/collection/G03/current/ + id: seadatanet.g03 + name: CI_PresentationFormCode + prefix: g03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G03/current/$1 +seadatanet.g04: + authority: seadatanet + description: Function performed by the responsible party + homepage: http://vocab.nerc.ac.uk/collection/G04/current/ + id: seadatanet.g04 + name: CI_RoleCode + prefix: g04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G04/current/$1 +seadatanet.g05: + authority: seadatanet + description: Type or method for evaluating an identified data quality measure + homepage: http://vocab.nerc.ac.uk/collection/G05/current/ + id: seadatanet.g05 + name: DQ_EvaluationMethodTypeCode + prefix: g05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G05/current/$1 +seadatanet.g06: + authority: seadatanet + description: Justification for the correlation of two datasets + homepage: http://vocab.nerc.ac.uk/collection/G06/current/ + id: seadatanet.g06 + name: DS_AssociationTypeCode + prefix: g06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G06/current/$1 +seadatanet.g07: + authority: seadatanet + description: Type of aggregation activity in which datasets are related + homepage: http://vocab.nerc.ac.uk/collection/G07/current/ + id: seadatanet.g07 + name: DS_InitiativeTypeCode + prefix: g07 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G07/current/$1 +seadatanet.g08: + authority: seadatanet + description: Code indicating whether grid data are points or area + homepage: http://vocab.nerc.ac.uk/collection/G08/current/ + id: seadatanet.g08 + name: MD_CellGeometryCode + prefix: g08 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G08/current/$1 +seadatanet.g09: + authority: seadatanet + description: Name of the character coding standard used in the resource + homepage: http://vocab.nerc.ac.uk/collection/G09/current/ + id: seadatanet.g09 + name: MD_CharacterSetCode + prefix: g09 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G09/current/$1 +seadatanet.g10: + authority: seadatanet + description: Name of the handling restrictions on the dataset + homepage: http://vocab.nerc.ac.uk/collection/G10/current/ + id: seadatanet.g10 + name: MD_ClassificationCode + prefix: g10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G10/current/$1 +seadatanet.g11: + authority: seadatanet + description: Specific type of information represented in the cell + homepage: http://vocab.nerc.ac.uk/collection/G11/current/ + id: seadatanet.g11 + name: MD_CoverageContentTypeCode + prefix: g11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G11/current/$1 +seadatanet.g12: + authority: seadatanet + description: Datatype of element or entity + homepage: http://vocab.nerc.ac.uk/collection/G12/current/ + id: seadatanet.g12 + name: MD_DatatypeCode + prefix: g12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G12/current/$1 +seadatanet.g13: + authority: seadatanet + description: Name of the dimension + homepage: http://vocab.nerc.ac.uk/collection/G13/current/ + id: seadatanet.g13 + name: 'MD_DimensionNameTypeCode ' + prefix: g13 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G13/current/$1 +seadatanet.g14: + authority: seadatanet + description: Name of point or vector objects used to locate zero-, one-, two-, or three-dimensional spatial locations in the dataset + homepage: http://vocab.nerc.ac.uk/collection/G14/current/ + id: seadatanet.g14 + name: MD_GeometricObjectTypeCode + prefix: g14 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G14/current/$1 +seadatanet.g15: + authority: seadatanet + description: Code which indicates conditions which may affect the image + homepage: http://vocab.nerc.ac.uk/collection/G15/current/ + id: seadatanet.g15 + name: 'MD_ImagingConditionCode ' + prefix: g15 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G15/current/$1 +seadatanet.g17: + authority: seadatanet + description: Frequency with which modifications and deletions are made to the data after they are first produced + homepage: http://vocab.nerc.ac.uk/collection/G17/current/ + id: seadatanet.g17 + name: MD_MaintenanceFrequencyCode + prefix: g17 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G17/current/$1 +seadatanet.g18: + authority: seadatanet + description: Method used to write to the medium + homepage: http://vocab.nerc.ac.uk/collection/G18/current/ + id: seadatanet.g18 + name: MD_MediumFormatCode + prefix: g18 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G18/current/$1 +seadatanet.g20: + authority: seadatanet + description: Obligation of the element or entity + homepage: http://vocab.nerc.ac.uk/collection/G20/current/ + id: seadatanet.g20 + name: MD_ObligationCode + prefix: g20 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G20/current/$1 +seadatanet.g21: + authority: seadatanet + description: Point in a pixel corresponding to the Earth location of the pixel + homepage: http://vocab.nerc.ac.uk/collection/G21/current/ + id: seadatanet.g21 + name: MD_PixelOrientationCode + prefix: g21 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G21/current/$1 +seadatanet.g22: + authority: seadatanet + description: Status of the dataset or progress of a review + homepage: http://vocab.nerc.ac.uk/collection/G22/current/ + id: seadatanet.g22 + name: MD_ProgressCode + prefix: g22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G22/current/$1 +seadatanet.g23: + authority: seadatanet + description: Limitation(s) placed upon the access or use of the data + homepage: http://vocab.nerc.ac.uk/collection/G23/current/ + id: seadatanet.g23 + name: MD_RestrictionCode + prefix: g23 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G23/current/$1 +seadatanet.g25: + authority: seadatanet + description: Class of information to which the referencing entity applies + homepage: http://vocab.nerc.ac.uk/collection/G25/current/ + id: seadatanet.g25 + name: MD_ScopeCode + prefix: g25 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G25/current/$1 +seadatanet.g26: + authority: seadatanet + description: >- + Terms used to represent geographic information in a dataset; + + ISO codelist extracted from 'Codelists for description of metadata datasets compliant with ISO/TC 211 19115:2003 and 19139' at http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml; last checked on 24Sep2018. + homepage: http://vocab.nerc.ac.uk/collection/G26/current/ + id: seadatanet.g26 + name: MD_SpatialRepresentationTypeCode + prefix: g26 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G26/current/$1 +seadatanet.g28: + authority: seadatanet + description: Degree of complexity of the spatial relationships + homepage: http://vocab.nerc.ac.uk/collection/G28/current/ + id: seadatanet.g28 + name: MD_TopologyLevelCode + prefix: g28 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G28/current/$1 +seadatanet.g29: + authority: seadatanet + description: Extension of MD_ScopeCode for the needs of GMX application schemas and in the context of a transfer + homepage: http://vocab.nerc.ac.uk/collection/G29/current/ + id: seadatanet.g29 + name: MX_ScopeCode + prefix: g29 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G29/current/$1 +seadatanet.g30: + authority: seadatanet + description: Terms used to represent geographic information in a dataset; ISO codelist extracted from 'Codelists for description of metadata datasets compliant with ISO/TC 211 19115:2003 and 19139' at http://www.isotc211.org/2005/resources/Codelist/gmxCodelists.xml. on 24Sep2018. + homepage: http://vocab.nerc.ac.uk/collection/G30/current/ + id: seadatanet.g30 + name: MD_SpatialRepresentationTypeCode (DO NOT USE - use G26 instead) + prefix: g30 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/G30/current/$1 +seadatanet.gbx: + authority: seadatanet + description: System used to control text displayed on BODC web pages on dynamic applications. The text stored in the description field is displayed in response to a CODVAL instance in the application code. + homepage: http://vocab.nerc.ac.uk/collection/GBX/current/ + id: seadatanet.gbx + name: I18n system English (UK) language terms + prefix: gbx + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GBX/current/$1 +seadatanet.ggb: + authority: seadatanet + description: Source data type information for the data sets used in the generation of the GEBCO_2019 Grid. + homepage: http://vocab.nerc.ac.uk/collection/GGB/current/ + id: seadatanet.ggb + name: GEBCO_2019 Grid source data types + prefix: ggb + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GGB/current/$1 +seadatanet.ggs: + authority: seadatanet + description: Provenance attributes of data source files used in the production of the GEBCO 30-second grid. + homepage: http://vocab.nerc.ac.uk/collection/GGS/current/ + id: seadatanet.ggs + name: GEBCO 30-second grid data sources + prefix: ggs + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GGS/current/$1 +seadatanet.ggt: + authority: seadatanet + description: Source data type information for the data sets used in the generation of the GEBCO Global Grid. + homepage: http://vocab.nerc.ac.uk/collection/GGT/current/ + id: seadatanet.ggt + name: GEBCO Grid Source Data Type Identifier + prefix: ggt + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GGT/current/$1 +seadatanet.gs1: + authority: seadatanet + description: Terms used to populate the featureOfInterest name field in the Geo-Seas data object Observations and Measurments documents. + homepage: http://vocab.nerc.ac.uk/collection/GS1/current/ + id: seadatanet.gs1 + name: Geo-Seas features of interest + prefix: gs1 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS1/current/$1 +seadatanet.gs2: + authority: seadatanet + description: Terms used to populate the observedProperty name field in the Geo-Seas data object Observations and Measurments documents. + homepage: http://vocab.nerc.ac.uk/collection/GS2/current/ + id: seadatanet.gs2 + name: Geo-Seas observed properties + prefix: gs2 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS2/current/$1 +seadatanet.gs3: + authority: seadatanet + description: Terms used to categorise sedimentary rocks and sediments in terms of the proportion of gravel, sand and mud. Initial terms proposed by Folk (1954) but subsequently revised by BGS and Flemming (2000). + homepage: http://vocab.nerc.ac.uk/collection/GS3/current/ + id: seadatanet.gs3 + name: Geo-Seas adjusted Folk sediment lithology classes + prefix: gs3 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS3/current/$1 +seadatanet.gs4: + authority: seadatanet + description: Terms used to describe rock and sediment colour in Geo-Seas based on the CGI GeologicUnitExposureColorTerms (https://www.seegrid.csiro.au/wiki/pub/CGIModel/GeologicUnitExposureColorTerms/Color.xls). + homepage: http://vocab.nerc.ac.uk/collection/GS4/current/ + id: seadatanet.gs4 + name: Geo-Seas geological sample colours + prefix: gs4 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS4/current/$1 +seadatanet.gs5: + authority: seadatanet + description: Terms used to describe sediment grain-size skewness coefficients in the Geo-Seas project. + homepage: http://vocab.nerc.ac.uk/collection/GS5/current/ + id: seadatanet.gs5 + name: Geo-Seas sediment grain-size skewness descriptors + prefix: gs5 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS5/current/$1 +seadatanet.gs6: + authority: seadatanet + description: Terms used to describe sediment grain-size kurtosis coefficients in the Geo-Seas project. + homepage: http://vocab.nerc.ac.uk/collection/GS6/current/ + id: seadatanet.gs6 + name: Geo-Seas sediment grain-size kurtosis descriptors + prefix: gs6 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS6/current/$1 +seadatanet.gs8: + authority: seadatanet + description: Concepts that describe techniques used in fieldwork in the geophysical discipline of seismics + homepage: http://vocab.nerc.ac.uk/collection/GS8/current/ + id: seadatanet.gs8 + name: Geo-Seas Seismic Methods + prefix: gs8 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS8/current/$1 +seadatanet.gs9: + authority: seadatanet + description: Concepts that describe dimensionality of field surveys in the geophysical discipline of seismics + homepage: http://vocab.nerc.ac.uk/collection/GS9/current/ + id: seadatanet.gs9 + name: Geo-Seas Seismic Survey Dimensionality + prefix: gs9 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GS9/current/$1 +seadatanet.gsa: + authority: seadatanet + description: Concepts that describe standard types of data product produced in the geophysical discipline of seismics + homepage: http://vocab.nerc.ac.uk/collection/GSA/current/ + id: seadatanet.gsa + name: Geo-Seas Seismic Data Product Types + prefix: gsa + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GSA/current/$1 +seadatanet.gsb: + authority: seadatanet + description: Concepts that describe instrument types used to measure reflected and refracted acoustic signals in the geophysical discipline of seismics + homepage: http://vocab.nerc.ac.uk/collection/GSB/current/ + id: seadatanet.gsb + name: Geo-Seas Seismic Receiver Types + prefix: gsb + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GSB/current/$1 +seadatanet.gsc: + authority: seadatanet + description: Terms used to describe sound velocity correction applied to bathymetric data in the MGD77 format + homepage: http://vocab.nerc.ac.uk/collection/GSC/current/ + id: seadatanet.gsc + name: MGD77 Bathymetry Sound Velocity Correction Codes + prefix: gsc + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GSC/current/$1 +seadatanet.gxm: + authority: seadatanet + description: The purpose, such as an application, for which a given BODC I18n term in the GBX controlled vocabulary is used. + homepage: http://vocab.nerc.ac.uk/collection/GXM/current/ + id: seadatanet.gxm + name: BODC I18n term usage + prefix: gxm + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/GXM/current/$1 +seadatanet.h01: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for micro-litter particle types in the EMODnet Chemistry data reporting system. The categories only reflect types based on morphological criteria (e.g. pellets, fragments, etc.) and all reference to the material they were made of was removed from this vocabulary as agreed in https://nvs-vocabs/EMODnetChemVocabs#19. + homepage: http://vocab.nerc.ac.uk/collection/H01/current/ + id: seadatanet.h01 + name: EMODnet micro-litter types + prefix: h01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/H01/current/$1 +seadatanet.h02: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for micro-litter particle shapes in the EMODnet Chemistry data reporting system. + homepage: http://vocab.nerc.ac.uk/collection/H02/current/ + id: seadatanet.h02 + name: EMODnet micro-litter shapes + prefix: h02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/H02/current/$1 +seadatanet.h03: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for micro-litter particle size classes in the EMODnet Chemistry data reporting system. + homepage: http://vocab.nerc.ac.uk/collection/H03/current/ + id: seadatanet.h03 + name: EMODnet micro-litter size classes + prefix: h03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/H03/current/$1 +seadatanet.h04: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for micro-litter particle colour classes in the EMODnet Chemistry data reporting system. + homepage: http://vocab.nerc.ac.uk/collection/H04/current/ + id: seadatanet.h04 + name: EMODnet micro-litter colour classes + prefix: h04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/H04/current/$1 +seadatanet.h05: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for micro-litter particle characterisation according to the type of non-plastic material or the type of plastic polymer in the EMODnet Chemistry data reporting system. + homepage: http://vocab.nerc.ac.uk/collection/H05/current/ + id: seadatanet.h05 + name: EMODnet micro-litter material or polymer type + prefix: h05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/H05/current/$1 +seadatanet.h06: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for micro-litter particle transparency categories in the EMODnet Chemistry data reporting format. + homepage: http://vocab.nerc.ac.uk/collection/H06/current/ + id: seadatanet.h06 + name: EMODnet micro-litter transparency classes + prefix: h06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/H06/current/$1 +seadatanet.ha2: + authority: seadatanet + description: Terms agreed within the EU EMODnet Human Activities community to describe categories of human activities, structures or organisational boundaries in or near the marine environment. + homepage: http://vocab.nerc.ac.uk/collection/HA2/current/ + id: seadatanet.ha2 + name: EMODnet human activity categories + prefix: ha2 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/HA2/current/$1 +seadatanet.i01: + authority: seadatanet + description: 'Extract of definitions from World Meteorological Organisation GRIB2 Table 4.2: meteorological parameter number by product discipline and parameter category.' + homepage: http://vocab.nerc.ac.uk/collection/I01/current/ + id: seadatanet.i01 + name: Subset of GRIB Table 4.2 - Parameter number by product discipline and parameter category + prefix: i01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I01/current/$1 +seadatanet.i02: + authority: seadatanet + description: 'World Meteorological Organisation GRIB2 Table 4.201: precipitation type.' + homepage: http://vocab.nerc.ac.uk/collection/I02/current/ + id: seadatanet.i02 + name: GRIB Table 4.201 (Precipitation type) + prefix: i02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I02/current/$1 +seadatanet.i03: + authority: seadatanet + description: Controlled vocabulary terms used within the Wisconsin Coastal Atlas. + homepage: http://vocab.nerc.ac.uk/collection/I03/current/ + id: seadatanet.i03 + name: Wisconsin Coastal Atlas Vocabulary + prefix: i03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I03/current/$1 +seadatanet.i10: + authority: seadatanet + description: Terms used in the INSPIRE infrastructure to tell a client what type of service to expect at the other end of a URL. + homepage: http://vocab.nerc.ac.uk/collection/I10/current/ + id: seadatanet.i10 + name: INSPIRE service types + prefix: i10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I10/current/$1 +seadatanet.i11: + authority: seadatanet + description: Types of control used to manage activities within a Management Area, Restriction or Regulation Zone. + homepage: http://vocab.nerc.ac.uk/collection/I11/current/ + id: seadatanet.i11 + name: INSPIRE Management and Reporting Control Type + prefix: i11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I11/current/$1 +seadatanet.i12: + authority: seadatanet + description: Terms used to describe temporal periods within which an activity is scheduled to be controlled. + homepage: http://vocab.nerc.ac.uk/collection/I12/current/ + id: seadatanet.i12 + name: INSPIRE Management and Reporting Day Type + prefix: i12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I12/current/$1 +seadatanet.i13: + authority: seadatanet + description: Environmental domain area within which a Management Area, Restriction or Regulation Zone was established. + homepage: http://vocab.nerc.ac.uk/collection/I13/current/ + id: seadatanet.i13 + name: INSPIRE Management and Reporting Environmental Domain Area + prefix: i13 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I13/current/$1 +seadatanet.i14: + authority: seadatanet + description: Classification of the types of activities controlled within a Management Area, Restriction or Regulation Zone. + homepage: http://vocab.nerc.ac.uk/collection/I14/current/ + id: seadatanet.i14 + name: INSPIRE Management and Reporting Controlled Activity Type + prefix: i14 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I14/current/$1 +seadatanet.i15: + authority: seadatanet + description: High-level classification defining the type of Management Area, Restriction or Regulation Zone. + homepage: http://vocab.nerc.ac.uk/collection/I15/current/ + id: seadatanet.i15 + name: INSPIRE Management and Reporting Zone Type + prefix: i15 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/I15/current/$1 +seadatanet.l02: + authority: seadatanet + description: SeaDataNet profile of ISO MD_GeometricObjectTypeCodeTerms code list. Known in SEA-SEARCH as 'Library 2' or cdi_measurement_codes. + homepage: http://vocab.nerc.ac.uk/collection/L02/current/ + id: seadatanet.l02 + name: SeaDataNet Geospatial Feature Types + prefix: l02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L02/current/$1 +seadatanet.l03: + authority: seadatanet + description: Terms used to express a classification of measurement periodicity in the SeaDataNet project. + homepage: http://vocab.nerc.ac.uk/collection/L03/current/ + id: seadatanet.l03 + name: SeaDataNet Measurement Periodicity Categories + prefix: l03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L03/current/$1 +seadatanet.l04: + authority: seadatanet + description: Terms used to group features or objects (sometimes called features of interest) in which measurements or observations may be made or of which samples may be collected. + homepage: http://vocab.nerc.ac.uk/collection/L04/current/ + id: seadatanet.l04 + name: Matrix Categories + prefix: l04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L04/current/$1 +seadatanet.l05: + authority: seadatanet + description: Terms used to classify groups of sensors, instruments, sources of algorithmically computed data (numerical models) or samplers (collectors of water, SPM, sediment, rock, air or biota samples). + homepage: http://vocab.nerc.ac.uk/collection/L05/current/ + id: seadatanet.l05 + name: SeaDataNet device categories + prefix: l05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L05/current/$1 +seadatanet.l06: + authority: seadatanet + description: 2-level grouping term hierarchy used for vehicles, structures or organisms capable of bearing instruments or tools for the collection of physical, chemical, geological or biological samples or data. + homepage: http://vocab.nerc.ac.uk/collection/L06/current/ + id: seadatanet.l06 + name: SeaVoX Platform Categories + prefix: l06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L06/current/$1 +seadatanet.l07: + authority: seadatanet + description: Terms for mechanisms by which data objects described by SeaDataNet Central Data Index (CDI) records may be obtained before SeaDataNet is fully implemented. + homepage: http://vocab.nerc.ac.uk/collection/L07/current/ + id: seadatanet.l07 + name: SeaDataNet data access mechanisms + prefix: l07 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L07/current/$1 +seadatanet.l08: + authority: seadatanet + description: Terms used to represent and classify data access policies in operation in the SeaDataNet project. + homepage: http://vocab.nerc.ac.uk/collection/L08/current/ + id: seadatanet.l08 + name: SeaDataNet Data Access Restriction Policies + prefix: l08 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L08/current/$1 +seadatanet.l10: + authority: seadatanet + description: Co-ordinate reference systems used for positions (latitude/longitude or grid references) in SeaDataNet metadata. May include 3D co-ordinate systems, but not vertical elevation datums like OD Newlyn. + homepage: http://vocab.nerc.ac.uk/collection/L10/current/ + id: seadatanet.l10 + name: SeaDataNet geographic co-ordinate reference frames + prefix: l10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L10/current/$1 +seadatanet.l11: + authority: seadatanet + description: Terms used to describe the zero point for vertical co-ordinate reference systems (datums). + homepage: http://vocab.nerc.ac.uk/collection/L11/current/ + id: seadatanet.l11 + name: SeaDataNet depth measurement reference planes + prefix: l11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L11/current/$1 +seadatanet.l12: + authority: seadatanet + description: Terms that are used to describe quality control procedures applied to data parameters. + homepage: http://vocab.nerc.ac.uk/collection/L12/current/ + id: seadatanet.l12 + name: SeaDataNet parameter quality control procedures + prefix: l12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L12/current/$1 +seadatanet.l13: + authority: seadatanet + description: Terms used to describe data coverage over the vertical (z) co-ordinate. + homepage: http://vocab.nerc.ac.uk/collection/L13/current/ + id: seadatanet.l13 + name: SeaVoX Vertical Co-ordinate Coverages + prefix: l13 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L13/current/$1 +seadatanet.l14: + authority: seadatanet + description: Terms used to describe the operational status of data collection activities within the SeaDataNet project. + homepage: http://vocab.nerc.ac.uk/collection/L14/current/ + id: seadatanet.l14 + name: SeaDataNet Activity Operational Stati + prefix: l14 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L14/current/$1 +seadatanet.l15: + authority: seadatanet + description: Terms used to by SeaDataNet to describe formally recognised standards for data acquisition and handling procedures. + homepage: http://vocab.nerc.ac.uk/collection/L15/current/ + id: seadatanet.l15 + name: SeaDataNet quality management system accreditations + prefix: l15 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L15/current/$1 +seadatanet.l18: + authority: seadatanet + description: Terms used as units in the quantification of what was collected or measured in a Cruise Summary Report (ROSCOP) record. + homepage: http://vocab.nerc.ac.uk/collection/L18/current/ + id: seadatanet.l18 + name: SeaDataNet Cruise Summary Report quantification units + prefix: l18 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L18/current/$1 +seadatanet.l19: + authority: seadatanet + description: Terms used in SeaDataNet metadata to describe the purpose of a keyword. An extension of the ISO19115 KeywordTypeCode codelist. + homepage: http://vocab.nerc.ac.uk/collection/L19/current/ + id: seadatanet.l19 + name: SeaDataNet keyword types + prefix: l19 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L19/current/$1 +seadatanet.l20: + authority: seadatanet + description: Flags used to provide additional information, usually referring to data quality, about data values in SeaDataNet data files. + homepage: http://vocab.nerc.ac.uk/collection/L20/current/ + id: seadatanet.l20 + name: SeaDataNet measurand qualifier flags + prefix: l20 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L20/current/$1 +seadatanet.l21: + authority: seadatanet + description: High-level classification of devices based on function and mode of deployment. + homepage: http://vocab.nerc.ac.uk/collection/L21/current/ + id: seadatanet.l21 + name: SeaDataNet device category types + prefix: l21 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L21/current/$1 +seadatanet.l22: + authority: seadatanet + description: Terms for distinct sampling or measuring devices that may be identified in the real world in terms of manufacturer and model number. + homepage: http://vocab.nerc.ac.uk/collection/L22/current/ + id: seadatanet.l22 + name: SeaVoX Device Catalogue + prefix: l22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L22/current/$1 +seadatanet.l23: + authority: seadatanet + description: Types of metadata record in the SeaDataNet metadata catalogue repositories + homepage: http://vocab.nerc.ac.uk/collection/L23/current/ + id: seadatanet.l23 + name: SeaDataNet metadata entities + prefix: l23 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L23/current/$1 +seadatanet.l24: + authority: seadatanet + description: Formats used for data delivery by SeaDataNet. + homepage: http://vocab.nerc.ac.uk/collection/L24/current/ + id: seadatanet.l24 + name: SeaDataNet data transport formats + prefix: l24 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L24/current/$1 +seadatanet.l26: + authority: seadatanet + description: Units of measure (P06 subset) that may be used for sampling intervals in the EDIOS metadata schema. Required to prevent times with units of kilograms! + homepage: http://vocab.nerc.ac.uk/collection/L26/current/ + id: seadatanet.l26 + name: EDIOS permitted sampling interval units + prefix: l26 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L26/current/$1 +seadatanet.l27: + authority: seadatanet + description: 'A catalogue including standardised labels of encoding schemes used for data value qualifying information such as data quality ' + homepage: http://vocab.nerc.ac.uk/collection/L27/current/ + id: seadatanet.l27 + name: SeaVoX data quality control flagging conventions + prefix: l27 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L27/current/$1 +seadatanet.l30: + authority: seadatanet + description: Organisations supplying or holding data concerned with the EU MEDATLAS project. + homepage: http://vocab.nerc.ac.uk/collection/L30/current/ + id: seadatanet.l30 + name: MEDATLAS Data Centres + prefix: l30 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L30/current/$1 +seadatanet.l31: + authority: seadatanet + description: Flags representing concepts used to specify quality of Geo-Seas data objects. These are a subset of SeaDataNet measurand qualifier flags. + homepage: http://vocab.nerc.ac.uk/collection/L31/current/ + id: seadatanet.l31 + name: Geo-Seas data object quality flags + prefix: l31 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L31/current/$1 +seadatanet.l33: + authority: seadatanet + description: Terms specified by WMO to label XBT data with the type of probe used and the algorithm used to compute depth. + homepage: http://vocab.nerc.ac.uk/collection/L33/current/ + id: seadatanet.l33 + name: WMO C3 vocabulary of XBT data types + prefix: l33 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L33/current/$1 +seadatanet.l34: + authority: seadatanet + description: Quality flags used for the primary level of the IODE Quality Flag Scheme for the Exchange of Oceanographic and Marine Meteorological Data, IODE Manuals and Guides 54, Vol. 3. + homepage: http://vocab.nerc.ac.uk/collection/L34/current/ + id: seadatanet.l34 + name: IODE Primary Level quality flags + prefix: l34 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L34/current/$1 +seadatanet.l35: + authority: seadatanet + description: A collection of terms which denote the manufacturers or developers of devices (includes manufacturer and/or developer collaborations). + homepage: http://vocab.nerc.ac.uk/collection/L35/current/ + id: seadatanet.l35 + name: SenseOcean device developers and manufacturers + prefix: l35 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/L35/current/$1 +seadatanet.m01: + authority: seadatanet + description: Terms describing what types of data formats exist in a data set so a human can identify if the data is likely to be of use and select a tool to interrogate that data. + homepage: http://vocab.nerc.ac.uk/collection/M01/current/ + id: seadatanet.m01 + name: MEDIN data format categories + prefix: m01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M01/current/$1 +seadatanet.m03: + authority: seadatanet + description: Terms used to describe different areas within an offshore renewable energy development. + homepage: http://vocab.nerc.ac.uk/collection/M03/current/ + id: seadatanet.m03 + name: The Crown Estate Renewable Energy Development Areas + prefix: m03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M03/current/$1 +seadatanet.m04: + authority: seadatanet + description: Terms used to describe different development phases of an offshore renewable energy development. + homepage: http://vocab.nerc.ac.uk/collection/M04/current/ + id: seadatanet.m04 + name: The Crown Estate Renewable Energy Development Phases + prefix: m04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M04/current/$1 +seadatanet.m05: + authority: seadatanet + description: Categories in a classification of the purpose and anticipated outcome of activities by governing bodies. + homepage: http://vocab.nerc.ac.uk/collection/M05/current/ + id: seadatanet.m05 + name: MEDIN socio-economic governance objective categories + prefix: m05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M05/current/$1 +seadatanet.m06: + authority: seadatanet + description: Categories in a classification of the purpose of activities in which the state of something at different times is determined. + homepage: http://vocab.nerc.ac.uk/collection/M06/current/ + id: seadatanet.m06 + name: MEDIN monitoring activity categories + prefix: m06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M06/current/$1 +seadatanet.m09: + authority: seadatanet + description: Terms used to classify techniques used to assess the socio-economic value of an ecosystem. + homepage: http://vocab.nerc.ac.uk/collection/M09/current/ + id: seadatanet.m09 + name: MEDIN ecosystem valuation method types + prefix: m09 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M09/current/$1 +seadatanet.m10: + authority: seadatanet + description: Terms used to describe techniques used to assess the socio-economic value of an ecosystem. + homepage: http://vocab.nerc.ac.uk/collection/M10/current/ + id: seadatanet.m10 + name: MEDIN ecosystem valuation methods + prefix: m10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M10/current/$1 +seadatanet.m11: + authority: seadatanet + description: Terms used to classify the conditions and processes through which natural ecosystems sustain and fulfil human life. + homepage: http://vocab.nerc.ac.uk/collection/M11/current/ + id: seadatanet.m11 + name: MEDIN ecosystem service types + prefix: m11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M11/current/$1 +seadatanet.m12: + authority: seadatanet + description: 'Categories of activity carried out by humans which exert an impact on the marine environment, as defined by the Joint Nature Conservation Committee (JNCC) ' + homepage: http://vocab.nerc.ac.uk/collection/M12/current/ + id: seadatanet.m12 + name: JNCC categories of human activity in the marine environment + prefix: m12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M12/current/$1 +seadatanet.m13: + authority: seadatanet + description: The standard list activities carried out by humans to manage the coastal environment, as defined by the Joint Nature Conservation Committee (JNCC) + homepage: http://vocab.nerc.ac.uk/collection/M13/current/ + id: seadatanet.m13 + name: JNCC standard list of human activities in the marine environment + prefix: m13 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M13/current/$1 +seadatanet.m14: + authority: seadatanet + description: 'List of defined pressures (stated by the Joint Nature Conservation Committee (JNCC) to be the mechanisms through which activities impact the marine environment) as specified by the Convention for the Protection of the Marine Environment for the North-East Atlantic (OSPAR) International Correspondence Group on Cumulative Effects (ICG-C) and distributed by the Joint Nature Conservation Committee ' + homepage: http://vocab.nerc.ac.uk/collection/M14/current/ + id: seadatanet.m14 + name: OSPAR list of defined pressures on the marine environment + prefix: m14 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M14/current/$1 +seadatanet.m15: + authority: seadatanet + description: 'Themes under which defined pressures in M14 are categorised by the Convention for the Protection of the Marine Environment for the North-East Atlantic (OSPAR) International Correspondence Group on Cumulative Effects (ICG-C) and distributed by the Joint Nature Conservation Committee (JNCC) ' + homepage: http://vocab.nerc.ac.uk/collection/M15/current/ + id: seadatanet.m15 + name: OSPAR list of themes of defined pressures on the marine environment + prefix: m15 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M15/current/$1 +seadatanet.m16: + authority: seadatanet + description: Terms used to describe techniques used by marine engineers to investigate marine earth materials. Used in the MEDIN Geotechnical Data Guideline to categorise what type of investigations are carried out at a particular location of interest. + homepage: http://vocab.nerc.ac.uk/collection/M16/current/ + id: seadatanet.m16 + name: Type of geotechnical investigation carried out at a site + prefix: m16 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M16/current/$1 +seadatanet.m17: + authority: seadatanet + description: Terms used to classify types of samples collected by marine engineers during geotechnical site investigations in the marine environment. + homepage: http://vocab.nerc.ac.uk/collection/M17/current/ + id: seadatanet.m17 + name: Type of sample collected during a geotechnical investigation + prefix: m17 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M17/current/$1 +seadatanet.m18: + authority: seadatanet + description: Terms used to classify types of container used by marine engineers to store physical specimens collected during marine geotechnical site investigations. + homepage: http://vocab.nerc.ac.uk/collection/M18/current/ + id: seadatanet.m18 + name: Type of container used to hold a physical sample collected during a geotechnical site investigation + prefix: m18 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M18/current/$1 +seadatanet.m20: + authority: seadatanet + description: Version 04.05 of the Marine Habitat Classification for Britain and Ireland (Connor et al. 2004), a hierarchical standard list of seabed habitats occurring within the marine, coastal and estuarine waters of Britain and Ireland. Connor, D.W., J.H. Allen, N.Golding, K.L.Howell, L.M. Lieberknecht, K.O. Northen And J.B. Reker (2004) The Marine Habitat Classification for Britain and Ireland Version 04.05. ISBN 1 861 07561 8. + homepage: http://vocab.nerc.ac.uk/collection/M20/current/ + id: seadatanet.m20 + name: Marine Habitat Classification for Britain and Ireland Version 04.05 + prefix: m20 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M20/current/$1 +seadatanet.m21: + authority: seadatanet + description: Version 15.03 of the Marine Habitat Classification for Britain and Ireland (JNCC 2015), a hierarchical standard list of seabed habitats occurring within the marine, coastal and estuarine waters of Britain and Ireland. JNCC (2015) The Marine Habitat Classification for Britain and Ireland Version 15.03 [Online]. + homepage: http://vocab.nerc.ac.uk/collection/M21/current/ + id: seadatanet.m21 + name: Marine Habitat Classification for Britain and Ireland Version 15.03 + prefix: m21 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M21/current/$1 +seadatanet.m22: + authority: seadatanet + description: List of species and habitats that are considered to be priorities for protection by the OSPAR Commission (see https://www.ospar.org/work-areas/bdc/species-habitats/list-of-threatened-declining-species-habitats) + homepage: http://vocab.nerc.ac.uk/collection/M22/current/ + id: seadatanet.m22 + name: OSPAR List of Threatened and/or Declining Species and Habitats + prefix: m22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M22/current/$1 +seadatanet.m23: + authority: seadatanet + description: The HELCOM Underwater biotope and habitat classification system (HELCOM HUB) provides a framework for defining biotopes in the whole Baltic Sea. Defining biotopes by the same split-rules, enables comparison of the biotopes in different regions of the Baltic Sea (see http://www.helcom.fi/baltic-sea-trends/biodiversity/helcom-hub). + homepage: http://vocab.nerc.ac.uk/collection/M23/current/ + id: seadatanet.m23 + name: HELCOM 'HUB' Underwater Biotope and Habitat Classification System + prefix: m23 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M23/current/$1 +seadatanet.m24: + authority: seadatanet + description: Version 97.07 of the Marine Habitat Classification for Britain and Ireland (Connor et al, 1997), a hierarchical standard list of seabed habitats occurring within the marine, coastal and estuarine waters of Britain and Ireland. Volume 1 (JNCC Report No 229) and Volume 2 (JNCC Report No 230). + homepage: http://vocab.nerc.ac.uk/collection/M24/current/ + id: seadatanet.m24 + name: Marine Habitat Classification for Britain and Ireland Version 97.06 + prefix: m24 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M24/current/$1 +seadatanet.m25: + authority: seadatanet + description: Terms that define standards recognised by MEDIN as being used to generate metadata records with the aim of enabling the discovery of geospatial data through online resources such as portals. Standard in this definition also covers specifications and profiles. Terms include both international and UK standards. + homepage: http://vocab.nerc.ac.uk/collection/M25/current/ + id: seadatanet.m25 + name: Geospatial discovery metadata standards, specifications and profiles recognised by MEDIN + prefix: m25 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M25/current/$1 +seadatanet.m26: + authority: seadatanet + description: Terms used to describe different phases within an offshore development or seabed activity. + homepage: http://vocab.nerc.ac.uk/collection/M26/current/ + id: seadatanet.m26 + name: The Crown Estate Seabed Development Phases + prefix: m26 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M26/current/$1 +seadatanet.m27: + authority: seadatanet + description: Terms used to describe different areas within an offshore development or seabed activity site. + homepage: http://vocab.nerc.ac.uk/collection/M27/current/ + id: seadatanet.m27 + name: The Crown Estate Seabed Development Areas + prefix: m27 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M27/current/$1 +seadatanet.m28: + authority: seadatanet + description: A collection of terms used to group wetland habitats into three upper-category types, as specified by the Ramsar Convention's (Ramsar, Iran, 1971) Classification System for Wetland Type, approved by Recommendation 4.7 and amended by Resolutions VI.5 and VII.11 of the Conference of the Contracting Parties. + homepage: http://vocab.nerc.ac.uk/collection/M28/current/ + id: seadatanet.m28 + name: Ramsar Classification System for Wetland Type upper categories + prefix: m28 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M28/current/$1 +seadatanet.m29: + authority: seadatanet + description: A collection of terms used to classify wetland habitat types, as specified by the Ramsar Convention's (Ramsar, Iran, 1971) Classification System for Wetland Type, approved by Recommendation 4.7 and amended by Resolutions VI.5 and VII.11 of the Conference of the Contracting Parties. + homepage: http://vocab.nerc.ac.uk/collection/M29/current/ + id: seadatanet.m29 + name: Ramsar Classification System for Wetland Type + prefix: m29 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/M29/current/$1 +seadatanet.mvb: + authority: seadatanet + description: Terms used to describe on-animal sensor data stored in the Movebank database (movebank.org), including individual measurements (events), reference data (animals, tags, deployments) and studies. + homepage: http://vocab.nerc.ac.uk/collection/MVB/current/ + id: seadatanet.mvb + name: Movebank Attribute Dictionary + prefix: mvb + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/MVB/current/$1 +seadatanet.n01: + authority: seadatanet + description: Terms used to describe portals to which a MEDIN discovery metadata record carrying the keyword should be made available. + homepage: http://vocab.nerc.ac.uk/collection/N01/current/ + id: seadatanet.n01 + name: MEDIN metadata record availability + prefix: n01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/N01/current/$1 +seadatanet.n02: + authority: seadatanet + description: Formats recognised by NDG, where this may allow conditional treatment. See also http://proj.badc.rl.ac.uk/ndg/browser/TI07-MOLES/trunk/Documents/NDG_MOLES_Instructions_for_Creation.doc + homepage: http://vocab.nerc.ac.uk/collection/N02/current/ + id: seadatanet.n02 + name: NERC DataGrid Recognised Formats + prefix: n02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/N02/current/$1 +seadatanet.n03: + authority: seadatanet + description: Terms used to specify the feature types available for coverages in the Climate Science Modelling Language (CSML). + homepage: http://vocab.nerc.ac.uk/collection/N03/current/ + id: seadatanet.n03 + name: Climate Science Modelling Language supported feature types + prefix: n03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/N03/current/$1 +seadatanet.n04: + authority: seadatanet + description: Terms describing types of on-line references in NERC DataGrid service bindings + homepage: http://vocab.nerc.ac.uk/collection/N04/current/ + id: seadatanet.n04 + name: NERC DataGrid on-line reference types + prefix: n04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/N04/current/$1 +seadatanet.n05: + authority: seadatanet + description: Terms used to describe the standard, profile and version number of XML documents that may be uploaded to the NERC DDS. + homepage: http://vocab.nerc.ac.uk/collection/N05/current/ + id: seadatanet.n05 + name: NERC data discovery service input metadata document standards + prefix: n05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/N05/current/$1 +seadatanet.n06: + authority: seadatanet + description: >- + Controlled list of terms used by the NERC Environmnetal Data Centres for + submission of DOI metadata records to DataCite. The list is used to + populate + + http://purl.org/spar/datacite/hasGeneralResourceType from the EDC's GEMINI profiles. + homepage: http://vocab.nerc.ac.uk/collection/N06/current/ + id: seadatanet.n06 + name: NERC Environmental Data Centres DataCite General Resource Types + prefix: n06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/N06/current/$1 +seadatanet.od1: + authority: seadatanet + description: Collection of terms used within the French Ocean Data and Services Cluster ODATIS for data discovery and product or dataset aggregation. Whenever applicable, Essential Variable terms are linked to the authoritative source of Essential Climate Ocean and Biodiversity Variable definitions maintained by the Global Observing System for Climate (GCOS), the Global Ocean Observing System (GOOS) and the Group on Earth Observations Biodiversity Observation Network (GEO BON). + homepage: http://vocab.nerc.ac.uk/collection/OD1/current/ + id: seadatanet.od1 + name: ODATIS aggregation parameters and Essential Variable names + prefix: od1 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/OD1/current/$1 +seadatanet.og1: + authority: seadatanet + description: Terms in this vocabulary are under the content governance of the OceanGliders Data Management Task Team (OGDMTT) on behalf of the OceanGliders community and Everyone's Gliding Observatories (EGO). Terms describe measured phenomena within the OG/EGO format. + homepage: http://vocab.nerc.ac.uk/collection/OG1/current/ + id: seadatanet.og1 + name: OceanGliders Parameter Usage Vocabulary + prefix: og1 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/OG1/current/$1 +seadatanet.p01: + authority: seadatanet + description: Terms built using the BODC parameter semantic model designed to describe individual measured phenomena. May be used to mark up sets of data such as a NetCDF array or spreadsheet column. Units must be specified when using a P01 code. The P06 unit that is linked to individual P01 in the NVS is the one used in BODC's systems but external users can use any appropriate units. + homepage: http://vocab.nerc.ac.uk/collection/P01/current/ + id: seadatanet.p01 + name: BODC Parameter Usage Vocabulary + prefix: p01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P01/current/$1 +seadatanet.p02: + authority: seadatanet + description: Terms describing fine-grained related groups of measurement phenomena designed to be used in dataset discovery interfaces. + homepage: http://vocab.nerc.ac.uk/collection/P02/current/ + id: seadatanet.p02 + name: SeaDataNet Parameter Discovery Vocabulary + prefix: p02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P02/current/$1 +seadatanet.p03: + authority: seadatanet + description: Terms agreed within the EU SeaDataNet community to describe coarse-grained groupings of related measurement phenomena. + homepage: http://vocab.nerc.ac.uk/collection/P03/current/ + id: seadatanet.p03 + name: SeaDataNet Agreed Parameter Groups + prefix: p03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P03/current/$1 +seadatanet.p04: + authority: seadatanet + description: Concatenated category, topic, term and variable separated by '>'. From Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3. + homepage: http://vocab.nerc.ac.uk/collection/P04/current/ + id: seadatanet.p04 + name: Global Change Master Directory Science Keywords V5 + prefix: p04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P04/current/$1 +seadatanet.p05: + authority: seadatanet + description: Terms defined by ISO describing data themes. Used to populate the mandatory ISO19115 topic category field. + homepage: http://vocab.nerc.ac.uk/collection/P05/current/ + id: seadatanet.p05 + name: International Standards Organisation ISO19115 Topic Categories + prefix: p05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P05/current/$1 +seadatanet.p06: + authority: seadatanet + description: Terms approved for use by BODC to describe the measurement units for data held in its repositories. + homepage: http://vocab.nerc.ac.uk/collection/P06/current/ + id: seadatanet.p06 + name: BODC-approved data storage units + prefix: p06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P06/current/$1 +seadatanet.p07: + authority: seadatanet + description: Terms used for definitive but not necessarily comprehensive descriptions of measured phenomena in the CF conventions (a content standard for data stored in NetCDF). + homepage: http://vocab.nerc.ac.uk/collection/P07/current/ + id: seadatanet.p07 + name: Climate and Forecast Standard Names + prefix: p07 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P07/current/$1 +seadatanet.p08: + authority: seadatanet + description: Terms used to classify SeaDataNet Agreed Parameter Groups to provide topic/theme level terms in a hierarchical parameter discovery interface. + homepage: http://vocab.nerc.ac.uk/collection/P08/current/ + id: seadatanet.p08 + name: SeaDataNet Parameter Disciplines + prefix: p08 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P08/current/$1 +seadatanet.p09: + authority: seadatanet + description: Terms under the content governance of SISMER used to describe measured phenomena within the MEDATLAS project. + homepage: http://vocab.nerc.ac.uk/collection/P09/current/ + id: seadatanet.p09 + name: MEDATLAS Parameter Usage Vocabulary + prefix: p09 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P09/current/$1 +seadatanet.p10: + authority: seadatanet + description: Terms used to describe sensors, instruments and other pieces of scientific equipment in the NASA Global Change Master Directory metadatabase. + homepage: http://vocab.nerc.ac.uk/collection/P10/current/ + id: seadatanet.p10 + name: Global Change Master Directory Instrument Keywords + prefix: p10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P10/current/$1 +seadatanet.p11: + authority: seadatanet + description: Category level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3. + homepage: http://vocab.nerc.ac.uk/collection/P11/current/ + id: seadatanet.p11 + name: Global Change Master Directory Science Keyword categories + prefix: p11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P11/current/$1 +seadatanet.p12: + authority: seadatanet + description: Topic level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3. + homepage: http://vocab.nerc.ac.uk/collection/P12/current/ + id: seadatanet.p12 + name: Global Change Master Directory Science Keyword topics + prefix: p12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P12/current/$1 +seadatanet.p13: + authority: seadatanet + description: Term level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3. + homepage: http://vocab.nerc.ac.uk/collection/P13/current/ + id: seadatanet.p13 + name: Global Change Master Directory Science Keyword terms + prefix: p13 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P13/current/$1 +seadatanet.p14: + authority: seadatanet + description: Variable level terms from the Science Keywords from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3. + homepage: http://vocab.nerc.ac.uk/collection/P14/current/ + id: seadatanet.p14 + name: Global Change Master Directory Science Keyword variables + prefix: p14 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P14/current/$1 +seadatanet.p15: + authority: seadatanet + description: Terms used to describe measured phenomena derivation algorithms in the CF conventions (a content standard for data stored in NetCDF), primarily targeted at statistical parameters. + homepage: http://vocab.nerc.ac.uk/collection/P15/current/ + id: seadatanet.p15 + name: Climate and Forecast Cell Methods + prefix: p15 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P15/current/$1 +seadatanet.p17: + authority: seadatanet + description: Research vessels deemed to be of interest to POGO. 'Of interest' is defined as active ocean-going research vessels greater than 60m in length + homepage: http://vocab.nerc.ac.uk/collection/P17/current/ + id: seadatanet.p17 + name: Partnership for Observation of the Global Ocean ships of interest + prefix: p17 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P17/current/$1 +seadatanet.p18: + authority: seadatanet + description: Chronostratigraphic unit terms from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3. + homepage: http://vocab.nerc.ac.uk/collection/P18/current/ + id: seadatanet.p18 + name: Global Change Master Directory Chronostratigraphic Units + prefix: p18 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P18/current/$1 +seadatanet.p19: + authority: seadatanet + description: Terms used to describe sensor-bearing platforms from Olsen L.M. et. al (2006) NASA/GCMD Earth Science Keywords Version 5.3.3. + homepage: http://vocab.nerc.ac.uk/collection/P19/current/ + id: seadatanet.p19 + name: Global Change Master Directory platforms + prefix: p19 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P19/current/$1 +seadatanet.p20: + authority: seadatanet + description: Terms used in NASA's GCMD to describe the function of related URLs embedded in DIF metadata records. Also used for NERC DataGrid service bindings. + homepage: http://vocab.nerc.ac.uk/collection/P20/current/ + id: seadatanet.p20 + name: Global Change Master Directory URL content types + prefix: p20 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P20/current/$1 +seadatanet.p21: + authority: seadatanet + description: Base terms (all hierarchical levels) interlinked by a relationship network to build the Marisaurus thesaurus. + homepage: http://vocab.nerc.ac.uk/collection/P21/current/ + id: seadatanet.p21 + name: Marisaurus Thesaurus + prefix: p21 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P21/current/$1 +seadatanet.p22: + authority: seadatanet + description: Groupings of spatial data according to Annex I, II and III of the INSPIRE Directive [DS-D2.5] + homepage: http://vocab.nerc.ac.uk/collection/P22/current/ + id: seadatanet.p22 + name: GEMET - INSPIRE themes, version 1.0 + prefix: p22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P22/current/$1 +seadatanet.p23: + authority: seadatanet + description: Coarse grained grouping terms designed by MEDIN to provide the top level for a parameter discovery thesaurus. + homepage: http://vocab.nerc.ac.uk/collection/P23/current/ + id: seadatanet.p23 + name: MEDIN Parameter Discipline Keywords + prefix: p23 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P23/current/$1 +seadatanet.p24: + authority: seadatanet + description: Classification concepts for units of measure based upon the fundamental SI quantities upon which they are based. + homepage: http://vocab.nerc.ac.uk/collection/P24/current/ + id: seadatanet.p24 + name: Units of measure dimensions + prefix: p24 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P24/current/$1 +seadatanet.p25: + authority: seadatanet + description: Terms used to describe phenomena within the NETMAR project at a granularity level suitable for labelling data aggregations or assessing whether the parameter is appropriate as an input to a given WPS. + homepage: http://vocab.nerc.ac.uk/collection/P25/current/ + id: seadatanet.p25 + name: NETMAR aggregation parameters + prefix: p25 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P25/current/$1 +seadatanet.p26: + authority: seadatanet + description: A collection of categories and sub-categories developed by ISO to classify services that display or process spatial data + homepage: http://vocab.nerc.ac.uk/collection/P26/current/ + id: seadatanet.p26 + name: ISO19119 geographic services taxonomy + prefix: p26 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P26/current/$1 +seadatanet.p27: + authority: seadatanet + description: Terms used to describe the environmental spatial location of an aliquot of a simulated oil spill by the METEO France MOTHY model. + homepage: http://vocab.nerc.ac.uk/collection/P27/current/ + id: seadatanet.p27 + name: Oil spill spillet location + prefix: p27 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P27/current/$1 +seadatanet.p28: + authority: seadatanet + description: Terms used to describe the operational stati of pollution cleanup sites in the Cedre cleanup site service. + homepage: http://vocab.nerc.ac.uk/collection/P28/current/ + id: seadatanet.p28 + name: Cedre pollution site cleanup operational stati + prefix: p28 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P28/current/$1 +seadatanet.p29: + authority: seadatanet + description: Terms used to describe the characteristics of regions of the Earth's Surface or their representation in a numerical simulation in the CF metadata conventions for data stored in NetCDF. + homepage: http://vocab.nerc.ac.uk/collection/P29/current/ + id: seadatanet.p29 + name: Climate and Forecast Area Types + prefix: p29 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P29/current/$1 +seadatanet.p30: + authority: seadatanet + description: Terms used to label regions of the Earth's Surface or their representation in a numerical simulation in the CF metadata conventions for data stored in NetCDF. + homepage: http://vocab.nerc.ac.uk/collection/P30/current/ + id: seadatanet.p30 + name: Climate and Forecast Standardized Region Names + prefix: p30 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P30/current/$1 +seadatanet.p31: + authority: seadatanet + description: Terms used to define the recognised metadata attributes for the description of CF-compliant data stored in NetCDF files. + homepage: http://vocab.nerc.ac.uk/collection/P31/current/ + id: seadatanet.p31 + name: Climate and Forecast Attribute Names + prefix: p31 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P31/current/$1 +seadatanet.p35: + authority: seadatanet + description: Labels used for aggregated parameters in the EMODNET chemistry lot + homepage: http://vocab.nerc.ac.uk/collection/P35/current/ + id: seadatanet.p35 + name: EMODnet Chemistry aggregated parameter names + prefix: p35 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P35/current/$1 +seadatanet.p36: + authority: seadatanet + description: Terms based on the EU MSFD used by the EMODNET chemistry lot to provide coarse granularity groupings of the chemical parameters it covers. + homepage: http://vocab.nerc.ac.uk/collection/P36/current/ + id: seadatanet.p36 + name: EMODnet Chemistry chemical groups + prefix: p36 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P36/current/$1 +seadatanet.p37: + authority: seadatanet + description: Terms used by the CF community to describe the calendar systems used for time co-ordinates in CF-compliant data files + homepage: http://vocab.nerc.ac.uk/collection/P37/current/ + id: seadatanet.p37 + name: Climate and Forecast Calendars + prefix: p37 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P37/current/$1 +seadatanet.p38: + authority: seadatanet + description: Terms used by the CF community to describe the data coverage over the vertical (z) co-ordinate. This is used to describe the Earth Realm in the CF Standard Name semantic model. + homepage: http://vocab.nerc.ac.uk/collection/P38/current/ + id: seadatanet.p38 + name: Climate and Forecast Vertical Co-ordinate Coverages + prefix: p38 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P38/current/$1 +seadatanet.p64: + authority: seadatanet + description: Concatenated category, topic, term and variable separated by '>'. From Olsen L.M. et. al (2007) NASA/GCMD Earth Science Keywords Version 6.0.0.0 + homepage: http://vocab.nerc.ac.uk/collection/P64/current/ + id: seadatanet.p64 + name: Global Change Master Directory Science Keywords V6 + prefix: p64 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/P64/current/$1 +seadatanet.q01: + authority: seadatanet + description: Collection of terms used by the Ocean Biogeographic Information System to standardise attributes related to sampling instruments and methods. + homepage: http://vocab.nerc.ac.uk/collection/Q01/current/ + id: seadatanet.q01 + name: OBIS sampling instruments and methods attributes + prefix: q01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/Q01/current/$1 +seadatanet.r01: + authority: seadatanet + description: Terms describing the type of data contained in an Argo netCDF file. Argo netCDF variable DATA_TYPE is populated by R01 prefLabel. + homepage: http://vocab.nerc.ac.uk/collection/R01/current/ + id: seadatanet.r01 + name: Argo data type + prefix: r01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R01/current/$1 +seadatanet.r03: + authority: seadatanet + description: Terms describing individual measured phenomena, used to mark up sets of data in Argo netCDF arrays. Argo netCDF variables PARAMETER and TRAJECTORY_PARAMETERS are populated by R03 altLabel; R03 altLabel is also used to name netCDF profile files parameter variables . + homepage: http://vocab.nerc.ac.uk/collection/R03/current/ + id: seadatanet.r03 + name: Argo parameter codes + prefix: r03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R03/current/$1 +seadatanet.r04: + authority: seadatanet + description: Codes for data centres and institutions handling or managing Argo data. Argo netCDF variable DATA_CENTRE is populated by R04 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R04/current/ + id: seadatanet.r04 + name: Argo data centres and institutions + prefix: r04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R04/current/$1 +seadatanet.r05: + authority: seadatanet + description: Accuracy in latitude and longitude measurements received from the positioning system, grouped by location accuracy classes. + homepage: http://vocab.nerc.ac.uk/collection/R05/current/ + id: seadatanet.r05 + name: Argo position accuracy + prefix: r05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R05/current/$1 +seadatanet.r06: + authority: seadatanet + description: Processing stage of the data based on the concatenation of processing level and class indicators. Argo netCDF variable DATA_STATE_INDICATOR is populated by R06 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R06/current/ + id: seadatanet.r06 + name: Argo data state indicators + prefix: r06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R06/current/$1 +seadatanet.r07: + authority: seadatanet + description: Coded history information for each action performed on each profile by a data centre. Argo netCDF variable HISTORY_ACTION is populated by R07 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R07/current/ + id: seadatanet.r07 + name: Argo history action codes + prefix: r07 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R07/current/$1 +seadatanet.r08: + authority: seadatanet + description: "Subset of instrument type codes from the World Meteorological Organization (WMO) Common Code Table C-3 (CCT C-3) 1770, named 'Instrument make and type for water temperature profile measurement with fall rate equation coefficients' and available here: https://library.wmo.int/doc_num.php?explnum_id=11283. Argo netCDF variable WMO_INST_TYPE is populated by R08 altLabel." + homepage: http://vocab.nerc.ac.uk/collection/R08/current/ + id: seadatanet.r08 + name: Argo instrument types + prefix: r08 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R08/current/$1 +seadatanet.r09: + authority: seadatanet + description: List of float location measuring systems. Argo netCDF variable POSITIONING_SYSTEM is populated by R09 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R09/current/ + id: seadatanet.r09 + name: Argo positioning system + prefix: r09 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R09/current/$1 +seadatanet.r10: + authority: seadatanet + description: List of telecommunication systems. Argo netCDF variable TRANS_SYSTEM is populated by R10 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R10/current/ + id: seadatanet.r10 + name: Argo transmission systems + prefix: r10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R10/current/$1 +seadatanet.r11: + authority: seadatanet + description: List of real-time quality-control tests and corresponding binary identifiers, used as reference to populate the Argo netCDF HISTORY_QCTEST variable. + homepage: http://vocab.nerc.ac.uk/collection/R11/current/ + id: seadatanet.r11 + name: Argo real-time quality-control test identifiers + prefix: r11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R11/current/$1 +seadatanet.r12: + authority: seadatanet + description: Data processing step codes for history record. Argo netCDF variable TRANS_SYSTEM is populated by R12 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R12/current/ + id: seadatanet.r12 + name: Argo history processing step codes + prefix: r12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R12/current/$1 +seadatanet.r13: + authority: seadatanet + description: Ocean area codes assigned to each profile in the Metadata directory (index) file of the Argo Global Assembly Centre. + homepage: http://vocab.nerc.ac.uk/collection/R13/current/ + id: seadatanet.r13 + name: Argo ocean area codes and boundary definitions + prefix: r13 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R13/current/$1 +seadatanet.r14: + authority: seadatanet + description: List of technical parameters reported by a float at every cycle. Technical parameter names follow a naming convention to indicate what is being reported (category), where or when (descriptor), and in what units, delimited by an underscore. They are stored in the float 'tech.nc' file, under TECHNICAL_PARAMETER_NAME. Each technical parameter name has an associated value, stored in TECHNICAL_PARAMTER_VALUE. Argo netCDF variable TECHNICAL_PARAMETER_NAME is populated by R14 prefLabel. + homepage: http://vocab.nerc.ac.uk/collection/R14/current/ + id: seadatanet.r14 + name: Argo technical parameter names + prefix: r14 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R14/current/$1 +seadatanet.r15: + authority: seadatanet + description: Measurement code IDs used in Argo Trajectory netCDF files. Argo netCDF variable MEASUREMENT_CODE is populated by R15 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R15/current/ + id: seadatanet.r15 + name: Argo trajectory measurement code identifiers + prefix: r15 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R15/current/$1 +seadatanet.r16: + authority: seadatanet + description: Profile sampling schemes and sampling methods. Argo netCDF variable VERTICAL_SAMPLING_SCHEME is populated by R16 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R16/current/ + id: seadatanet.r16 + name: Argo vertical sampling schemes + prefix: r16 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R16/current/$1 +seadatanet.r18: + authority: seadatanet + description: List of float configuration settings selected by the float Principal Investigator (PI). Configuration parameters may or may not be reported by the float, and do not constitute float measurements. Configuration parameters selected for a float are stored in the float 'meta.nc' file, under CONFIG_PARAMETER_NAME. Each configuration parameter name has an associated value, stored in CONFIG_PARAMETER_VALUE. Argo netCDF variable CONFIG_PARAMETER_NAME is populated by R18 prefLabel. + homepage: http://vocab.nerc.ac.uk/collection/R18/current/ + id: seadatanet.r18 + name: Argo configuration parameter names + prefix: r18 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R18/current/$1 +seadatanet.r19: + authority: seadatanet + description: Flag scale for values in all Argo netCDF cycle timing variables. Argo netCDF cycle timing variables JULD__STATUS are populated by R19 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R19/current/ + id: seadatanet.r19 + name: Argo STATUS flags + prefix: r19 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R19/current/$1 +seadatanet.r20: + authority: seadatanet + description: Codes to indicate the best estimate of whether the float touched the ground during a specific cycle. Argo netCDF variable GROUNDED in the Trajectory file is populated by R20 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R20/current/ + id: seadatanet.r20 + name: Argo GROUNDED flags + prefix: r20 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R20/current/$1 +seadatanet.r21: + authority: seadatanet + description: Argo status flag on the Representative Park Pressure (RPP). Argo netCDF variable REPRESENTATIVE_PARK_PRESSURE_STATUS in the Trajectory file is populated by R21 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R21/current/ + id: seadatanet.r21 + name: Argo status flag on the Representative Park Pressure (RPP) + prefix: r21 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R21/current/$1 +seadatanet.r22: + authority: seadatanet + description: List of platform family/category of Argo floats. Argo netCDF variable PLATFORM_FAMILY is populated by R22 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R22/current/ + id: seadatanet.r22 + name: Argo platform family + prefix: r22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R22/current/$1 +seadatanet.r23: + authority: seadatanet + description: List of Argo float types. Argo netCDF variable PLATFORM_TYPE is populated by R23 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R23/current/ + id: seadatanet.r23 + name: Argo platform type + prefix: r23 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R23/current/$1 +seadatanet.r24: + authority: seadatanet + description: List of Argo float manufacturers. Argo netCDF variable PLATFORM_MAKER is populated by R24 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R24/current/ + id: seadatanet.r24 + name: Argo platform maker + prefix: r24 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R24/current/$1 +seadatanet.r25: + authority: seadatanet + description: Terms describing sensor types mounted on Argo floats. Argo netCDF variable SENSOR is populated by R25 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R25/current/ + id: seadatanet.r25 + name: Argo sensor types + prefix: r25 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R25/current/$1 +seadatanet.r26: + authority: seadatanet + description: Terms describing developers and manufacturers of sensors mounted on Argo floats. Argo netCDF variable SENSOR_MAKER is populated by R26 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R26/current/ + id: seadatanet.r26 + name: Argo sensor manufacturers + prefix: r26 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R26/current/$1 +seadatanet.r27: + authority: seadatanet + description: 'Terms listing models of sensors mounted on Argo floats. Note: avoid using the manufacturer name and sensor firmware version in new entries when possible. Argo netCDF variable SENSOR_MODEL is populated by R27 altLabel.' + homepage: http://vocab.nerc.ac.uk/collection/R27/current/ + id: seadatanet.r27 + name: Argo sensor models + prefix: r27 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R27/current/$1 +seadatanet.r28: + authority: seadatanet + description: List of Argo floats controller board types and generations. Argo netCDF variables CONTROLLER_BOARD_TYPE_PRIMARY and, when needed, CONTROLLER_BOARD_TYPE_SECONDARY, are populated by R28 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R28/current/ + id: seadatanet.r28 + name: Argo controller board types and generations + prefix: r28 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R28/current/$1 +seadatanet.r40: + authority: seadatanet + description: List of Principal Investigator (PI) names in charge of Argo floats. Argo netCDF variable PI_NAME is populated by R40 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/R40/current/ + id: seadatanet.r40 + name: Argo Principal Investigator (PI) names + prefix: r40 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/R40/current/$1 +seadatanet.rd2: + authority: seadatanet + description: Quality flag scale for delayed-mode measurements. Argo netCDF variables _ADJUSTED_QC in 'D' mode are populated by RD2 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/RD2/current/ + id: seadatanet.rd2 + name: Argo delayed-mode quality control measurement flags + prefix: rd2 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/RD2/current/$1 +seadatanet.rmc: + authority: seadatanet + description: Categories of trajectory measurement codes listed in NVS collection 'R15' + homepage: http://vocab.nerc.ac.uk/collection/RMC/current/ + id: seadatanet.rmc + name: Argo measurement code categories + prefix: rmc + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/RMC/current/$1 +seadatanet.rp2: + authority: seadatanet + description: Quality control flag scale for whole profiles. Argo netCDF variables PROFILE__QC are populated by RP2 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/RP2/current/ + id: seadatanet.rp2 + name: Argo profile quality control flags + prefix: rp2 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/RP2/current/$1 +seadatanet.rr2: + authority: seadatanet + description: Quality flag scale for real-time measurements. Argo netCDF variables _QC in 'R' mode and _ADJUSTED_QC in 'A' mode are populated by RR2 altLabel. + homepage: http://vocab.nerc.ac.uk/collection/RR2/current/ + id: seadatanet.rr2 + name: Argo real-time quality control measurement flags + prefix: rr2 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/RR2/current/$1 +seadatanet.rtv: + authority: seadatanet + description: Timing variables representing stages of an Argo float profiling cycle, most of which are associated with a trajectory measurement code ID listed in NVS collection 'R15'. Argo netCDF cycle timing variable names JULD__STATUS are constructed by RTV altLabel. + homepage: http://vocab.nerc.ac.uk/collection/RTV/current/ + id: seadatanet.rtv + name: Argo float cycle timing variables + prefix: rtv + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/RTV/current/$1 +seadatanet.s01: + authority: seadatanet + description: Terms used to describe the information entities that are combined in the BODC semantic model to produce a phenomenon description. + homepage: http://vocab.nerc.ac.uk/collection/S01/current/ + id: seadatanet.s01 + name: BODC parameter semantic model component names + prefix: s01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S01/current/$1 +seadatanet.s02: + authority: seadatanet + description: Terms used to describe the relationship between the 'where theme' and the 'what theme' in the BODC semantic model for measured phenomena descriptions. + homepage: http://vocab.nerc.ac.uk/collection/S02/current/ + id: seadatanet.s02 + name: BODC parameter semantic model relationships between what theme and where theme + prefix: s02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S02/current/$1 +seadatanet.s03: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for a sample preparation entity (part of the how theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S03/current/ + id: seadatanet.s03 + name: BODC parameter semantic model sample preparation entity descriptions + prefix: s03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S03/current/$1 +seadatanet.s04: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for an analytical method entity (part of the how theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S04/current/ + id: seadatanet.s04 + name: BODC parameter semantic model analytical method entity descriptions + prefix: s04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S04/current/$1 +seadatanet.s05: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for data processing description (part of the how theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S05/current/ + id: seadatanet.s05 + name: BODC parameter semantic model data processing entity descriptions + prefix: s05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S05/current/$1 +seadatanet.s06: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used to specify the property element of a parameter (part of the 'what' theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S06/current/ + id: seadatanet.s06 + name: BODC parameter semantic model parameter entity names + prefix: s06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S06/current/$1 +seadatanet.s07: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for a parameter statistic (part of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S07/current/ + id: seadatanet.s07 + name: BODC parameter semantic model parameter statistic + prefix: s07 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S07/current/$1 +seadatanet.s09: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for biological entity size (part of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S09/current/ + id: seadatanet.s09 + name: BODC parameter semantic model biological entity size terms + prefix: s09 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S09/current/$1 +seadatanet.s10: + authority: seadatanet + description: Controlled vocabulary defining terms used to refer to a biological entity sex category (part of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S10/current/ + id: seadatanet.s10 + name: BODC parameter semantic model biological entity sex category terms + prefix: s10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S10/current/$1 +seadatanet.s11: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used to specify the development or life cycle stage of a biological entity (part of the 'what' theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S11/current/ + id: seadatanet.s11 + name: BODC parameter semantic model biological entity development stage terms + prefix: s11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S11/current/$1 +seadatanet.s12: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for biological entity (component of the what theme) plant or animal parts in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S12/current/ + id: seadatanet.s12 + name: BODC parameter semantic model biological entity subcomponent terms + prefix: s12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S12/current/$1 +seadatanet.s13: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for ad-hoc qualification of a biological entity (component of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S13/current/ + id: seadatanet.s13 + name: BODC parameter semantic model biological entity subgroup terms + prefix: s13 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S13/current/$1 +seadatanet.s14: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for morphology of a biological entity (component of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S14/current/ + id: seadatanet.s14 + name: BODC parameter semantic model biological entity morphology terms + prefix: s14 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S14/current/$1 +seadatanet.s15: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for colour or optical appearance of a biological entity (component of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S15/current/ + id: seadatanet.s15 + name: BODC parameter semantic model biological entity colour terms + prefix: s15 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S15/current/$1 +seadatanet.s18: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used for a physical entity (part of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S18/current/ + id: seadatanet.s18 + name: BODC parameter semantic model physical entity names + prefix: s18 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S18/current/$1 +seadatanet.s19: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used to qualify a generic physical entity (part of the what theme) in the BODC parameter semantic model. + homepage: http://vocab.nerc.ac.uk/collection/S19/current/ + id: seadatanet.s19 + name: BODC parameter semantic model physical entity subgroup names + prefix: s19 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S19/current/$1 +seadatanet.s20: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used to describe the reference with respect to which a physical entity (part of the what theme) in the BODC parameter. semantic model is specified. + homepage: http://vocab.nerc.ac.uk/collection/S20/current/ + id: seadatanet.s20 + name: BODC parameter semantic model physical entity datum names + prefix: s20 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S20/current/$1 +seadatanet.s21: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used to describe the sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme. + homepage: http://vocab.nerc.ac.uk/collection/S21/current/ + id: seadatanet.s21 + name: BODC parameter semantic model sphere names + prefix: s21 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S21/current/$1 +seadatanet.s22: + authority: seadatanet + description: Controlled vocabulary defining the terms that may be used to describe subgroupings of the sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme. + homepage: http://vocab.nerc.ac.uk/collection/S22/current/ + id: seadatanet.s22 + name: BODC parameter semantic model sphere subgroup names + prefix: s22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S22/current/$1 +seadatanet.s23: + authority: seadatanet + description: Controlled vocabulary defining the terms for phase (dissolved, particulate etc.) within a sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme. + homepage: http://vocab.nerc.ac.uk/collection/S23/current/ + id: seadatanet.s23 + name: BODC semantic model sphere phase names + prefix: s23 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S23/current/$1 +seadatanet.s24: + authority: seadatanet + description: Concepts describing physical or logical (i.e. categories) subdivisions of a phase (i.e. subcomponent) of a sphere (SWEET EarthRealm) in the BODC parameter semantic model. Part of the where theme. + homepage: http://vocab.nerc.ac.uk/collection/S24/current/ + id: seadatanet.s24 + name: BODC semantic model sphere phase subgroup names + prefix: s24 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S24/current/$1 +seadatanet.s25: + authority: seadatanet + description: Terms used to describe biological entities (organisms or parts thereof) in the BODC Parameter Usage Vocabulary + homepage: http://vocab.nerc.ac.uk/collection/S25/current/ + id: seadatanet.s25 + name: BODC parameter semantic model biological entity names + prefix: s25 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S25/current/$1 +seadatanet.s26: + authority: seadatanet + description: Terms used to describe the medium in which a measurement was made in the semantic model that underpins the BODC parameter discovery vocabulary + homepage: http://vocab.nerc.ac.uk/collection/S26/current/ + id: seadatanet.s26 + name: BODC parameter semantic model matrices + prefix: s26 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S26/current/$1 +seadatanet.s27: + authority: seadatanet + description: Terms for chemicals whose quantity in a matrix is determined to generate measurements in the BODC parameter usage vocabulary semantic model. Includes elements, compounds, isotopes and mixtures. + homepage: http://vocab.nerc.ac.uk/collection/S27/current/ + id: seadatanet.s27 + name: BODC parameter semantic model chemical substances + prefix: s27 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S27/current/$1 +seadatanet.s28: + authority: seadatanet + description: The six encoded modes of operation for a deployed Seaglider. + homepage: http://vocab.nerc.ac.uk/collection/S28/current/ + id: seadatanet.s28 + name: Seaglider Guidance and Control Phase Settings + prefix: s28 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S28/current/$1 +seadatanet.s29: + authority: seadatanet + description: Terms used to describe physical entities in the BODC Parameter Usage Vocabulary + homepage: http://vocab.nerc.ac.uk/collection/S29/current/ + id: seadatanet.s29 + name: BODC parameter semantic model physical entity compound names + prefix: s29 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S29/current/$1 +seadatanet.s30: + authority: seadatanet + description: Controlled vocabulary defining the relationship between two biological entities in the BODC parameter semantic model for biological parameters related to e.g. predator-prey interactions. + homepage: http://vocab.nerc.ac.uk/collection/S30/current/ + id: seadatanet.s30 + name: BODC parameter semantic model relationships between biological entities + prefix: s30 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/S30/current/$1 +seadatanet.t01: + authority: seadatanet + description: Standardised list of major research areas within the British Antarctic Survey for classifying materials and activities. + homepage: http://vocab.nerc.ac.uk/collection/T01/current/ + id: seadatanet.t01 + name: British Antarctic Survey research topics + prefix: t01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/T01/current/$1 +seadatanet.v12: + authority: seadatanet + description: Controlled vocabularies deemed to be of interest to the SeaDataNet project or users of its standards + homepage: http://vocab.nerc.ac.uk/collection/V12/current/ + id: seadatanet.v12 + name: SeaDataNet Vocabularies + prefix: v12 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/V12/current/$1 +seadatanet.v22: + authority: seadatanet + description: Concept collections used within ISO Code List representations for ISO19139 encoding of SeaDataNet CDIs and CSRs + homepage: http://vocab.nerc.ac.uk/collection/V22/current/ + id: seadatanet.v22 + name: SeaDataNet CDI/CSR ISO Code List collections + prefix: v22 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/V22/current/$1 +seadatanet.v23: + authority: seadatanet + description: Concept collections used within ISOTC211/19115 namespace of ISO Code List representations for ISO19139 encoding of SeaDataNet CDIs and CSRs + homepage: http://vocab.nerc.ac.uk/collection/V23/current/ + id: seadatanet.v23 + name: SeaDataNet GMX and imported ISO Code List collections + prefix: v23 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/V23/current/$1 +seadatanet.w01: + authority: seadatanet + description: Vocabulary in support of SeaDataNet's implementation of OGC Sensor Web Enablement. This is the top level vocabulary with many narrower concepts from other vocabularies. + homepage: http://vocab.nerc.ac.uk/collection/W01/current/ + id: seadatanet.w01 + name: SeaDataNet Sensor Web Enablement and SensorML type vocabulary + prefix: w01 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W01/current/$1 +seadatanet.w02: + authority: seadatanet + description: Vocabulary in support of SeaDataNet's (SDN) implementation of OGC Sensor Web Enablement (SWE). This is the lower level SDN SEW specific vocabulary. + homepage: http://vocab.nerc.ac.uk/collection/W02/current/ + id: seadatanet.w02 + name: SeaDataNet Sensor Web Enablement and SensorML sub-type vocabulary + prefix: w02 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W02/current/$1 +seadatanet.w03: + authority: seadatanet + description: Terms used to describe events or operations that have taken place during the life of an observation system (e.g. a sensor, a platform, an instrument, a network). + homepage: http://vocab.nerc.ac.uk/collection/W03/current/ + id: seadatanet.w03 + name: SensorML History Event Types + prefix: w03 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W03/current/$1 +seadatanet.w04: + authority: seadatanet + description: Terms used in SensorML to describe properties of an observation system that further qualify or quantify its output values. + homepage: http://vocab.nerc.ac.uk/collection/W04/current/ + id: seadatanet.w04 + name: SensorML Capability Section Terms + prefix: w04 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W04/current/$1 +seadatanet.w05: + authority: seadatanet + description: Terms used in SensorML to describe properties of an observation system that do not further qualify or quantify its output values. + homepage: http://vocab.nerc.ac.uk/collection/W05/current/ + id: seadatanet.w05 + name: SensorML Characteristic Section Terms + prefix: w05 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W05/current/$1 +seadatanet.w06: + authority: seadatanet + description: Terms used in SensorML to describe aspects of an observation system (e.g. the type of process, the type of sensor, or its intended applications). + homepage: http://vocab.nerc.ac.uk/collection/W06/current/ + id: seadatanet.w06 + name: SensorML Classification Section Terms + prefix: w06 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W06/current/$1 +seadatanet.w07: + authority: seadatanet + description: Terms used in SensorML to identify an observation system. + homepage: http://vocab.nerc.ac.uk/collection/W07/current/ + id: seadatanet.w07 + name: SensorML Identification Section Terms + prefix: w07 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W07/current/$1 +seadatanet.w08: + authority: seadatanet + description: Terms used in SensorML to describe the role and contact information for an observation system. + homepage: http://vocab.nerc.ac.uk/collection/W08/current/ + id: seadatanet.w08 + name: SensorML Contact Section Terms + prefix: w08 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W08/current/$1 +seadatanet.w09: + authority: seadatanet + description: Terms used in SWE Observations and Measurements that describe the measurements made by an observing system and the features involved in this process. + homepage: http://vocab.nerc.ac.uk/collection/W09/current/ + id: seadatanet.w09 + name: Sensor Web Enablement Observations and Measurements Section Terms + prefix: w09 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W09/current/$1 +seadatanet.w10: + authority: seadatanet + description: Terms used in SensorML to describe the software interactions with an observing system. The terms are typically used in the SensorML Outputs section. + homepage: http://vocab.nerc.ac.uk/collection/W10/current/ + id: seadatanet.w10 + name: SensorML Output Section Data Interface Terms + prefix: w10 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W10/current/$1 +seadatanet.w11: + authority: seadatanet + description: Terms used in SensorML to describe aspects of an Event. + homepage: http://vocab.nerc.ac.uk/collection/W11/current/ + id: seadatanet.w11 + name: SensorML Event Classification Terms + prefix: w11 + source: http://vocab.nerc.ac.uk + subjects: + - earth and related environmental sciences + - oceanography + uri_format: http://vocab.nerc.ac.uk/collection/W11/current/$1 diff --git a/fuji_server/data/linked_vocabs/sweet_ontologies.json b/fuji_server/data/linked_vocabs/sweet_ontologies.json deleted file mode 100644 index 3463135b..00000000 --- a/fuji_server/data/linked_vocabs/sweet_ontologies.json +++ /dev/null @@ -1,2477 +0,0 @@ -{ - 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"prefix": "sostsp", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateSpace/$1" - }, - "sweet.sostss": { - "authority": "sweet", - "id": "sweet.sostss", - "name": "SWEET Ontology State Space Scale", - "prefix": "sostss", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateSpaceScale/$1" - }, - "sweet.sostst": { - "authority": "sweet", - "id": "sweet.sostst", - "name": "SWEET Ontology State Storm", - "prefix": "sostst", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateStorm/$1" - }, - "sweet.sostsy": { - "authority": "sweet", - "id": "sweet.sostsy", - "name": "SWEET Ontology State System", - "prefix": "sostsy", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateSystem/$1" - }, - "sweet.sosttc": { - "authority": "sweet", - "id": "sweet.sosttc", - "name": "SWEET Ontology State Time Cycle", - "prefix": "sosttc", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateTimeCycle/$1" - }, - "sweet.sosttf": { - "authority": "sweet", - "id": "sweet.sosttf", - "name": "SWEET Ontology State Time Frequency", - "prefix": "sosttf", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateTimeFrequency/$1" - }, - "sweet.sosttg": { - "authority": "sweet", - "id": "sweet.sosttg", - "name": "SWEET Ontology State Time Geologic", - "prefix": "sosttg", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateTimeGeologic/$1" - }, - "sweet.sostth": { - "authority": "sweet", - "id": "sweet.sostth", - "name": "SWEET Ontology State Thermodynamic", - "prefix": "sostth", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateThermodynamic/$1" - }, - "sweet.sostti": { - "authority": "sweet", - "id": "sweet.sostti", - "name": "SWEET Ontology State Time", - "prefix": "sostti", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateTime/$1" - }, - "sweet.sostv": { - "authority": "sweet", - "id": "sweet.sostv", - "name": "SWEET Ontology State Visibility", - "prefix": "sostv", - "source": "sweetontology.net", - "subjects": [ - "earth and related environmental sciences" - ], - "uri_format": "http://sweetontology.net/stateVisibility/$1" - } -} diff --git a/fuji_server/data/linked_vocabs/sweet_ontologies.yaml b/fuji_server/data/linked_vocabs/sweet_ontologies.yaml new file mode 100644 index 00000000..811362fb --- /dev/null +++ b/fuji_server/data/linked_vocabs/sweet_ontologies.yaml @@ -0,0 +1,2025 @@ +sweet.soall: + authority: sweet + id: sweet.soall + name: SWEET Ontology + prefix: soall + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/sweetAll/$1 +sweet.sohu: + authority: sweet + id: sweet.sohu + name: SWEET Ontology Human + prefix: sohu + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/human/$1 +sweet.sohua: + authority: sweet + id: sweet.sohua + name: SWEET Ontology Human Agriculture + prefix: sohua + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanAgriculture/$1 +sweet.sohuc: + authority: sweet + id: sweet.sohuc + name: SWEET Ontology Human Commerce + prefix: sohuc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanCommerce/$1 +sweet.sohud: + authority: sweet + id: sweet.sohud + name: SWEET Ontology Human Decision + prefix: sohud + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanDecision/$1 +sweet.sohuea: + authority: sweet + id: sweet.sohuea + name: SWEET Ontology Human Environmental Assessment + prefix: sohuea + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanEnvirAssessment/$1 +sweet.sohueccont: + authority: sweet + id: sweet.sohueccont + name: SWEET Ontology Human Environmental Control + prefix: sohueccont + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanEnvirControl/$1 +sweet.sohuecons: + authority: sweet + id: sweet.sohuecons + name: SWEET Ontology Human Environmental Conservation + prefix: sohuecons + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanEnvirConservation/$1 +sweet.sohues: + authority: sweet + id: sweet.sohues + name: SWEET Ontology Human Environmental Standards + prefix: sohues + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanEnvirStandards/$1 +sweet.sohuj: + authority: sweet + id: sweet.sohuj + name: SWEET Ontology Human Jurisdiction + prefix: sohuj + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanJurisdiction/$1 +sweet.sohukd: + authority: sweet + id: sweet.sohukd + name: SWEET Ontology Human Knowledge Domain + prefix: sohukd + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanKnowledgeDomain/$1 +sweet.sohur: + authority: sweet + id: sweet.sohur + name: SWEET Ontology Human Research + prefix: sohur + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanResearch/$1 +sweet.sohut: + authority: sweet + id: sweet.sohut + name: SWEET Ontology Human Transportation + prefix: sohut + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanTransportation/$1 +sweet.sohutr: + authority: sweet + id: sweet.sohutr + name: SWEET Ontology Human Technology Readiness + prefix: sohutr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/humanTechReadiness/$1 +sweet.soma: + authority: sweet + id: sweet.soma + name: SWEET Ontology Materials + prefix: soma + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matr/$1 +sweet.somaae: + authority: sweet + id: sweet.somaae + name: SWEET Ontology Material Aerosol + prefix: somaae + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrAerosol/$1 +sweet.somab: + authority: sweet + id: sweet.somab + name: SWEET Ontology Material Biomass + prefix: somab + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrBiomass/$1 +sweet.somac: + authority: sweet + id: sweet.somac + name: SWEET Ontology Material Compound + prefix: somac + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrCompound/$1 +sweet.somael: + authority: sweet + id: sweet.somael + name: SWEET Ontology Material Element + prefix: somael + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrElement/$1 +sweet.somaem: + authority: sweet + id: sweet.somaem + name: SWEET Ontology Material Elemental Molecule + prefix: somaem + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrElementalMolecule/$1 +sweet.somaen: + authority: sweet + id: sweet.somaen + name: SWEET Ontology Material Energy + prefix: somaen + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrEnergy/$1 +sweet.somaeq: + authority: sweet + id: sweet.somaeq + name: SWEET Ontology Material Equipment + prefix: somaeq + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrEquipment/$1 +sweet.somaf: + authority: sweet + id: sweet.somaf + name: SWEET Ontology Material Facility + prefix: somaf + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrFacility/$1 +sweet.somaind: + authority: sweet + id: sweet.somaind + name: SWEET Ontology Material Industrial + prefix: somaind + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrIndustrial/$1 +sweet.somains: + authority: sweet + id: sweet.somains + name: SWEET Ontology Material Instrument + prefix: somains + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrInstrument/$1 +sweet.somaio: + authority: sweet + id: sweet.somaio + name: SWEET Ontology Material Ion + prefix: somaio + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrIon/$1 +sweet.somais: + authority: sweet + id: sweet.somais + name: SWEET Ontology Material Isotope + prefix: somais + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrIsotope/$1 +sweet.somamic: + authority: sweet + id: sweet.somamic + name: SWEET Ontology Material Microbiota + prefix: somamic + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrMicrobiota/$1 +sweet.somamin: + authority: sweet + id: sweet.somamin + name: SWEET Ontology Material Mineral + prefix: somamin + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrMineral/$1 +sweet.soman: + authority: sweet + id: sweet.soman + name: SWEET Ontology Material Animal + prefix: soman + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrAnimal/$1 +sweet.somanr: + authority: sweet + id: sweet.somanr + name: SWEET Ontology Material Natural Resource + prefix: somanr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrNaturalResource/$1 +sweet.somaoc: + authority: sweet + id: sweet.somaoc + name: SWEET Ontology Material Organic Compound + prefix: somaoc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrOrganicCompound/$1 +sweet.somapa: + authority: sweet + id: sweet.somapa + name: SWEET Ontology Material Particle + prefix: somapa + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrParticle/$1 +sweet.somapl: + authority: sweet + id: sweet.somapl + name: SWEET Ontology Material Plant + prefix: somapl + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrPlant/$1 +sweet.somarock: + authority: sweet + id: sweet.somarock + name: SWEET Ontology Material Rock + prefix: somarock + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrRock/$1 +sweet.somarocki: + authority: sweet + id: sweet.somarocki + name: SWEET Ontology Material Rock Igneous + prefix: somarocki + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrRockIgneous/$1 +sweet.somas: + authority: sweet + id: sweet.somas + name: SWEET Ontology Material Sediment + prefix: somas + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrSediment/$1 +sweet.somaw: + authority: sweet + id: sweet.somaw + name: SWEET Ontology Material Water + prefix: somaw + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/matrWater/$1 +sweet.soph: + authority: sweet + id: sweet.soph + name: SWEET Ontology Phenomena + prefix: soph + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phen/$1 +sweet.sophatmo: + authority: sweet + id: sweet.sophatmo + name: SWEET Ontology Phenomena Atmosphere + prefix: sophatmo + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmo/$1 +sweet.sophatmoc: + authority: sweet + id: sweet.sophatmoc + name: SWEET Ontology Phenomena Atmosphere Cloud + prefix: sophatmoc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoCloud/$1 +sweet.sophatmofo: + authority: sweet + id: sweet.sophatmofo + name: SWEET Ontology Phenomena Atmosphere Fog + prefix: sophatmofo + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoFog/$1 +sweet.sophatmofr: + authority: sweet + id: sweet.sophatmofr + name: SWEET Ontology Phenomena Atmosphere Front + prefix: sophatmofr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoFront/$1 +sweet.sophatmol: + authority: sweet + id: sweet.sophatmol + name: SWEET Ontology Phenomena Atmosphere Lightning + prefix: sophatmol + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoLightning/$1 +sweet.sophatmopc: + authority: sweet + id: sweet.sophatmopc + name: SWEET Ontology Phenomena Atmosphere Precipitation + prefix: sophatmopc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoPrecipitation/$1 +sweet.sophatmops: + authority: sweet + id: sweet.sophatmops + name: SWEET Ontology Phenomena Atmosphere Pressure + prefix: sophatmops + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoPressure/$1 +sweet.sophatmos: + authority: sweet + id: sweet.sophatmos + name: SWEET Ontology Phenomena Atmosphere Sky + prefix: sophatmos + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoSky/$1 +sweet.sophatmot: + authority: sweet + id: sweet.sophatmot + name: SWEET Ontology Phenomena Atmosphere Transport + prefix: sophatmot + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoTransport/$1 +sweet.sophatmow: + authority: sweet + id: sweet.sophatmow + name: SWEET Ontology Phenomena Atmosphere Wind + prefix: sophatmow + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoWind/$1 +sweet.sophatmowm: + authority: sweet + id: sweet.sophatmowm + name: SWEET Ontology Phenomena Atmosphere Wind Mesoscale + prefix: sophatmowm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenAtmoWindMesoscale/$1 +sweet.sophb: + authority: sweet + id: sweet.sophb + name: SWEET Ontology Phenomena Biology + prefix: sophb + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenBiol/$1 +sweet.sophcm: + authority: sweet + id: sweet.sophcm + name: SWEET Ontology Phenomena Cycle Material + prefix: sophcm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenCycleMaterial/$1 +sweet.sophcr: + authority: sweet + id: sweet.sophcr + name: SWEET Ontology Phenomena Cryosphere + prefix: sophcr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenCryo/$1 +sweet.sophcy: + authority: sweet + id: sweet.sophcy + name: SWEET Ontology Phenomena Cycle + prefix: sophcy + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenCycle/$1 +sweet.sophec: + authority: sweet + id: sweet.sophec + name: SWEET Ontology Phenomena Ecology + prefix: sophec + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenEcology/$1 +sweet.sophei: + authority: sweet + id: sweet.sophei + name: SWEET Ontology Phenomena Environmental Impact + prefix: sophei + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenEnvirImpact/$1 +sweet.sophel: + authority: sweet + id: sweet.sophel + name: SWEET Ontology Phenomena ElectroMagnetic + prefix: sophel + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenElecMag/$1 +sweet.sophen: + authority: sweet + id: sweet.sophen + name: SWEET Ontology Phenomena Energy + prefix: sophen + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenEnergy/$1 +sweet.sophfd: + authority: sweet + id: sweet.sophfd + name: SWEET Ontology Phenomena Fluid Dynamics + prefix: sophfd + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenFluidDynamics/$1 +sweet.sophfi: + authority: sweet + id: sweet.sophfi + name: SWEET Ontology Phenomena Fluid Instability + prefix: sophfi + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenFluidInstability/$1 +sweet.sophft: + authority: sweet + id: sweet.sophft + name: SWEET Ontology Phenomena Fluid Transport + prefix: sophft + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenFluidTransport/$1 +sweet.sophg: + authority: sweet + id: sweet.sophg + name: SWEET Ontology Phenomena Geologic + prefix: sophg + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenGeol/$1 +sweet.sophgf: + authority: sweet + id: sweet.sophgf + name: SWEET Ontology Phenomena Geologic Fault + prefix: sophgf + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenGeolFault/$1 +sweet.sophgg: + authority: sweet + id: sweet.sophgg + name: SWEET Ontology Phenomena Geologic Geomorphology + prefix: sophgg + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenGeolGeomorphology/$1 +sweet.sophgs: + authority: sweet + id: sweet.sophgs + name: SWEET Ontology Phenomena Geologic Seismicity + prefix: sophgs + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenGeolSeismicity/$1 +sweet.sophgt: + authority: sweet + id: sweet.sophgt + name: SWEET Ontology Phenomena Geologic Tectonic + prefix: sophgt + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenGeolTectonic/$1 +sweet.sophgv: + authority: sweet + id: sweet.sophgv + name: SWEET Ontology Phenomena Geologic Volcano + prefix: sophgv + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenGeolVolcano/$1 +sweet.sophhe: + authority: sweet + id: sweet.sophhe + name: SWEET Ontology Phenomena Heliosphere + prefix: sophhe + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenHelio/$1 +sweet.sophhy: + authority: sweet + id: sweet.sophhy + name: SWEET Ontology Phenomena Hydrosphere + prefix: sophhy + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenHydro/$1 +sweet.sophm: + authority: sweet + id: sweet.sophm + name: SWEET Ontology Phenomena Mixing + prefix: sophm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenMixing/$1 +sweet.sopho: + authority: sweet + id: sweet.sopho + name: SWEET Ontology Phenomena Ocean + prefix: sopho + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenOcean/$1 +sweet.sophoc: + authority: sweet + id: sweet.sophoc + name: SWEET Ontology Phenomena Ocean Coastal + prefix: sophoc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenOceanCoastal/$1 +sweet.sophod: + authority: sweet + id: sweet.sophod + name: SWEET Ontology Phenomena Ocean Dynamics + prefix: sophod + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenOceanDynamics/$1 +sweet.sophpc: + authority: sweet + id: sweet.sophpc + name: SWEET Ontology Phenomena Planetary Climate + prefix: sophpc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenPlanetClimate/$1 +sweet.sophr: + authority: sweet + id: sweet.sophr + name: SWEET Ontology Phenomena Reaction + prefix: sophr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenReaction/$1 +sweet.sophso: + authority: sweet + id: sweet.sophso + name: SWEET Ontology Phenomena Solid + prefix: sophso + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenSolid/$1 +sweet.sophst: + authority: sweet + id: sweet.sophst + name: SWEET Ontology Phenomena Star + prefix: sophst + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenStar/$1 +sweet.sophsy: + authority: sweet + id: sweet.sophsy + name: SWEET Ontology Phenomena System + prefix: sophsy + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenSystem/$1 +sweet.sophsyc: + authority: sweet + id: sweet.sophsyc + name: SWEET Ontology Phenomena System Complexity + prefix: sophsyc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenSystemComplexity/$1 +sweet.sophw: + authority: sweet + id: sweet.sophw + name: SWEET Ontology Phenomena Wave + prefix: sophw + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenWave/$1 +sweet.sophwn: + authority: sweet + id: sweet.sophwn + name: SWEET Ontology Phenomena Wave Noise + prefix: sophwn + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/phenWaveNoise/$1 +sweet.soproc: + authority: sweet + id: sweet.soproc + name: SWEET Ontology Process + prefix: soproc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/proc/$1 +sweet.soprocc: + authority: sweet + id: sweet.soprocc + name: SWEET Ontology Process Chemical + prefix: soprocc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/procChemical/$1 +sweet.soprocp: + authority: sweet + id: sweet.soprocp + name: SWEET Ontology Process Physical + prefix: soprocp + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/procPhysical/$1 +sweet.soprocsc: + authority: sweet + id: sweet.soprocsc + name: SWEET Ontology Process State Change + prefix: soprocsc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/procStateChange/$1 +sweet.soprocw: + authority: sweet + id: sweet.soprocw + name: SWEET Ontology Process Wave + prefix: soprocw + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/procWave/$1 +sweet.soprop: + authority: sweet + id: sweet.soprop + name: SWEET Ontology Property + prefix: soprop + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/prop/$1 +sweet.sopropb: + authority: sweet + id: sweet.sopropb + name: SWEET Ontology Property Binary + prefix: sopropb + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propBinary/$1 +sweet.sopropcap: + authority: sweet + id: sweet.sopropcap + name: SWEET Ontology Property Capacity + prefix: sopropcap + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propCapacity/$1 +sweet.sopropcat: + authority: sweet + id: sweet.sopropcat + name: SWEET Ontology Property Categorical + prefix: sopropcat + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propCategorical/$1 +sweet.sopropcha: + authority: sweet + id: sweet.sopropcha + name: SWEET Ontology Property Charge + prefix: sopropcha + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propCharge/$1 +sweet.sopropche: + authority: sweet + id: sweet.sopropche + name: SWEET Ontology Property Chemical + prefix: sopropche + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propChemical/$1 +sweet.sopropcon: + authority: sweet + id: sweet.sopropcon + name: SWEET Ontology Property Conductivity + prefix: sopropcon + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propConductivity/$1 +sweet.sopropcou: + authority: sweet + id: sweet.sopropcou + name: SWEET Ontology Property Count + prefix: sopropcou + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propCount/$1 +sweet.sopropdife: + authority: sweet + id: sweet.sopropdife + name: SWEET Ontology Property Difference + prefix: sopropdife + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propDifference/$1 +sweet.sopropdifu: + authority: sweet + id: sweet.sopropdifu + name: SWEET Ontology Property Diffusivity + prefix: sopropdifu + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propDiffusivity/$1 +sweet.sopropdr: + authority: sweet + id: sweet.sopropdr + name: SWEET Ontology Property Dimensionless Ratio + prefix: sopropdr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propDimensionlessRatio/$1 +sweet.soprope: + authority: sweet + id: sweet.soprope + name: SWEET Ontology Property Energy + prefix: soprope + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propEnergy/$1 +sweet.sopropef: + authority: sweet + id: sweet.sopropef + name: SWEET Ontology Property Energy Flux + prefix: sopropef + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propEnergyFlux/$1 +sweet.sopropfr: + authority: sweet + id: sweet.sopropfr + name: SWEET Ontology Property Fraction + prefix: sopropfr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propFraction/$1 +sweet.sopropfu: + authority: sweet + id: sweet.sopropfu + name: SWEET Ontology Property Function + prefix: sopropfu + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propFunction/$1 +sweet.sopropi: + authority: sweet + id: sweet.sopropi + name: SWEET Ontology Property Index + prefix: sopropi + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propIndex/$1 +sweet.sopropm: + authority: sweet + id: sweet.sopropm + name: SWEET Ontology Property Mass + prefix: sopropm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propMass/$1 +sweet.sopropmf: + authority: sweet + id: sweet.sopropmf + name: SWEET Ontology Property Mass Flux + prefix: sopropmf + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propMassFlux/$1 +sweet.sopropo: + authority: sweet + id: sweet.sopropo + name: SWEET Ontology Property Ordinal + prefix: sopropo + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propOrdinal/$1 +sweet.sopropp: + authority: sweet + id: sweet.sopropp + name: SWEET Ontology Property Pressure + prefix: sopropp + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propPressure/$1 +sweet.sopropq: + authority: sweet + id: sweet.sopropq + name: SWEET Ontology Property Quantity + prefix: sopropq + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propQuantity/$1 +sweet.sopropr: + authority: sweet + id: sweet.sopropr + name: SWEET Ontology Property Rotation + prefix: sopropr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propRotation/$1 +sweet.soprops: + authority: sweet + id: sweet.soprops + name: SWEET Ontology Property Space + prefix: soprops + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpace/$1 +sweet.sopropsdir: + authority: sweet + id: sweet.sopropsdir + name: SWEET Ontology Property Space Direction + prefix: sopropsdir + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpaceDirection/$1 +sweet.sopropsdis: + authority: sweet + id: sweet.sopropsdis + name: SWEET Ontology Property Space Distance + prefix: sopropsdis + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpaceDistance/$1 +sweet.sopropsh: + authority: sweet + id: sweet.sopropsh + name: SWEET Ontology Property Space Height + prefix: sopropsh + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpaceHeight/$1 +sweet.sopropsl: + authority: sweet + id: sweet.sopropsl + name: SWEET Ontology Property Space Location + prefix: sopropsl + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpaceLocation/$1 +sweet.sopropsm: + authority: sweet + id: sweet.sopropsm + name: SWEET Ontology Property Space Multidimensional + prefix: sopropsm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpaceMultidimensional/$1 +sweet.sopropsp: + authority: sweet + id: sweet.sopropsp + name: SWEET Ontology Property Speed + prefix: sopropsp + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpeed/$1 +sweet.sopropst: + authority: sweet + id: sweet.sopropst + name: SWEET Ontology Property Space Thickness + prefix: sopropst + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propSpaceThickness/$1 +sweet.sopropt: + authority: sweet + id: sweet.sopropt + name: SWEET Ontology Property Temperature + prefix: sopropt + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propTemperature/$1 +sweet.soproptf: + authority: sweet + id: sweet.soproptf + name: SWEET Ontology Property Time Frequency + prefix: soproptf + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propTimeFrequency/$1 +sweet.soproptg: + authority: sweet + id: sweet.soproptg + name: SWEET Ontology Property Temperature Gradient + prefix: soproptg + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propTemperatureGradient/$1 +sweet.sopropti: + authority: sweet + id: sweet.sopropti + name: SWEET Ontology Property Time + prefix: sopropti + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/propTime/$1 +sweet.sorea: + authority: sweet + id: sweet.sorea + name: SWEET Ontology Realm + prefix: sorea + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realm/$1 +sweet.soreaa: + authority: sweet + id: sweet.soreaa + name: SWEET Ontology Realm Atmospheric + prefix: soreaa + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmAtmo/$1 +sweet.soreaab: + authority: sweet + id: sweet.soreaab + name: SWEET Ontology Realm Astrophysical Body + prefix: soreaab + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmAstroBody/$1 +sweet.soreaabl: + authority: sweet + id: sweet.soreaabl + name: SWEET Ontology Realm Atmospheric Boundary Layer + prefix: soreaabl + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmAtmoBoundaryLayer/$1 +sweet.soreaah: + authority: sweet + id: sweet.soreaah + name: SWEET Ontology Realm Astrophysical Heliosphere + prefix: soreaah + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmAstroHelio/$1 +sweet.soreaas: + authority: sweet + id: sweet.soreaas + name: SWEET Ontology Realm Astrophysical + prefix: soreaas + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmAstroStar/$1 +sweet.soreaaw: + authority: sweet + id: sweet.soreaaw + name: SWEET Ontology Realm Atmospheric Weather + prefix: soreaaw + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmAtmoWeather/$1 +sweet.soreabb: + authority: sweet + id: sweet.soreabb + name: SWEET Ontology Realm Biologic Biome + prefix: soreabb + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmBiolBiome/$1 +sweet.soreac: + authority: sweet + id: sweet.soreac + name: SWEET Ontology Realm Cryosphere + prefix: soreac + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmCryo/$1 +sweet.soreacz: + authority: sweet + id: sweet.soreacz + name: SWEET Ontology Realm Climate Zone + prefix: soreacz + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmClimateZone/$1 +sweet.soreaer: + authority: sweet + id: sweet.soreaer + name: SWEET Ontology Realm Earth Reference + prefix: soreaer + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmEarthReference/$1 +sweet.soreag: + authority: sweet + id: sweet.soreag + name: SWEET Ontology Realm Geologic + prefix: soreag + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmGeol/$1 +sweet.soreagb: + authority: sweet + id: sweet.soreagb + name: SWEET Ontology Realm Geologic Basin + prefix: soreagb + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmGeolBasin/$1 +sweet.soreagcons: + authority: sweet + id: sweet.soreagcons + name: SWEET Ontology Realm Geologic Constituent + prefix: soreagcons + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmGeolConstituent/$1 +sweet.soreagcont: + authority: sweet + id: sweet.soreagcont + name: SWEET Ontology Realm Geologic Continental + prefix: soreagcont + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmGeolContinental/$1 +sweet.soreagoc: + authority: sweet + id: sweet.soreagoc + name: SWEET Ontology Realm Geologic Oceanic + prefix: soreagoc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmGeolOceanic/$1 +sweet.soreagor: + authority: sweet + id: sweet.soreagor + name: SWEET Ontology Realm Geologic Orogen + prefix: soreagor + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmGeolOrogen/$1 +sweet.soreah: + authority: sweet + id: sweet.soreah + name: SWEET Ontology Realm Hydrosphere + prefix: soreah + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmHydro/$1 +sweet.soreahb: + authority: sweet + id: sweet.soreahb + name: SWEET Ontology Realm Hydrosphere Body + prefix: soreahb + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmHydroBody/$1 +sweet.soreal: + authority: sweet + id: sweet.soreal + name: SWEET Ontology Realm Landform + prefix: soreal + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandform/$1 +sweet.soreala: + authority: sweet + id: sweet.soreala + name: SWEET Ontology Realm Land Aeolian + prefix: soreala + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandAeolian/$1 +sweet.sorealc: + authority: sweet + id: sweet.sorealc + name: SWEET Ontology Realm Land Coastal + prefix: sorealc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandCoastal/$1 +sweet.sorealf: + authority: sweet + id: sweet.sorealf + name: SWEET Ontology Realm Land Fluvial + prefix: sorealf + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandFluvial/$1 +sweet.sorealg: + authority: sweet + id: sweet.sorealg + name: SWEET Ontology Realm Land Glacial + prefix: sorealg + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandGlacial/$1 +sweet.sorealo: + authority: sweet + id: sweet.sorealo + name: SWEET Ontology Realm Land Orographic + prefix: sorealo + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandOrographic/$1 +sweet.sorealp: + authority: sweet + id: sweet.sorealp + name: SWEET Ontology Realm Land Protected + prefix: sorealp + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandProtected/$1 +sweet.sorealt: + authority: sweet + id: sweet.sorealt + name: SWEET Ontology Realm Land Tectonic + prefix: sorealt + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandTectonic/$1 +sweet.sorealv: + authority: sweet + id: sweet.sorealv + name: SWEET Ontology Realm Land Volcanic + prefix: sorealv + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmLandVolcanic/$1 +sweet.soreao: + authority: sweet + id: sweet.soreao + name: SWEET Ontology Realm Ocean + prefix: soreao + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmOcean/$1 +sweet.soreaofe: + authority: sweet + id: sweet.soreaofe + name: SWEET Ontology Realm Ocean Feature + prefix: soreaofe + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmOceanFeature/$1 +sweet.soreaofl: + authority: sweet + id: sweet.soreaofl + name: SWEET Ontology Realm Ocean Floor + prefix: soreaofl + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmOceanFloor/$1 +sweet.sorear: + authority: sweet + id: sweet.sorear + name: SWEET Ontology Realm Region + prefix: sorear + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmRegion/$1 +sweet.soreas: + authority: sweet + id: sweet.soreas + name: SWEET Ontology Realm Soil + prefix: soreas + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/realmSoil/$1 +sweet.sorel: + authority: sweet + id: sweet.sorel + name: SWEET Ontology Relationships + prefix: sorel + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/rela/$1 +sweet.sorelch: + authority: sweet + id: sweet.sorelch + name: SWEET Ontology Relationships Chemical + prefix: sorelch + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaChemical/$1 +sweet.sorelcl: + authority: sweet + id: sweet.sorelcl + name: SWEET Ontology Relationships Climate + prefix: sorelcl + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaClimate/$1 +sweet.sorelh: + authority: sweet + id: sweet.sorelh + name: SWEET Ontology Relationships Human + prefix: sorelh + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaHuman/$1 +sweet.sorelm: + authority: sweet + id: sweet.sorelm + name: SWEET Ontology Relationships Mathematical + prefix: sorelm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaMath/$1 +sweet.sorelph: + authority: sweet + id: sweet.sorelph + name: SWEET Ontology Relationships Physical + prefix: sorelph + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaPhysical/$1 +sweet.sorelpr: + authority: sweet + id: sweet.sorelpr + name: SWEET Ontology Relationships Provenance + prefix: sorelpr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaProvenance/$1 +sweet.sorelsc: + authority: sweet + id: sweet.sorelsc + name: SWEET Ontology Relationships Scientific + prefix: sorelsc + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaSci/$1 +sweet.sorelsp: + authority: sweet + id: sweet.sorelsp + name: SWEET Ontology Relationships Space + prefix: sorelsp + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaSpace/$1 +sweet.sorelt: + authority: sweet + id: sweet.sorelt + name: SWEET Ontology Relationships Time + prefix: sorelt + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/relaTime/$1 +sweet.sorep: + authority: sweet + id: sweet.sorep + name: SWEET Ontology Representation + prefix: sorep + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/repr/$1 +sweet.sorepdf: + authority: sweet + id: sweet.sorepdf + name: SWEET Ontology Representation Data Format + prefix: sorepdf + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataFormat/$1 +sweet.sorepdm: + authority: sweet + id: sweet.sorepdm + name: SWEET Ontology Representation Data Model + prefix: sorepdm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataModel/$1 +sweet.sorepdp: + authority: sweet + id: sweet.sorepdp + name: SWEET Ontology Representation Data Product + prefix: sorepdp + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataProduct/$1 +sweet.sorepds: + authority: sweet + id: sweet.sorepds + name: SWEET Ontology Representation Data Service + prefix: sorepds + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataService/$1 +sweet.sorepdsa: + authority: sweet + id: sweet.sorepdsa + name: SWEET Ontology Representation Data Servcie Analysis + prefix: sorepdsa + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataServiceAnalysis/$1 +sweet.sorepdsg: + authority: sweet + id: sweet.sorepdsg + name: SWEET Ontology Representation Data Service Geospatial + prefix: sorepdsg + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataServiceGeospatial/$1 +sweet.sorepdsr: + authority: sweet + id: sweet.sorepdsr + name: SWEET Ontology Representation Data Service Reduction + prefix: sorepdsr + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataServiceReduction/$1 +sweet.sorepdsv: + authority: sweet + id: sweet.sorepdsv + name: SWEET Ontology Representation Data Service Validation + prefix: sorepdsv + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprDataServiceValidation/$1 +sweet.sorepm: + authority: sweet + id: sweet.sorepm + name: SWEET Ontology Representation Mathematics + prefix: sorepm + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprMath/$1 +sweet.sorepmf: + authority: sweet + id: sweet.sorepmf + name: SWEET Ontology Representation Mathematics Function + prefix: sorepmf + source: sweetontology.net + subjects: + - earth and related environmental sciences + uri_format: http://sweetontology.net/reprMathFunction/$1 +sweet.sorepmfo: + authority: sweet + id: sweet.sorepmfo + name: SWEET Ontology Representation Mathematics Function Orthogonal + prefix: sorepmfo + source: sweetontology.net + subjects: + - 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{ - "type": "schema", - "value": "https://schemas.opengis.net/waterml/2.0/waterml2.xsd" - }, - { - "type": "namespace", - "value": "http://www.opengis.net/waterml/2.0" - } - ], - "subject_areas": [ - "Hydrology" - ], - "urls": [ - "http://www.opengeospatial.org/standards/waterml", - "https://schemas.opengis.net/waterml/2.0/waterml2.xsd", - "http://www.opengis.net/waterml/2.0" - ] - }, - "XOAI, a DSPACE Metadata Format": { - "acronym": "XOAI", - "field_of_science": [], - "id": "xoai-metadata-format", - "identifier": [ - { - "type": "local", - "value": "fuji:m6" - }, - { - "type": "homepage", - "value": "https://github.com/DSpace/xoai" - }, - { - "type": "namespace", - "value": "http://www.lyncode.com/xoai" - } - ], - "subject_areas": null, - "urls": [ - "https://github.com/DSpace/xoai", - "http://www.lyncode.com/xoai" - ] - }, - "XmetaDiss": { - "acronym": "xmetadiss", - "field_of_science": [ - "library sciences", - "sciences", - "humanities" - ], - "id": "xmetadiss-schema", - "identifier": [ - { - "type": "local", - "value": "fuji:m43" - }, - { - "type": "schema", - "value": "https://d-nb.info/standards/schema/xmetadissplus.xsd" - }, - { - "type": "namespace", - "value": "http://www.d-nb.de/standards/xmetadissplus/" - }, - { - "type": "namespace", - "value": "http://www.d-nb.de/standards/xMetaDiss/" - }, - { - "type": "homepage", - "value": "http://www.d-nb.de/standards/xMetaDiss/" - } - ], - "subject_areas": [ - "Multidisciplinary", - "Bibliographic standards", - "Information/library standards" - ], - "urls": [ - "https://d-nb.info/standards/schema/xmetadissplus.xsd", - "http://www.d-nb.de/standards/xmetadissplus/", - "http://www.d-nb.de/standards/xMetaDiss/", - "http://www.d-nb.de/standards/xMetaDiss/", - "https://d-nb.info/1260521133/34" - ] - }, - "da|ra Metadata Schema": { - "acronym": "da|ra", - "field_of_science": [ - "sociology", - "social sciences", - "political sciences" - ], - "id": "dara-metadata-schema", - "identifier": [ - { - "type": "local", - "value": "fuji:m10" - }, - { - "type": "local", - "value": "https://fairsharing.org/4651" - }, - { - "type": "namespace", - "value": "http://da-ra.de/schema/kernel-4" - }, - { - "type": "schema", - "value": "http://da-ra.de/dara/schemadefinitions/dara.xsd" - }, - { - "type": "schema", - "value": "dara_v2.2.1_de_en_19112012.xsd" - }, - { - "type": "schema", - "value": "http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd" - }, - { - "type": "homepage", - "value": "https://www.da-ra.de/downloads#metadata" - } - ], - "subject_areas": [ - "Social policy", - "Sociology" - ], - "urls": [ - "http://da-ra.de/schema/kernel-4", - "http://da-ra.de/dara/schemadefinitions/dara.xsd", - "dara_v2.2.1_de_en_19112012.xsd", - "http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd", - "https://www.da-ra.de/downloads#version-3-0", - "https://www.da-ra.de/downloads#metadata" - ] - }, - "eBank UK Metadata Application Profile": { - "acronym": null, - "field_of_science": [ - "crystallography", - "natural sciences" - ], - "id": "ebank-uk-metadata-application-profile", - "identifier": [ - { - "type": "local", - "value": "msc:m57" - }, - { - "type": "local", - "value": "https://doi.org/10.25504/FAIRsharing.ad4856" - }, - { - "type": "homepage", - "value": "http://ecrystals.chem.soton.ac.uk" - }, - { - "type": "schema", - "value": "http://naca.central.cranfield.ac.uk/ethos-oai/2.0/uketd_dc.xsd" - }, - { - "type": "namespace", - "value": "http://naca.central.cranfield.ac.uk/ethos-oai/uketd_dc/" - } - ], - "subject_areas": [ - "Crystallography" - ], - "urls": [ - "http://ecrystals.chem.soton.ac.uk", - "http://naca.central.cranfield.ac.uk/ethos-oai/2.0/uketd_dc.xsd", - "http://naca.central.cranfield.ac.uk/ethos-oai/uketd_dc/" - ] - }, - "isaconfig-diXa": { - "acronym": null, - "field_of_science": [ - "medical and health sciences", - "toxicology", - "genetics", - "natural sciences" - ], - "id": "isaconfig-dixa", - "identifier": [ - { - "type": "local", - "value": "msc:m68" - }, - { - "type": "homepage", - "value": "https://bitbucket.org/kanterae/isaconfig-dixa" - } - ], - "subject_areas": [ - "Genetics", - "Toxicology" - ], - "urls": [ - "https://bitbucket.org/kanterae/isaconfig-dixa" - ] - }, - "museumdat": { - "acronym": "museumdat", - "field_of_science": [ - "humanities" - ], - "id": "museumdat-schema", - "identifier": [ - { - "type": "local", - "value": "fuji:m31" - }, - { - "type": "local", - "value": "https://fairsharing.org/4671" - }, - { - "type": "schema", - "value": "http://museum.zib.de/museumdat/museumdat-v1.0.xsd" - }, - { - "type": "homepage", - "value": "http://museum.zib.de/museumdat/" - } - ], - "subject_areas": [ - "Humanities", - "Cultural heritage" - ], - "urls": [ - "http://museum.zib.de/museumdat/museumdat-v1.0.xsd", - "http://museum.zib.de/museumdat/" - ] - }, - "null": { - "acronym": "scholix", - "field_of_science": [], - "id": "scholix-metadata-schema", - "identifier": [ - { - "type": "local", - "value": "fuji:m28" - }, - { - "type": "local", - "value": "https://doi.org/10.25504/FAIRsharing.B0d5Kn" - }, - { - "type": "homepage", - "value": "http://www.scholix.org/schema" - }, - { - "type": "namespace", - "value": "http://www.scholix.org" - }, - { - "type": "schema", - "value": "https://github.com/scholix/schema/blob/master/xsd/v3/schema.xsd" - }, - { - "type": "schema", - "value": "https://github.com/scholix/schema/blob/master/xsd/v1/scholix.xsd" - } - ], - "subject_areas": null, - "urls": [ - "http://www.scholix.org/schema", - "http://www.scholix.org", - "https://github.com/scholix/schema/blob/master/xsd/v3/schema.xsd", - "https://github.com/scholix/schema/blob/master/xsd/v1/scholix.xsd" - ] - }, - "xepicur": { - "acronym": "epicur", - "field_of_science": [], - "id": "epicur-metadata-schema", - "identifier": [ - { - "type": "local", - "value": "fuji:m21" - }, - { - "type": "local", - "value": "https://fairsharing.org/4659" - }, - { - "type": "namespace", - "value": "urn:nbn:de:1111-2004033116" - }, - { - "type": "schema", - "value": "https://files.dnb.de/Web/xepicur.xsd" - }, - { - "type": "homepage", - "value": "https://wiki.dnb.de/display/URNSERVDOK/xepicur+-+XML-Datentransferformat+zur+Verwaltung+von+URN" - } - ], - "subject_areas": null, - "urls": [ - "urn:nbn:de:1111-2004033116", - " https://files.dnb.de/Web/xepicur.xsd", - "https://wiki.dnb.de/display/URNSERVDOK/xepicur+-+XML-Datentransferformat+zur+Verwaltung+von+URN" - ] - } -} diff --git a/fuji_server/data/metadata_standards.yaml b/fuji_server/data/metadata_standards.yaml new file mode 100644 index 00000000..9e7d55c9 --- /dev/null +++ b/fuji_server/data/metadata_standards.yaml @@ -0,0 +1,4010 @@ +ABCD (Access to Biological Collection Data): + acronym: ABCD + field_of_science: + - zoology + - geology + - botany + - biological sciences + - palaeontology + - earth and related environmental sciences + - genetics + - natural sciences + id: abcd-access-biological-collection-data + identifier: + - type: local + value: msc:m1 + - type: local + value: https://doi.org/10.25504/FAIRsharing.kr3215 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/abcd-access-biological-collection-data + - type: homepage + value: http://wiki.tdwg.org/ABCD + - type: schema + value: https://abcd.tdwg.org/xml/ABCD_3.0.xsd + - type: namespace + value: http://www.tdwg.org/schemas/abcd/3.0 + - type: schema + value: https://abcd.tdwg.org/xml/ABCD_2.1.xsd + - type: namespace + value: http://www.tdwg.org/schemas/abcd/2.1 + - type: schema + value: https://abcd.tdwg.org/xml/ABCD_2.06.xsd + - type: namespace + value: http://www.tdwg.org/schemas/abcd/2.06 + subject_areas: + - Biological diversity + - Botany + - Earth sciences + - Genetics + - Geology + - Palaeontology + - Zoology + urls: + - http://www.tdwg.org/standards/115/ + - http://wiki.tdwg.org/ABCD + - https://abcd.tdwg.org/xml/ABCD_3.0.xsd + - http://www.tdwg.org/schemas/abcd/3.0 + - https://abcd.tdwg.org/xml/ABCD_2.1.xsd + - http://www.tdwg.org/schemas/abcd/2.1 + - https://abcd.tdwg.org/xml/ABCD_2.06.xsd + - http://www.tdwg.org/schemas/abcd/2.06 +ABCDDNA: + acronym: ABCDDNA + field_of_science: + - genetics + - natural sciences + id: abcddna + identifier: + - type: local + value: msc:m42 + - type: local + value: https://doi.org/10.25504/FAIRsharing.7tx4ac + - type: homepage + value: http://www.tdwg.org/standards/640/ + - type: schema + value: http://www.dnabank-network.org/schemas/ABCDDNA/ABCDDNA.xsd + - type: namespace + value: http://www.dnabank-network.org/schemas/ABCDDNA + subject_areas: + - Genetics + urls: + - http://www.tdwg.org/standards/640/ + - http://www.dnabank-network.org/schemas/ABCDDNA/ABCDDNA.xsd + - http://www.dnabank-network.org/schemas/ABCDDNA +ABCDEFG (Access to Biological Collection Databases Extended for Geosciences): + acronym: ABCDEFG + field_of_science: + - earth and related environmental sciences + - mineralogy + - natural sciences + - palaeontology + id: abcdefg-access-biological-collection-databases-extended-geosciences + identifier: + - type: local + value: msc:m43 + - type: local + value: https://fairsharing.org/1396 + - type: homepage + value: http://www.geocase.eu/efg + - type: schema + value: http://www.geocase.eu/sites/geocase.biodiv.naturkundemuseum-berlin.de/documentation/abcdefg.xsd + - type: namespace + value: http://www.synthesys.info/ABCDEFG/1.0 + subject_areas: + - Earth sciences + - Mineralogy + - Palaeontology + urls: + - http://www.geocase.eu/efg + - http://www.geocase.eu/sites/geocase.biodiv.naturkundemuseum-berlin.de/documentation/abcdefg.xsd + - http://www.synthesys.info/ABCDEFG/1.0 +AGLS Metadata Profile: + acronym: AGLS + field_of_science: + - sciences + id: agls-metadata-profile + identifier: + - type: local + value: msc:m44 + - type: local + value: https://fairsharing.org/751 + - type: homepage + value: http://www.agls.gov.au + - type: namespace + value: http://www.agls.gov.au/agls/terms/ + subject_areas: + - Multidisciplinary + urls: + - http://www.agls.gov.au + - http://www.agls.gov.au/agls/terms/ +AGRIS Application Profile: + acronym: AGRIS + field_of_science: + - animal and dairy science + - agriculture + - agricultural sciences + - fisheries + id: agris-application-profile + identifier: + - type: local + value: msc:m45 + - type: local + value: https://doi.org/10.25504/FAIRsharing.32e620 + - type: homepage + value: http://www.fao.org/docrep/008/ae909e/ae909e00.htm + - type: namespace + value: http://www.fao.org/agris + subject_areas: + - Agricultural economics + - Agriculture + - Aquaculture + - Livestock + urls: + - http://www.fao.org/docrep/008/ae909e/ae909e00.htm + - http://www.fao.org/agris +ANZLIC Metadata Profile: + acronym: ANZLIC + field_of_science: + - physical geography + - natural sciences + - cartography + id: anzlic-metadata-profile + identifier: + - type: local + value: msc:m46 + - type: local + value: https://fairsharing.org/820 + - type: homepage + value: https://www.anzlic.gov.au/resources/anzlic-metadata-profile + subject_areas: + - Cartography + - Geography + - Topography + urls: + - https://www.anzlic.gov.au/resources/anzlic-metadata-profile +AODN Marine Community Profile: + acronym: AODN + field_of_science: + - glaciology + - climatology + - oceanography + - meteorology + - earth and related environmental sciences + - natural sciences + - hydrology + id: marine-community-profile + identifier: + - type: local + value: msc:m71 + - type: local + value: https://doi.org/10.25504/FAIRsharing.18b8b4 + - type: homepage + value: http://www.aodc.org.au/index.php?id=37 + - type: namespace + value: http://schemas.aodn.org.au/mcp-2.0 + - type: namespace + value: http://schemas.aodn.org.au + - type: schema + value: http://schemas.aodn.org.au/mcp-2.0/schema.xsd + subject_areas: + - Climatology + - Earth sciences + - Glaciology + - Hydrology + - Meteorology + - Oceanography + urls: + - https://mcp-profile-docs.readthedocs.io/en/stable/ + - http://www.aodc.org.au/index.php?id=37 + - http://schemas.aodn.org.au/mcp-2.0 + - http://schemas.aodn.org.au + - http://schemas.aodn.org.au/mcp-2.0/schema.xsd +ARIADNE Dataset Catalogue Model (ACDM): + acronym: ACDM + field_of_science: + - humanities + - archaeology + id: ariadne-dataset-catalogue-model + identifier: + - type: local + value: fuji:m19 + - type: local + value: https://fairsharing.org/4647 + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - type: namespace + value: http://registry.ariadne-infrastructure.eu/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/ + - type: namespace + value: http://ariadne-registry.dcu.gr/schema-definition + - type: homepage + value: http://ariadne-registry.dcu.gr/ + subject_areas: + - Archaeology + urls: + - http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - http://registry.ariadne-infrastructure.eu/ + - https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - https://www.ariadne-infrastructure.eu/resource/ao/ + - http://ariadne-registry.dcu.gr/schema-definition + - http://ariadne-registry.dcu.gr/ +AVM (Astronomy Visualization Metadata): + acronym: AVM + field_of_science: + - natural sciences + - astronomy + id: avm-astronomy-visualization-metadata + identifier: + - type: local + value: msc:m3 + - type: local + value: https://doi.org/10.25504/FAIRsharing.338ze0 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/avm-astronomy-visualization-metadata + - type: homepage + value: http://www.virtualastronomy.org/avm_metadata.php + - type: namespace + value: http://www.communicatingastronomy.org/avm/1.0/ + subject_areas: + - Astronomy + urls: + - http://www.virtualastronomy.org/avm_metadata.php#2 + - http://www.virtualastronomy.org/avm_metadata.php + - http://www.communicatingastronomy.org/avm/1.0/ +Academic Metadata Format: + acronym: AMF + field_of_science: + - sciences + id: amf-academic-metadata-format + identifier: + - type: local + value: fuji:m25 + - type: local + value: https://fairsharing.org/4646 + - type: namespace + value: http://amf.openlib.org + - type: homepage + value: http://amf.openlib.org + - type: schema + value: http://amf.openlib.org/2001/amf.xsd + subject_areas: + - Multidisciplinary + urls: + - http://openlib.org/home/krichel/ebisu.html + - http://amf.openlib.org + - http://amf.openlib.org + - http://amf.openlib.org/2001/amf.xsd +AgMES (Agricultural Metadata Element Set): + acronym: AgMES + field_of_science: + - animal and dairy science + - agriculture + - agricultural sciences + - fisheries + id: agmes-agricultural-metadata-element-set + identifier: + - type: local + value: msc:m2 + - type: local + value: https://doi.org/10.25504/FAIRsharing.vd694s + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/agmes-agricultural-metadata-element-set + - type: homepage + value: http://aims.fao.org/standards/agmes + - type: namespace + value: http://purl.org/agmes/1.1/ + subject_areas: + - Agricultural economics + - Agriculture + - Aquaculture + - Livestock + urls: + - http://aims.fao.org/es/standards/agmes/namespace-specification + - http://aims.fao.org/standards/agmes + - http://purl.org/agmes/1.1/ + - http://purl.org/agmes/1.1/ +Apple Core: + acronym: aDwC + field_of_science: + - natural sciences + - botany + id: apple-core + identifier: + - type: local + value: msc:m47 + - type: local + value: https://fairsharing.org/726 + - type: homepage + value: http://code.google.com/p/applecore/wiki/Introduction + subject_areas: + - Botany + urls: + - http://code.google.com/p/applecore/wiki/Introduction +Asset Description Metadata Schema (ADMS): + acronym: ADMS + field_of_science: + - social sciences + - political sciences + id: asset-description-metadata-schema-adms + identifier: + - type: local + value: msc:m48 + - type: local + value: https://doi.org/10.25504/FAIRsharing.es2t25 + - type: homepage + value: http://www.w3.org/TR/vocab-adms/ + - type: namespace + value: http://www.w3.org/ns/adms# + subject_areas: + - Social policy + urls: + - http://www.w3.org/TR/vocab-adms/ + - http://www.w3.org/ns/adms# +BibTeX: + acronym: BibTeX + field_of_science: [] + id: bibtex-format + identifier: + - type: local + value: fuji:m34 + - type: local + value: https://doi.org/10.25504/FAIRsharing.bdf2fe + - type: homepage + value: http://www.bibtex.org/ + - type: namespace + value: http://clarin-pl.eu/ns/experimental/bibtex + - type: namespace + value: http://lindat.mff.cuni.cz/ns/experimental/bibtex + - type: namespace + value: http://repository.clarin.dk/ns/experimental/bibtex + subject_areas: + urls: + - http://www.bibtex.org/ + - http://clarin-pl.eu/ns/experimental/bibtex + - http://lindat.mff.cuni.cz/ns/experimental/bibtex + - http://repository.clarin.dk/ns/experimental/bibtex +CARARE metadata schema: + acronym: CARARE + field_of_science: + - architectural design + - humanities + - archaeology + - history + id: carare-metadata-schema + identifier: + - type: local + value: msc:m49 + - type: local + value: https://doi.org/10.25504/FAIRsharing.ba7c93 + - type: homepage + value: https://pro.carare.eu/doku.php?id=support:metadata-schema + - type: namespace + value: http://www.carare.eu/carareSchema + - type: schema + value: https://pro.carare.eu/lib/exe/fetch.php?media=support:carare-v1_0_6_1.xsd + subject_areas: + - Archaeology + - Architecture + - Cultural heritage + - Cultural property preservation + - History + urls: + - https://pro.carare.eu/doku.php?id=support:metadata-schema + - http://www.carare.eu/carareSchema + - https://pro.carare.eu/lib/exe/fetch.php?media=support:carare-v1_0_6_1.xsd +CDWA Lite: + acronym: cdwa-lite + field_of_science: + - humanities + id: cdwa-lite-schema + identifier: + - type: local + value: fuji:m30 + - type: local + value: https://fairsharing.org/4649 + - type: homepage + value: https://www.getty.edu/research/publications/electronic_publications/cdwa/cdwalite.html + - type: namespace + value: https://www.getty.edu/CDWA/CDWALite + - type: schema + value: http://www.getty.edu/CDWA/CDWALite/CDWALite-xsd-public-v1-1.xsd + - type: schema + value: http://www.getty.edu/CDWA/CDWALite/CDWALite-xsd-public-v1-0.xsd + subject_areas: + - Humanities + - Cultural heritage + urls: + - https://www.getty.edu/research/publications/electronic_publications/cdwa/cdwalite.pdf + - https://www.getty.edu/research/publications/electronic_publications/cdwa/cdwalite.html + - https://www.getty.edu/CDWA/CDWALite + - http://www.getty.edu/CDWA/CDWALite/CDWALite-xsd-public-v1-1.xsd + - http://www.getty.edu/CDWA/CDWALite/CDWALite-xsd-public-v1-0.xsd +CEDAR Template Model: + acronym: CEDAR + field_of_science: + - earth and related environmental sciences + - clinical medicine + - engineering and technology + - agricultural sciences + - medical and health sciences + - agriculture + - social sciences + - public administration + - natural sciences + - medical engineering + id: cedar-template-model + identifier: + - type: local + value: msc:m94 + - type: local + value: https://doi.org/10.25504/FAIRsharing.V527H4 + - type: homepage + value: https://more.metadatacenter.org/tools-training/outreach/cedar-template-model + subject_areas: + - Administration + - Agricultural research + - Clinical medicine + - Earth sciences + - Medical information systems + urls: + - https://more.metadatacenter.org/tools-training/outreach/cedar-template-model + - https://more.metadatacenter.org/sites/default/files/artifact/CEDAR%20Template%20Model%20v1.5.0_0.pdf +CERIF (Common European Research Information Format): + acronym: CERIF + field_of_science: + - sciences + id: cerif + identifier: + - type: local + value: msc:m4 + - type: local + value: https://doi.org/10.25504/FAIRsharing.6945dq + - type: homepage + value: http://www.eurocris.org/cerif/main-features-cerif + - type: schema + value: https://www.eurocris.org/Uploads/Web%20pages/CERIF-1.6/CERIF_1.6_2.xsd + - type: schema + value: https://www.eurocris.org/Uploads/Web%20pages/CERIF-1.5/CERIF_1.5_1.xsd + - type: schema + value: https://www.openaire.eu/schema/cris/1.1/openaire-cerif-profile.xsd + - type: namespace + value: urn:xmlns:org:eurocris:cerif-1.6-2 + - type: namespace + value: urn:xmlns:org:eurocris:cerif-1.5-1 + - type: namespace + value: urn:xmlns:org:eurocris:cerif-1.4-0 + - type: namespace + value: http://www.eurocris.org/ontologies/cerif/1.3# + - type: namespace + value: https://www.openaire.eu/cerif-profile/1.1/ + subject_areas: + - Multidisciplinary + urls: + - http://www.eurocris.org/Uploads/Web%20pages/CERIF-1.6/documentation/MInfo.html + - http://www.eurocris.org/cerif/main-features-cerif + - https://www.eurocris.org/Uploads/Web%20pages/CERIF-1.6/CERIF_1.6_2.xsd + - https://www.eurocris.org/Uploads/Web%20pages/CERIF-1.5/CERIF_1.5_1.xsd + - https://www.openaire.eu/schema/cris/1.1/openaire-cerif-profile.xsd + - urn:xmlns:org:eurocris:cerif-1.6-2 + - urn:xmlns:org:eurocris:cerif-1.5-1 + - urn:xmlns:org:eurocris:cerif-1.4-0 + - http://www.eurocris.org/ontologies/cerif/1.3# + - https://www.openaire.eu/cerif-profile/1.1/ +CESSDA MLI - Council of European Social Science Data Archives Minimum Level of Information: + acronym: + field_of_science: + - social geography + - demography + - sociology + - economics + - social sciences + id: cessda-mli-council-european-social-science-data-archives-minimum-level-inf + identifier: + - type: local + value: msc:m50 + - type: local + value: https://fairsharing.org/4272 + - type: homepage + value: http://www.cessda.org/sharing/managing/3/ + subject_areas: + - Demography + - Economics + - Land use + - Sociology + urls: + - http://www.cessda.org/sharing/managing/3/ +CF (Climate and Forecast) Metadata Conventions: + acronym: CF + field_of_science: + - climatology + - oceanography + - natural sciences + - meteorology + id: cf-climate-and-forecast-metadata-conventions + identifier: + - type: local + value: msc:m5 + - type: local + value: https://doi.org/10.25504/FAIRsharing.f8cd83 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/cf-climate-and-forecast-metadata-conventions + - type: homepage + value: http://cfconventions.org/ + subject_areas: + - Climatology + - Meteorology + - Oceanography + urls: + - http://cfconventions.org/documents.html + - http://cfconventions.org/ +CIF (Crystallographic Information Framework): + acronym: CIF + field_of_science: + - crystallography + - engineering and technology + - materials engineering + - chemical sciences + - natural sciences + id: cif-crystallographic-information-framework + identifier: + - type: local + value: msc:m6 + - type: local + value: https://doi.org/10.25504/FAIRsharing.zr52g5 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/cif-crystallographic-information-framework + - type: homepage + value: http://www.iucr.org/resources/cif + subject_areas: + - Chemistry + - Crystallography + - Materials engineering + urls: + - http://www.iucr.org/resources/cif/spec + - http://www.iucr.org/resources/cif +CIM (Common Information Model): + acronym: CIM + field_of_science: + - climatology + - natural sciences + id: cim-common-information-model + identifier: + - type: local + value: msc:m7 + - type: local + value: https://doi.org/10.25504/FAIRsharing.k3z4q9 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/cim-common-information-model + - type: homepage + value: https://earthsystemcog.org/projects/es-doc-models/cim + - type: schema + value: https://github.com/ES-DOC/esdoc-cim/blob/v1.10.0/cim.xsd + subject_areas: + - Climatology + urls: + - https://earthsystemcog.org/projects/es-doc-models/cim_versions + - https://earthsystemcog.org/projects/es-doc-models/cim + - https://github.com/ES-DOC/esdoc-cim/blob/v1.10.0/cim.xsd +COARDS Conventions: + acronym: + field_of_science: + - climatology + - oceanography + - natural sciences + - meteorology + id: coards-conventions + identifier: + - type: local + value: msc:m51 + - type: local + value: https://doi.org/10.25504/FAIRsharing.9614ca + - type: homepage + value: http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html + subject_areas: + - Climatology + - Meteorology + - Oceanography + urls: + - http://ferret.wrc.noaa.gov/noaa_coop/coop_cdf_profile.html +CSDGM Extensions for Remote Sensing Metadata: + acronym: CSDGM + field_of_science: + - meteorology + - climatology + - oceanography + - natural sciences + - hydrology + id: csdgm-extensions-remote-sensing-metadata + identifier: + - type: local + value: msc:m53 + - type: local + value: https://fairsharing.org/1445 + - type: homepage + value: http://www.fgdc.gov/standards/projects/FGDC-standards-projects/csdgm_rs_ex/MetadataRemoteSensingExtens.pdf + subject_areas: + - Climatology + - Hydrology + - Meteorology + - Oceanography + urls: + - http://www.fgdc.gov/standards/projects/FGDC-standards-projects/csdgm_rs_ex/MetadataRemoteSensingExtens.pdf +CSMD (Core Scientific Metadata Model): + acronym: CSMD + field_of_science: + - crystallography + - biochemistry + - engineering and technology + - materials engineering + - chemical sciences + - natural sciences + id: csmd-cclrc-core-scientific-metadata-model + identifier: + - type: local + value: msc:m8 + - type: local + value: https://doi.org/10.25504/FAIRsharing.30fk89 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/csmd-cclrc-core-scientific-metadata-model + - type: homepage + value: http://icatproject-contrib.github.io/CSMD/ + - type: namespace + value: http://www.purl.org/net/CSMD/4.0# + - type: namespace + value: http://www.escience.clrc.ac.uk/schemas/scientific + subject_areas: + - Biochemistry + - Chemistry + - Crystallography + - Materials engineering + urls: + - http://icatproject-contrib.github.io/CSMD/ + - http://www.purl.org/net/CSMD/4.0# + - http://www.escience.clrc.ac.uk/schemas/scientific +Catalogue Service for the Web: + acronym: CSW + field_of_science: + - earth and related environmental sciences + - natural sciences + - cartography + id: csw-catalogue-schema + identifier: + - type: local + value: fuji:m32 + - type: local + value: https://fairsharing.org/4650 + - type: schema + value: http://schemas.opengis.net/csw/2.0.2/CSW-publication.xsd + - type: namespace + value: http://www.opengis.net/cat/csw/2.0.2 + - type: namespace + value: http://www.opengis.net/cat/csw/3.0 + - type: schema + value: http://schemas.opengis.net/cat/csw/3.0/cswAll.xsd + - type: homepage + value: https://www.ogc.org/standard/cat/ + subject_areas: + - Cartography + - Earth sciences + urls: + - http://schemas.opengis.net/csw/2.0.2/CSW-publication.xsd + - http://www.opengis.net/cat/csw/2.0.2 + - http://www.opengis.net/cat/csw/3.0 + - http://schemas.opengis.net/cat/csw/3.0/cswAll.xsd + - https://www.ogc.org/standard/cat/ +CharDM, Data Model for Astronomical DataSet Characterisation: + acronym: CharDM + field_of_science: [] + id: chardm-astronomical-dataset-characterisation + identifier: + - type: local + value: fuji:m29 + - type: local + value: https://doi.org/10.25504/FAIRsharing.yYjZWb + - type: homepage + value: https://www.ivoa.net/documents/cover/CharacterisationDM-20070530.html + - type: schema + value: http://www.ivoa.net/xml/Characterisation/Characterisation-v1.11.xsd + subject_areas: + urls: + - https://www.ivoa.net/documents/cover/CharacterisationDM-20070530.html + - http://www.ivoa.net/xml/Characterisation/Characterisation-v1.11.xsd +Clarivate Data Citation Index Schema: + acronym: dci + field_of_science: + - library sciences + - humanities + id: clarivate-data-citation-index-schema + identifier: + - type: local + value: fuji:m39 + - type: namespace + value: https://clarivate.com/products/web-of-science/web-science-form/data-citation-index/ + - type: homepage + value: https://clarivate.com/products/scientific-and-academic-research/research-discovery-and-workflow-solutions/webofscience-platform/data-citation-index/ + subject_areas: + - Bibliographic standards + urls: + - https://clarivate.com/products/web-of-science/web-science-form/data-citation-index/ + - https://clarivate.com/products/scientific-and-academic-research/research-discovery-and-workflow-solutions/webofscience-platform/data-citation-index/ +Component MetaData Specification (CMDI): + acronym: CMDI + field_of_science: + - humanities + - linguistics + - languages and literature + id: cmd-component-metadata + identifier: + - type: local + value: fuji:m6 + - type: local + value: https://doi.org/10.25504/FAIRsharing.2e0599 + - type: namespace + value: http://www.clarin.eu/cmd/ + - type: namespace + value: https://www.clarin.eu/cmd/1 + - type: homepage + value: https://www.clarin.eu/content/component-metadata + - type: namespace + value: http://www.clarin.eu/cmd/1 + - type: schema + value: http://infra.clarin.eu/CMDI/1.x/xsd/cmd-envelop.xsd + - type: schema + value: http://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/profiles/clarin.eu:cr1:p_1290431694484/xsd + - type: schema + value: https://infra.clarin.eu/CMDI/1.x/xsd/cmd-envelop.xsd + - type: schema + value: http://www.clarin.eu/cmd/1/profiles/clarin.eu:cr1:p_1290431694484 + - type: schema + value: https://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/1.x/profiles/clarin.eu:cr1:p_1290431694484/xsd + subject_areas: + - Linguistics + - Languages + urls: + - http://www.clarin.eu/cmd/ + - https://www.clarin.eu/cmd/1 + - https://www.clarin.eu/content/component-metadata + - https://pure.mpg.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_1480943 + - http://www.clarin.eu/cmd/1 + - http://infra.clarin.eu/CMDI/1.x/xsd/cmd-envelop.xsd + - http://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/profiles/clarin.eu:cr1:p_1290431694484/xsd + - https://infra.clarin.eu/CMDI/1.x/xsd/cmd-envelop.xsd + - http://www.clarin.eu/cmd/1/profiles/clarin.eu:cr1:p_1290431694484 + - https://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/1.x/profiles/clarin.eu:cr1:p_1290431694484/xsd +Crossref Schema: + acronym: crossref + field_of_science: + - sciences + id: crossref-schema + identifier: + - type: local + value: fuji:m40 + - type: local + value: https://doi.org/10.25504/FAIRsharing.bbQbSW + - type: homepage + value: http://www.crossref.org/schema + - type: namespace + value: http://www.crossref.org/schema/4.4.0 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.0.xsd + - type: schema + value: https://data.crossref.org/schemas/crossref4.3.7.xsd + - type: namespace + value: http://www.crossref.org/schema/4.3.7 + - type: namespace + value: http://www.crossref.org/schema/4.4.1 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.1.xsd + - type: namespace + value: http://www.crossref.org/schema/4.4.2 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.2.xsd + - type: namespace + value: http://www.crossref.org/schema/4.8.1 + - type: schema + value: https://data.crossref.org/schemas/crossref4.8.1.xsd + - type: namespace + value: http://www.crossref.org/schema/5.3.1 + - type: schema + value: https://data.crossref.org/schemas/crossref5.3.1.xsd + subject_areas: + - Multidisciplinary + urls: + - http://www.crossref.org/schema + - http://www.crossref.org/schema/4.4.0 + - https://data.crossref.org/schemas/crossref4.4.0.xsd + - https://data.crossref.org/schemas/crossref4.3.7.xsd + - http://www.crossref.org/schema/4.3.7 + - http://www.crossref.org/schema/4.4.1 + - https://data.crossref.org/schemas/crossref4.4.1.xsd + - http://www.crossref.org/schema/4.4.2 + - https://data.crossref.org/schemas/crossref4.4.2.xsd + - http://www.crossref.org/schema/4.8.1 + - https://data.crossref.org/schemas/crossref4.8.1.xsd + - http://www.crossref.org/schema/5.3.1 + - https://data.crossref.org/schemas/crossref5.3.1.xsd +Cruise Summary Reports: + acronym: CSR + field_of_science: + - glaciology + - climatology + - oceanography + - meteorology + - earth and related environmental sciences + - natural sciences + - hydrology + id: cruise-summary-reports + identifier: + - type: local + value: msc:m52 + - type: local + value: https://doi.org/10.25504/FAIRsharing.e36460 + - type: homepage + value: http://www.seadatanet.org/Metadata/CSR + - type: namespace + value: http://www.seadatanet.org + - type: schema + value: http://schemas.seadatanet.org/Standards-Software/Metadata-formats/SDN_CSR_ISO19139_5.2.0.xsd + - type: schema + value: http://schemas.seadatanet.org/StandardsSoftware/Metadata-formats/SDN2_CSR_ISO19139_5.0.0.xsd + subject_areas: + - Climatology + - Earth sciences + - Glaciology + - Hydrology + - Meteorology + - Oceanography + urls: + - http://www.seadatanet.org/Metadata/CSR + - http://www.seadatanet.org + - http://schemas.seadatanet.org/Standards-Software/Metadata-formats/SDN_CSR_ISO19139_5.2.0.xsd + - ' http://schemas.seadatanet.org/StandardsSoftware/Metadata-formats/SDN2_CSR_ISO19139_5.0.0.xsd' +DCAT (Data Catalog Vocabulary): + acronym: DCAT + field_of_science: + - sciences + id: dcat-data-catalog-vocabulary + identifier: + - type: local + value: msc:m12 + - type: local + value: https://doi.org/10.25504/FAIRsharing.h4j3qm + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dcat-data-catalog-vocabulary + - type: homepage + value: http://www.w3.org/TR/vocab-dcat/ + - type: homepage + value: https://www.w3.org/2017/dxwg/wiki/Main_Page + - type: namespace + value: http://www.w3.org/ns/dcat# + subject_areas: + - Multidisciplinary + urls: + - https://www.w3.org/TR/vocab-dcat/#class-dataset + - https://www.w3.org/TR/vocab-dcat/#class-catalog + - http://www.w3.org/TR/vocab-dcat/ + - https://www.w3.org/ns/dcat.ttl + - https://www.w3.org/2017/dxwg/wiki/Main_Page + - http://www.w3.org/ns/dcat# +DDI (Data Documentation Initiative): + acronym: DDI + field_of_science: + - political sciences + - public health + - social geography + - history + - demography + - medical and health sciences + - sociology + - statistics and probability + - economics + - law + - social sciences + - humanities + - natural sciences + id: ddi-data-documentation-initiative + identifier: + - type: local + value: msc:m13 + - type: local + value: https://doi.org/10.25504/FAIRsharing.1t5ws6 + - type: local + value: https://doi.org/10.25504/FAIRsharing.EZCpPd + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/ddi-data-documentation-initiative + - type: homepage + value: http://www.ddialliance.org/ + - type: namespace + value: http://www.icpsr.umich.edu/DDI + - type: schema + value: http://www.ddialliance.org/DDI/schema/ddi3.1/dataset.xsd + - type: namespace + value: ddi:codebook:2_5 + - type: namespace + value: ddi:dataset:3_3 + - type: namespace + value: ddi:dataset:3_2 + - type: namespace + value: ddi:dataset:3_1 + - type: namespace + value: ddi:instance:3_1 + - type: namespace + value: ddi:instance:3_2 + - type: namespace + value: ddi:instance:3_3 + - type: namespace + value: ddi:dataset:3_0 + - type: namespace + value: ddi:studyunit:3_2 + - type: namespace + value: ddi:studyunit:3_1 + - type: schema + value: https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/codebook.xsd + - type: schema + value: https://ddialliance.org/Specification/DDI-Codebook/2.1/XMLSchema/codebook.xsd + - type: schema + value: https://ddialliance.org/Specification/DDI-Lifecycle/3.3/XMLSchema/instance.xsd + - type: schema + value: https://ddialliance.org/Specification/DDI-Lifecycle/3.2/XMLSchema/instance.xsd + - type: schema + value: https://ddialliance.org/Specification/DDI-Lifecycle/3.1/XMLSchema/instance.xsd + - type: schema + value: https://ddialliance.org/Specification/DDI-Lifecycle/3.0/XMLSchema/instance.xsd + subject_areas: + - Demography + - Economics + - Health policy + - History + - Human geography + - Land use + - Law + - Politics + - Social policy + - Sociology + - Statistics + urls: + - http://www.ddialliance.org/Specification/ + - http://www.ddialliance.org/ + - http://www.icpsr.umich.edu/DDI + - http://www.ddialliance.org/DDI/schema/ddi3.1/dataset.xsd + - ddi:codebook:2_5 + - ddi:dataset:3_3 + - ddi:dataset:3_2 + - ddi:dataset:3_1 + - ddi:instance:3_1 + - ddi:instance:3_2 + - ddi:instance:3_3 + - ddi:dataset:3_0 + - ddi:studyunit:3_2 + - ddi:studyunit:3_1 + - https://ddialliance.org/Specification/DDI-Codebook/2.5/XMLSchema/codebook.xsd + - https://ddialliance.org/Specification/DDI-Codebook/2.1/XMLSchema/codebook.xsd + - https://ddialliance.org/Specification/DDI-Lifecycle/3.3/XMLSchema/instance.xsd + - https://ddialliance.org/Specification/DDI-Lifecycle/3.2/XMLSchema/instance.xsd + - https://ddialliance.org/Specification/DDI-Lifecycle/3.1/XMLSchema/instance.xsd + - https://ddialliance.org/Specification/DDI-Lifecycle/3.0/XMLSchema/instance.xsd +DIF (Directory Interchange Format): + acronym: DIF + field_of_science: + - ecology + - meteorology + - glaciology + - biochemistry + - climatology + - agricultural sciences + - oceanography + - agriculture + - marine biology + - natural sciences + - hydrology + id: dif-directory-interchange-format + identifier: + - type: local + value: msc:m14 + - type: local + value: https://doi.org/10.25504/FAIRsharing.esxaaq + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dif-directory-interchange-format + - type: homepage + value: http://gcmd.nasa.gov/add/difguide/ + - type: schema + value: https://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v10.2.xsd + - type: schema + value: http://gcmd.nasa.gov/Aboutus/xml/dif/dif.xsd + - type: schema + value: https://git.earthdata.nasa.gov/projects/EMFD/repos/dif-schemas/browse/10.x/dif.xsd + - type: namespace + value: http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/ + - type: namespace + value: http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif + - type: schema + value: http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v9.4.xsd + subject_areas: + - Agriculture + - Biochemistry + - Climatology + - Ecology + - Glaciology + - Hydrology + - Marine biology + - Meteorology + - Oceanography + urls: + - http://gcmd.nasa.gov/add/difguide/WRITEADIF.pdf + - http://gcmd.nasa.gov/add/difguide/ + - https://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v10.2.xsd + - http://gcmd.nasa.gov/Aboutus/xml/dif/dif.xsd + - https://git.earthdata.nasa.gov/projects/EMFD/repos/dif-schemas/browse/10.x/dif.xsd + - http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/ + - http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif + - http://gcmd.gsfc.nasa.gov/Aboutus/xml/dif/dif_v9.4.xsd +DSpace Intermediate Metadata Format: + acronym: dspace-dim + field_of_science: [] + id: dim-dspace-intermediate-format + identifier: + - type: local + value: fuji:m36 + - type: namespace + value: http://www.dspace.org/xmlns/dspace/dim + - type: homepage + value: https://wiki.lyrasis.org/display/DSPACE/ + subject_areas: + urls: + - http://www.dspace.org/xmlns/dspace/dim + - https://wiki.lyrasis.org/display/DSPACE/ +Darwin Core: + acronym: DwC + field_of_science: + - ecology + - zoology + - botany + - biological sciences + - palaeontology + - oceanography + - physical geography + - marine biology + - earth and related environmental sciences + - natural sciences + - cartography + id: darwin-core + identifier: + - type: local + value: msc:m9 + - type: local + value: https://doi.org/10.25504/FAIRsharing.xvf5y3 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/darwin-core + - type: homepage + value: http://rs.tdwg.org/dwc/index.htm + - type: namespace + value: http://rs.tdwg.org/dwc/terms/ + - type: namespace + value: http://rs.tdwg.org/dwc/iri/ + - type: schema + value: http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd + subject_areas: + - Biogeography + - Biological diversity + - Botany + - Cartography + - Earth sciences + - Ecology + - Marine animals + - Oceanography + - Palaeontology + - Physical geography + - Topography + - Zoology + urls: + - http://www.tdwg.org/standards/450 + - http://rs.tdwg.org/dwc/index.htm + - http://rs.tdwg.org/dwc/terms/ + - http://rs.tdwg.org/dwc/iri/ + - http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd +Darwin Core Geospatial Extension: + acronym: DwC-S + field_of_science: + - biological sciences + - physical geography + - natural sciences + - cartography + id: darwin-core-geospatial-extension + identifier: + - type: local + value: msc:m54 + - type: local + value: https://doi.org/10.25504/FAIRsharing.76c06d + - type: homepage + value: http://wiki.tdwg.org/twiki/bin/view/DarwinCore/GeospatialExtension + subject_areas: + - Biogeography + - Cartography + - Topography + urls: + - http://wiki.tdwg.org/twiki/bin/view/DarwinCore/GeospatialExtension +Data Package: + acronym: + field_of_science: + - sciences + id: data-package + identifier: + - type: local + value: msc:m10 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3b861d + - type: homepage + value: https://frictionlessdata.io/data-packages/ + subject_areas: + - Multidisciplinary + urls: + - https://frictionlessdata.io/specs/data-package/ + - https://frictionlessdata.io/data-packages/ +DataCite Metadata Schema: + acronym: datacite + field_of_science: + - sciences + id: datacite-metadata-schema + identifier: + - type: local + value: msc:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.me4qwe + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/datacite-metadata-schema + - type: homepage + value: http://schema.datacite.org + - type: namespace + value: http://datacite.org/schema/kernel + subject_areas: + - Multidisciplinary + urls: + - http://schema.datacite.org + - http://datacite.org/schema/kernel + - http://schema.datacite.org/meta/kernel-2.1/doc/DataCite-MetadataKernel_v2.2.pdf + - http://schema.datacite.org/meta/kernel-2.1/metadata.xsd + - http://datacite.org/schema/kernel-2.1 + - http://schema.datacite.org/meta/kernel-2.2/doc/DataCite-MetadataKernel_v2.2.pdf + - http://schema.datacite.org/meta/kernel-2.2/metadata.xsd + - http://datacite.org/schema/kernel-2.2 + - http://schema.datacite.org/meta/kernel-3.0/doc/DataCite-MetadataKernel_v3.0.pdf + - http://schema.datacite.org/meta/kernel-3.0/metadata.xsd + - http://datacite.org/schema/kernel-3 + - http://schema.datacite.org/meta/kernel-3.1/doc/DataCite-MetadataKernel_v3.1.pdf + - http://schema.datacite.org/meta/kernel-3.1/metadata.xsd + - http://datacite.org/schema/kernel-3.1 + - http://schema.datacite.org/meta/kernel-4.0/doc/DataCite-MetadataKernel_v4.0.pdf + - http://schema.datacite.org/meta/kernel-4.0/metadata.xsd + - http://datacite.org/schema/kernel-4 +Digital Item Declaration Language (DIDL): + acronym: DIDL + field_of_science: + - sciences + id: didl-digital-item-declaration-language + identifier: + - type: local + value: fuji:m4 + - type: local + value: https://fairsharing.org/4652 + - type: namespace + value: urn:mpeg:mpeg21:2002:02-DIDL-NS + - type: homepage + value: https://www.iso.org/standard/35366.html + subject_areas: + - Multidisciplinary + urls: + - urn:mpeg:mpeg21:2002:02-DIDL-NS + - http://www.dlib.org/dlib/november03/bekaert/11bekaert.html + - https://www.iso.org/standard/35366.html +Dryad Metadata Application Profile: + acronym: + field_of_science: + - sciences + id: dryad-metadata-application-profile + identifier: + - type: local + value: msc:m55 + - type: homepage + value: http://wiki.datadryad.org/Metadata_Profile + - type: namespace + value: http://datadryad.org/metadata/ + - type: schema + value: http://datadryad.org/profile/v3.1/dryad.xsd + - type: schema + value: http://datadryad.org/profile/v3/dryad.xsd + - type: schema + value: http://ils.unc.edu/mrc/dryad/version1_0/dryad_1_0.xsd + subject_areas: + - Multidisciplinary + urls: + - http://wiki.datadryad.org/Metadata_Profile + - http://datadryad.org/metadata/ + - http://datadryad.org/profile/v3.1/dryad.xsd + - http://datadryad.org/profile/v3/dryad.xsd + - http://ils.unc.edu/mrc/dryad/version1_0/dryad_1_0.xsd +Dublin Core: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + urls: + - http://dublincore.org/specifications/ + - http://dublincore.org + - http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - http://dublincore.org/schemas/xmls/qdc/dc.xsd + - http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - http://purl.org/dc/elements/1.1/ + - http://purl.org/dc/terms/ + - http://purl.org/dc/dcmitype/ +DwC Germplasm: + acronym: + field_of_science: + - natural sciences + - botany + id: dwc-germplasm + identifier: + - type: local + value: msc:m56 + - type: local + value: https://doi.org/10.25504/FAIRsharing.hgsFLe + - type: homepage + value: http://code.google.com/p/darwincore-germplasm/ + - type: namespace + value: http://purl.org/germplasm# + - type: namespace + value: http://purl.org/germplasm/germplasmTerm# + subject_areas: + - Botany + urls: + - http://code.google.com/p/darwincore-germplasm/ + - http://purl.org/germplasm# + - http://purl.org/germplasm/germplasmTerm# +EAD (Encoded Archival Description): + acronym: ead + field_of_science: + - humanities + - history + id: ead-encoded-archival-description + identifier: + - type: local + value: msc:m96 + - type: local + value: https://doi.org/10.25504/FAIRsharing.95f59a + - type: homepage + value: https://www.loc.gov/ead/ + - type: namespace + value: urn:isbn:1-931666-22-9 + - type: namespace + value: http://ead3.archivists.org/schema + - type: namespace + value: http://ead3.archivists.org/schema/ + subject_areas: + - History + urls: + - https://www.loc.gov/ead/ + - urn:isbn:1-931666-22-9 + - http://ead3.archivists.org/schema + - http://ead3.archivists.org/schema/ + - https://www.loc.gov/ead/tglib1998/ + - https://www.loc.gov/ead/ag/aghome.html + - https://www.loc.gov/ead/ead.xsd + - ftp://ftp.loc.gov/pub/ead/ead.dtd + - https://www.loc.gov/ead/tglib/ + - https://www.loc.gov/ead/ead3.xsd + - https://www.loc.gov/ead/ead3.dtd + - https://www.loc.gov/ead/EAD3taglib/EAD3.html +EDMED Metadata Profile: + acronym: + field_of_science: + - ecology + - glaciology + - environmental sciences + - climatology + - oceanography + - soil sciences + - hydrogeology + - meteorology + - natural sciences + - hydrology + id: edmed-metadata-profile + identifier: + - type: local + value: msc:m58 + - type: local + value: https://doi.org/10.25504/FAIRsharing.ed7f20 + - type: homepage + value: https://www.bodc.ac.uk/data/information_and_inventories/edmed/ + - type: schema + value: EDMED_sdn_V1.2.xsd + subject_areas: + - Climatology + - Ecology + - Environmental sciences + - Glaciology + - Hydrogeology + - Hydrology + - Meteorology + - Oceanography + - Soil sciences + urls: + - https://www.bodc.ac.uk/data/information_and_inventories/edmed/ + - EDMED_sdn_V1.2.xsd +EML (Ecological Metadata Language): + acronym: EML + field_of_science: + - ecology + - botany + - biological sciences + - zoology + - natural sciences + id: eml-ecological-metadata-language + identifier: + - type: local + value: msc:m16 + - type: local + value: https://doi.org/10.25504/FAIRsharing.r3vtvx + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/eml-ecological-metadata-language + - type: homepage + value: https://eml.ecoinformatics.org/ + - type: namespace + value: eml://eml.ecoinformatics.org/eml-2.0.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.0.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.0.1 + - type: namespace + value: eml://ecoinformatics.org/eml-2.1.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.1.1 + - type: namespace + value: https://eml.ecoinformatics.org/eml-2.2.0 + - type: namespace + value: https://eml.ecoinformatics.org/eml-2.2.1 + - type: schema + value: https://eml.ecoinformatics.org/schema/eml_xsd + subject_areas: + - Biological diversity + - Botany + - Ecology + - Zoology + urls: + - https://eml.ecoinformatics.org/ + - https://eml.ecoinformatics.org/schema + - eml://eml.ecoinformatics.org/eml-2.0.0 + - eml://ecoinformatics.org/eml-2.0.0 + - eml://ecoinformatics.org/eml-2.0.1 + - eml://ecoinformatics.org/eml-2.1.0 + - eml://ecoinformatics.org/eml-2.1.1 + - https://eml.ecoinformatics.org/eml-2.2.0 + - https://eml.ecoinformatics.org/eml-2.2.1 + - https://eml.ecoinformatics.org/schema/eml_xsd +EPrints XML: + acronym: EPrints + field_of_science: + - sciences + id: eprints-xml + identifier: + - type: local + value: fuji:m23 + - type: namespace + value: http://eprints.org/ep2/data/2.0 + - type: homepage + value: https://wiki.eprints.org/w/XML_Export_Format + subject_areas: + - Multidisciplinary + urls: + - http://eprints.org/ep2/data/2.0 + - https://wiki.eprints.org/w/XML_Export_Format +ETD-MS an Interoperability Metadata Standard for Electronic Theses and Dissertations: + acronym: ETD-MS + field_of_science: + - sciences + id: etdms-metadata-schema + identifier: + - type: local + value: fuji:m17 + - type: local + value: https://fairsharing.org/4660 + - type: homepage + value: https://ndltd.org/metadata/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.1/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.0/ + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdms11.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdc.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdcterms.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.0/etdms.xsd + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1-0/ + subject_areas: + - Multidisciplinary + urls: + - https://ndltd.org/metadata/ + - http://www.ndltd.org/standards/metadata/etdms/1.1/ + - http://www.ndltd.org/standards/metadata/etdms/1.0/ + - http://www.ndltd.org/standards/metadata/etdms/1.1/etdms11.xsd + - http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdc.xsd + - http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdcterms.xsd + - http://www.ndltd.org/standards/metadata/etdms/1.0/etdms.xsd + - http://www.ndltd.org/standards/metadata/etdms/1-0/ +EURISCO Descriptors: + acronym: + field_of_science: [] + id: eurisco-descriptors + identifier: + - type: local + value: msc:m85 + - type: homepage + value: https://www.ecpgr.cgiar.org/resources/germplasm-databases/eurisco-catalogue + subject_areas: + urls: + - http://www.ecpgr.cgiar.org/fileadmin/templates/ecpgr.org/upload/MISC/EURISCO_Descriptors.pdf + - https://www.ecpgr.cgiar.org/resources/germplasm-databases/eurisco-catalogue +Emblem XML-Schema: + acronym: Emblem + field_of_science: + - humanities + id: emblem-metadata-schema + identifier: + - type: local + value: fuji:m16 + - type: local + value: https://fairsharing.org/4654 + - type: homepage + value: http://diglib.hab.de/rules/schema/emblem/ + - type: namespace + value: http://diglib.hab.de/rules/schema/emblem + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-3.xsd + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-2.xsd + subject_areas: + - Humanities + urls: + - http://diglib.hab.de/rules/schema/emblem/ + - http://diglib.hab.de/rules/schema/emblem + - http://diglib.hab.de/rules/schema/emblem/emblem-1-3.xsd + - http://diglib.hab.de/rules/schema/emblem/emblem-1-2.xsd +Europeana Data Model (EDM): + acronym: EDM + field_of_science: + - humanities + id: edm-europeana-data-model + identifier: + - type: local + value: fuji:m33 + - type: local + value: https://fairsharing.org/4653 + - type: homepage + value: https://pro.europeana.eu/page/edm-documentation + - type: namespace + value: http://www.europeana.eu/schemas/edm/ + - type: namespace + value: http://www.europeana.eu/schemas/edm + - type: namespace + value: http://www.europeana.eu/schemas/ese/ + subject_areas: + - Humanities + - Cultural heritage + urls: + - https://pro.europeana.eu/page/edm-documentation + - http://www.europeana.eu/schemas/edm/ + - http://www.europeana.eu/schemas/edm + - http://www.europeana.eu/schemas/ese/ +FGDC/CSDGM (Federal Geographic Data Committee Content Standard for Digital Geospatial Metadata): + acronym: fgdc + field_of_science: + - meteorology + - biochemistry + - climatology + - social geography + - oceanography + - physical geography + - marine biology + - social sciences + - natural sciences + - cartography + - hydrology + id: fgdccsdgm-federal-geographic-data-committee-content-standard-digital-ge + identifier: + - type: local + value: msc:m17 + - type: local + value: https://fairsharing.org/1445 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/fgdccsdgm-federal-geographic-data-committee-content-standard-digital-ge + - type: homepage + value: http://www.fgdc.gov/metadata/geospatial-metadata-standards/ + - type: schema + value: https://www.fgdc.gov/schemas/metadata/fgdc-std-001-1998.xsd + - type: schema + value: https://www.fgdc.gov/schemas/metadata/fgdc-std-001.2-2001.xsd + - type: namespace + value: https://www.fgdc.gov/schemas/metadata/ + - type: namespace + value: http://www.fgdc.gov/metadata/csdgm/index_html + subject_areas: + - Biochemistry + - Cartography + - Climatology + - Geography + - Hydrology + - Land use + - Marine biology + - Meteorology + - Oceanography + - Topography + urls: + - http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/base-metadata/v2_0698.pdf + - http://www.fgdc.gov/metadata/geospatial-metadata-standards/ + - https://www.fgdc.gov/schemas/metadata/fgdc-std-001-1998.xsd + - https://www.fgdc.gov/schemas/metadata/fgdc-std-001.2-2001.xsd + - https://www.fgdc.gov/schemas/metadata/ + - http://www.fgdc.gov/metadata/csdgm/index_html +FGDC/CSDGM Biological Data Profile: + acronym: + field_of_science: + - biological sciences + - natural sciences + id: fgdccsdgm-biological-data-profile + identifier: + - type: local + value: msc:m59 + - type: homepage + value: http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/biometadata/biodatap.pdf + subject_areas: + - Biogeography + urls: + - http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/biometadata/biodatap.pdf +FITS (Flexible Image Transport System): + acronym: + field_of_science: + - astrophysics + - natural sciences + - astronomy + id: fits-flexible-image-transport-system + identifier: + - type: local + value: msc:m18 + - type: local + value: https://doi.org/10.25504/FAIRsharing.xvash1 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/fits-flexible-image-transport-system + - type: homepage + value: http://fits.gsfc.nasa.gov/fits_standard.html + subject_areas: + - Astronomy + - Astrophysics + - Sun + urls: + - http://fits.gsfc.nasa.gov/fits_standard.html + - http://fits.gsfc.nasa.gov/fits_standard.html +FITS World Coordinate System (WCS): + acronym: + field_of_science: + - astrophysics + - natural sciences + - astronomy + id: fits-world-coordinate-system-wcs + identifier: + - type: local + value: msc:m60 + - type: homepage + value: http://fits.gsfc.nasa.gov/fits_wcs.html + subject_areas: + - Astronomy + - Astrophysics + - Sun + urls: + - http://fits.gsfc.nasa.gov/fits_wcs.html +Fast Healthcare Interoperability Resources: + acronym: FHIR + field_of_science: + - medical and health sciences + - clinical medicine + id: fhir-fast-healthcare-interoperability-resources + identifier: + - type: local + value: fuji:m47 + - type: local + value: https://doi.org/10.25504/FAIRsharing.25k4yp + - type: homepage + value: https://hl7.org/fhir/ + - type: namespace + value: http://hl7.org/fhir + subject_areas: + - Clinical medicine + urls: + - https://hl7.org/fhir/ + - http://hl7.org/fhir +GBIF Metadata Profile: + acronym: + field_of_science: + - ecology + - botany + - biological sciences + - zoology + - natural sciences + id: gbif-metadata-profile + identifier: + - type: local + value: msc:m61 + - type: homepage + value: http://rs.gbif.org/schema/eml-gbif-profile/ + subject_areas: + - Biogeography + - Biological diversity + - Botany + - Ecology + - Zoology + urls: + - http://rs.gbif.org/schema/eml-gbif-profile/ + - http://rs.gbif.org/schema/eml-gbif-profile/1.0.2/eml-gbif-profile.xsd + - http://rs.gbif.org/schema/eml-gbif-profile/1.1/eml-gbif-profile.xsd +GESMES/TS (Generic Statistical Message for Time Series): + acronym: + field_of_science: + - political sciences + - statistics and probability + - economics + - social sciences + - natural sciences + id: gesmests-generic-statistical-message-time-series + identifier: + - type: local + value: msc:m62 + - type: homepage + value: http://www.ecb.int/stats/services/sdmx/html/index.en.html + subject_areas: + - Economics + - Social policy + - Statistics + urls: + - http://www.ecb.int/stats/services/sdmx/html/index.en.html +GSIM (Generic Statistical Information Model): + acronym: + field_of_science: + - statistics and probability + - natural sciences + id: gsim-generic-statistical-information-model + identifier: + - type: local + value: msc:m63 + - type: local + value: https://doi.org/10.25504/FAIRsharing.22bb25 + - type: homepage + value: http://www1.unece.org/stat/platform/display/metis/Generic+Statistical+Information+Model + subject_areas: + - Statistics + urls: + - http://www1.unece.org/stat/platform/display/metis/Generic+Statistical+Information+Model +Genome Metadata: + acronym: + field_of_science: + - genetics + - natural sciences + id: genome-metadata + identifier: + - type: local + value: msc:m19 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/genome-metadata + - type: homepage + value: http://enews.patricbrc.org/faqs/genome-metadata-faqs/ + subject_areas: + - Genetics + urls: + - http://enews.patricbrc.org/faqs/genome-metadata-faqs/ +GeoRSS: + acronym: + field_of_science: + - earth and related environmental sciences + - natural sciences + id: georss-encoding-standard + identifier: + - type: local + value: fuji:m1 + - type: local + value: https://fairsharing.org/4663 + - type: homepage + value: http://www.georss.org + - type: namespace + value: http://www.georss.org/georss/ + - type: namespace + value: http://schemas.opengis.net/georss/1.0/ + subject_areas: + - Earth sciences + urls: + - http://www.georss.org + - http://www.georss.org/georss/ + - http://schemas.opengis.net/georss/1.0/ +Geography Markup Language: + acronym: + field_of_science: + - geology + - glaciology + - climatology + - oceanography + - physical geography + - hydrogeology + - meteorology + - earth and related environmental sciences + - natural sciences + - cartography + - hydrology + id: iso-19136 + identifier: + - type: local + value: fuji:m3 + - type: local + value: https://doi.org/10.25504/FAIRsharing.d69ee0 + - type: homepage + value: www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=32554 + - type: namespace + value: http://www.opengis.net/gml/3.2 + - type: namespace + value: http://schemas.opengis.net/gml/3.2.1/gml.xsd + subject_areas: + - Cartography + - Climatology + - Earth sciences + - Geography + - Geology + - Glaciology + - Hydrogeology + - Hydrology + - Meteorology + - Oceanography + - Topography + urls: + - https://www.ogc.org/standards/gml + - www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=32554 + - http://www.opengis.net/gml/3.2 + - http://schemas.opengis.net/gml/3.2.1/gml.xsd +HISPID (Herbarium Information Standards and Protocols for Interchange of Data): + acronym: + field_of_science: + - natural sciences + - botany + id: hispid-herbarium-information-standards-and-protocols-interchange-data + identifier: + - type: local + value: msc:m64 + - type: local + value: https://doi.org/10.25504/FAIRsharing.y49yj6 + - type: homepage + value: http://www.rbg.vic.gov.au/wiki/hiscom/index.php/HISPID_5 + subject_areas: + - Botany + urls: + - http://www.rbg.vic.gov.au/wiki/hiscom/index.php/HISPID_5 +IDF (International DOI Foundation) Metadata Kernel: + acronym: + field_of_science: [] + id: idf-international-doi-foundation-metadata-kernel + identifier: + - type: local + value: msc:m86 + - type: homepage + value: https://www.doi.org/the-identifier/resources/handbook/doi_kernel_xml_schema/ + - type: schema + value: https://www.doi.org/doi_schemas/DOIMetadataKernel.xsd + - type: namespace + value: http://www.doi.org/2010/DOISchema + subject_areas: + urls: + - https://www.doi.org/the-identifier/resources/handbook/doi_kernel_xml_schema/ + - https://www.doi.org/doi_schemas/DOIMetadataKernel.xsd + - http://www.doi.org/2010/DOISchema +IMDI Metadata Standard: + acronym: IMDI + field_of_science: + - humanities + - linguistics + id: imdi-metadata-schema + identifier: + - type: local + value: fuji:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.2cfb88 + - type: namespace + value: http://www.mpi.nl/IMDI/Schema/IMDI + - type: namespace + value: http://www.mpi.nl/IMDI/schemas/xsd/ + - type: schema + value: https://www.mpi.nl/IMDI/Schema/IMDI_3.0.xsd + - type: homepage + value: https://archive.mpi.nl/forums/t/imdi-metadata-information/2933 + subject_areas: + - Humanities + - Linguistics + urls: + - http://www.mpi.nl/IMDI/Schema/IMDI + - http://www.mpi.nl/IMDI/schemas/xsd/ + - https://www.mpi.nl/IMDI/Schema/IMDI_3.0.xsd + - https://archive.mpi.nl/forums/t/imdi-metadata-information/2933 +IMPEx Data Model: + acronym: + field_of_science: + - natural sciences + - astronomy + id: impex-data-model + identifier: + - type: local + value: msc:m65 + - type: homepage + value: http://meetingorganizer.copernicus.org/EPSC2012/EPSC2012-360.pdf + subject_areas: + - Astronomical systems + - Astronomy + - Sun + urls: + - http://meetingorganizer.copernicus.org/EPSC2012/EPSC2012-360.pdf +INSPIRE Metadata Regulation: + acronym: + field_of_science: + - glaciology + - climatology + - oceanography + - physical geography + - hydrogeology + - meteorology + - earth and related environmental sciences + - natural sciences + - cartography + - hydrology + id: inspire-metadata-regulation + identifier: + - type: local + value: msc:m66 + - type: local + value: https://doi.org/10.25504/FAIRsharing.nrx5kk + - type: homepage + value: http://inspire.ec.europa.eu/ + - type: namespace + value: http://inspire.ec.europa.eu/schemas/common/1.0/common.xsd + - type: namespace + value: http://inspire.ec.europa.eu/schemas/common/1.0/network.xsd + subject_areas: + - Cartography + - Climatology + - Earth sciences + - Geography + - Glaciology + - Hydrogeology + - Hydrology + - Meteorology + - Oceanography + - Topography + urls: + - http://inspire.ec.europa.eu/ + - http://inspire.ec.europa.eu/schemas/common/1.0/common.xsd + - http://inspire.ec.europa.eu/schemas/common/1.0/network.xsd +ISA-TAB Nano: + acronym: + field_of_science: + - biological sciences + - biochemistry + - engineering and technology + - natural sciences + id: isa-tab-nano + identifier: + - type: local + value: msc:m67 + - type: local + value: https://doi.org/10.25504/FAIRsharing.njqq5b + - type: homepage + value: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano#ISA-TAB-Nano-title + subject_areas: + - Biochemicals + - Biotechnology + urls: + - https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano#ISA-TAB-Nano-title +ISA-Tab: + acronym: + field_of_science: + - biological sciences + - biochemistry + - engineering and technology + - cell metabolism + - molecular biology + - biophysics + - cell biology + - genetics + - natural sciences + id: isa-tab + identifier: + - type: local + value: msc:m21 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/isa-tab + - type: homepage + value: http://isatab.sourceforge.net/format.html + subject_areas: + - Biochemicals + - Biochemistry + - Biophysics + - Biotechnology + - Cell biology + - Genetics + - Metabolism + - Molecular biology + urls: + - http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf + - http://isatab.sourceforge.net/format.html +ISO 19115: + acronym: ISO19115 + field_of_science: + - geology + - glaciology + - climatology + - oceanography + - physical geography + - hydrogeology + - meteorology + - earth and related environmental sciences + - natural sciences + - cartography + - hydrology + id: iso-19115 + identifier: + - type: local + value: msc:m22 + - type: local + value: https://doi.org/10.25504/FAIRsharing.t7mby9 + - type: homepage + value: http://www.iso.org/iso/catalogue_detail.htm?csnumber=53798 + - type: namespace + value: http://www.isotc211.org/2005/gmd/gmd.xsd + - type: namespace + value: http://www.isotc211.org/2005/gmd + - type: namespace + value: http://standards.iso.org/iso/19115/-3/mds/2.0 + - type: namespace + value: http://standards.iso.org/iso/19115/-3/mds/1.0 + - type: namespace + value: http://standards.iso.org/iso/19115/-3/mdb/2.0 + - type: namespace + value: http://bluenet3.antcrc.utas.edu.au/mcp + subject_areas: + - Cartography + - Climatology + - Earth sciences + - Geography + - Geology + - Glaciology + - Hydrogeology + - Hydrology + - Meteorology + - Oceanography + - Topography + urls: + - http://standards.iso.org/iso/19115/-3/ + - http://www.iso.org/iso/catalogue_detail.htm?csnumber=53798 + - http://www.isotc211.org/2005/gmd/gmd.xsd + - http://www.isotc211.org/2005/gmd + - http://standards.iso.org/iso/19115/-3/mds/2.0 + - http://standards.iso.org/iso/19115/-3/mds/1.0 + - http://standards.iso.org/iso/19115/-3/mdb/2.0 + - http://bluenet3.antcrc.utas.edu.au/mcp +ISO 19115 North American Profile: + acronym: + field_of_science: + - physical geography + - natural sciences + - cartography + id: iso-19115-north-american-profile + identifier: + - type: local + value: msc:m70 + - type: local + value: https://doi.org/10.25504/FAIRsharing.b4af3c + - type: homepage + value: http://www.fgdc.gov/standards/projects/incits-l1-standards-projects/NAP-Metadata + subject_areas: + - Cartography + - Geography + - Topography + urls: + - http://www.fgdc.gov/standards/projects/incits-l1-standards-projects/NAP-Metadata +ISO 19115-2 - Imagery and gridded data: + acronym: + field_of_science: + - glaciology + - climatology + - social geography + - oceanography + - physical geography + - social sciences + - meteorology + - earth and related environmental sciences + - natural sciences + - cartography + - hydrology + id: iso-19115-2-imagery-and-gridded-data + identifier: + - type: local + value: msc:m69 + - type: local + value: https://doi.org/10.25504/FAIRsharing.a6b18c + - type: homepage + value: http://www.iso.org/iso/catalogue_detail.htm?csnumber=39229 + subject_areas: + - Cartography + - Climatology + - Earth sciences + - Geography + - Glaciology + - Hydrology + - Land use + - Meteorology + - Oceanography + - Topography + urls: + - http://www.iso.org/iso/catalogue_detail.htm?csnumber=39229 +IVOA Registry Interfaces: + acronym: ivoa-reg + field_of_science: + - natural sciences + - astronomy + id: ivoa-registry-metdata + identifier: + - type: local + value: fuji:m35 + - type: local + value: https://doi.org/10.25504/FAIRsharing.RycpEU + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/international-virtual-observatory-alliance-technical-specifications + - type: namespace + value: http://www.ivoa.net/xml/VORegistry/v1.0 + - type: namespace + value: http://www.ivoa.net/xml/RegistryInterface/v1.0 + - type: homepage + value: https://www.ivoa.net/Documents/cover/RDFVORegistry-20070920.html + subject_areas: + - Astronomy + urls: + - https://www.ivoa.net/documents/RegistryInterface/20180723/REC-RegistryInterface-1.1.html + - http://www.ivoa.net/xml/VORegistry/v1.0 + - http://www.ivoa.net/xml/RegistryInterface/v1.0 + - https://www.ivoa.net/Documents/cover/RDFVORegistry-20070920.html +International Federation of Digital Seismograph Networks StationXML (FDSN StationXML): + acronym: + field_of_science: + - earth and related environmental sciences + - geophysics + - natural sciences + id: fdsn-seismograph + identifier: + - type: local + value: fuji:m8 + - type: local + value: https://fairsharing.org/1434 + - type: namespace + value: http://www.fdsn.org/xml/station/1 + - type: homepage + value: http://www.fdsn.org/xml/station/ + subject_areas: + - Earth sciences + - Geophysics + urls: + - http://www.fdsn.org/xml/station/1 + - http://www.fdsn.org/xml/station/ + - http://docs.fdsn.org/projects/stationxml/en/latest/ +International Virtual Observatory Alliance Technical Specifications: + acronym: IVOA + field_of_science: + - natural sciences + - astronomy + id: international-virtual-observatory-alliance-technical-specifications + identifier: + - type: local + value: msc:m20 + - type: homepage + value: http://ivoa.net/documents/ + subject_areas: + - Astronomy + urls: + - http://www.ivoa.net/documents/#specs + - http://ivoa.net/documents/ +Journal Publishing Tag Set (Jats): + acronym: jats + field_of_science: + - library sciences + - humanities + id: jats-schema + identifier: + - type: local + value: fuji:m41 + - type: local + value: https://doi.org/10.25504/FAIRsharing.smr0rh + - type: homepage + value: http://jats.nlm.nih.gov/publishing/ + - type: schema + value: https://jats.nlm.nih.gov/publishing/1.0/xsd/JATS-journalpublishing1.xsd + - type: namespace + value: http://jats.nlm.nih.gov/publishing/1.0 + subject_areas: + - Bibliographic standards + - Information/library standards + urls: + - http://jats.nlm.nih.gov/publishing/ + - https://jats.nlm.nih.gov/publishing/1.0/xsd/JATS-journalpublishing1.xsd + - http://jats.nlm.nih.gov/publishing/1.0 +LIDO, Lightweight Information Describing Objects: + acronym: LIDO + field_of_science: + - humanities + id: lido-lightweight-information-describing-objects + identifier: + - type: local + value: fuji:m18 + - type: local + value: https://doi.org/10.25504/FAIRsharing.73558b + - type: schema + value: www.lido-schema.org/schema/latest/lido.xsd + - type: schema + value: www.lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: schema + value: http://www.lido-schema.org/schema/v1.0/lido-v1.0.xsd + - type: schema + value: http://lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: namespace + value: http://www.lido-schema.org + - type: homepage + value: http://www.lido-schema.org + subject_areas: + - Humanities + - Cultural heritage + urls: + - www.lido-schema.org/schema/latest/lido.xsd + - www.lido-schema.org/schema/v1.1/lido-v1.1.xsd + - http://www.lido-schema.org/schema/v1.0/lido-v1.0.xsd + - http://lido-schema.org/schema/v1.1/lido-v1.1.xsd + - http://www.lido-schema.org + - http://www.lido-schema.org + - https://cidoc.mini.icom.museum/working-groups/lido/lido-overview/about-lido/what-is-lido/ +Learning Object Metadata (LOM): + acronym: LOM + field_of_science: [] + id: lom-higher-education-schema + identifier: + - type: local + value: fuji:m24 + - type: local + value: https://fairsharing.org/4664 + - type: homepage + value: http://www.imsglobal.org/metadata/index.html + - type: namespace + value: http://ltsc.ieee.org/xsd/LOMv1p0 + - type: namespace + value: http://ltsc.ieee.org/2002/09/lom-base# + - type: namespace + value: https://www.oerbw.de/hsoerlom + - type: schema + value: http://www.rdn.ac.uk/oai/lom/lom.xsd + - type: schema + value: https://w3id.org/kim/hs-oer-lom-profil/latest/schemas/hs-oer-lom.xsd + subject_areas: + urls: + - http://www.imsglobal.org/metadata/index.html + - https://dini-ag-kim.github.io/hs-oer-lom-profil/latest/ + - https://ieeexplore.ieee.org/document/1032843 + - http://ltsc.ieee.org/xsd/LOMv1p0 + - http://ltsc.ieee.org/2002/09/lom-base# + - https://www.oerbw.de/hsoerlom + - http://www.rdn.ac.uk/oai/lom/lom.xsd + - https://w3id.org/kim/hs-oer-lom-profil/latest/schemas/hs-oer-lom.xsd +MAGE-TAB: + acronym: + field_of_science: [] + id: mage-tab + identifier: + - type: local + value: msc:m87 + - type: local + value: https://fairsharing.org/4680 + - type: homepage + value: https://psidev.info/magetab + subject_areas: + urls: + - https://psidev.info/magetab +MARC (Machine-Readable Cataloging): + acronym: MARC + field_of_science: + - library sciences + - sciences + - humanities + id: marc-machine-readable-cataloging + identifier: + - type: local + value: msc:m88 + - type: local + value: https://doi.org/10.25504/FAIRsharing.217b1b + - type: homepage + value: http://www.loc.gov/marc/ + - type: schema + value: http://www.loc.gov/standards/marcxml/schema/MARC21slim.xsd + - type: schema + value: https://www.loc.gov/standards/marcxml/schema/MARC21slim.xsd + - type: namespace + value: http://www.loc.gov/MARC21/slim + - type: namespace + value: http://www.ddb.de/professionell/MARC21/plus + subject_areas: + - Multidisciplinary + - Bibliographic standards + - Information/library standards + urls: + - http://www.loc.gov/marc/ + - http://www.loc.gov/marc/bibliographic/ + - http://www.loc.gov/standards/marcxml/schema/MARC21slim.xsd + - https://www.loc.gov/standards/marcxml/schema/MARC21slim.xsd + - http://www.loc.gov/MARC21/slim + - http://www.ddb.de/professionell/MARC21/plus +METS - Metadata Encoding and Transmission Standard: + acronym: METS + field_of_science: + - sciences + id: mets-metadata-encoding-and-transmission-standard + identifier: + - type: local + value: fuji:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.921056 + - type: namespace + value: http://www.loc.gov/METS/ + - type: schema + value: https://www.loc.gov/standards/mets/profile_docs/mets.profile.v1-2.xsd + - type: schema + value: https://www.loc.gov/standards/mets/profile_docs/mets.profile.v2-1.xsd + - type: schema + value: https://www.loc.gov/standards/mets/profile_docs/mets.profile.v2-0.xsd + - type: homepage + value: https://www.loc.gov/standards/mets/mets-profiles.html + subject_areas: + - Multidisciplinary + urls: + - http://www.loc.gov/METS/ + - https://www.loc.gov/standards/mets/profile_docs/mets.profile.v1-2.xsd + - https://www.loc.gov/standards/mets/profile_docs/mets.profile.v2-1.xsd + - https://www.loc.gov/standards/mets/profile_docs/mets.profile.v2-0.xsd + - https://www.loc.gov/standards/mets/mets-profiles.html +MIBBI (Minimum Information for Biological and Biomedical Investigations): + acronym: + field_of_science: + - computer and information sciences + - biological sciences + - environmental sciences + - biochemistry + - engineering and technology + - cell metabolism + - proteins + - cell biology + - genetics + - natural sciences + id: mibbi-minimum-information-biological-and-biomedical-investigations + identifier: + - type: local + value: msc:m23 + - type: local + value: https://fairsharing.org/3518 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/mibbi-minimum-information-biological-and-biomedical-investigations + - type: homepage + value: http://mibbi.sourceforge.net/portal.shtml + subject_areas: + - Biochemistry + - Biology + - Biotechnology + - Cell biology + - Computer applications + - Environmental sciences + - Genetics + - Metabolism + - Proteins + urls: + - http://mibbi.sourceforge.net/foundry.shtml + - http://mibbi.sourceforge.net/portal.shtml +MIDAS-Heritage: + acronym: MIDAS + field_of_science: + - architectural design + - humanities + - archaeology + - history + id: midas-heritage + identifier: + - type: local + value: msc:m24 + - type: local + value: https://doi.org/10.25504/FAIRsharing.q0hgq + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/midas-heritage + - type: homepage + value: http://www.english-heritage.org.uk/publications/midas-heritage/ + - type: namespace + value: http://www.heritage-standards.org/midas/schema/1.0 + subject_areas: + - Archaeology + - Architecture + - Cultural heritage + - Cultural property preservation + - History + urls: + - http://www.english-heritage.org.uk/content/publications/publicationsNew/guidelines-standards/midas-heritage/midas-heritage-2012-v1_1.pdf + - https://historicengland.org.uk/images-books/publications/midas-heritage/ + - http://www.english-heritage.org.uk/publications/midas-heritage/ + - http://www.heritage-standards.org/midas/schema/1.0 +MODS (Metadata Object Description Schema): + acronym: MODS + field_of_science: + - library sciences + - humanities + id: mods-metadata-object-description-schema + identifier: + - type: local + value: msc:m97 + - type: local + value: https://doi.org/10.25504/FAIRsharing.o67X7e + - type: homepage + value: http://www.loc.gov/standards/mods/ + - type: namespace + value: http://www.loc.gov/mods/v3 + - type: namespace + value: http://www.loc.gov/mods/ + subject_areas: + - Bibliographic standards + - Information/library standards + urls: + - http://www.loc.gov/standards/mods/ + - http://www.loc.gov/mods/v3 + - http://www.loc.gov/mods/ + - http://www.loc.gov/standards/mods/v3/mods-3-3.xsd + - http://www.loc.gov/standards/mods/mods-outline-3-4.html + - http://www.loc.gov/standards/mods/v3/mods-3-4.xsd + - http://www.loc.gov/standards/mods/mods-outline-3-5.html + - http://www.loc.gov/standards/mods/v3/mods-3-5.xsd + - http://www.loc.gov/standards/mods/mods-outline-3-6.html + - http://www.loc.gov/standards/mods/v3/mods-3-6.xsd + - http://www.loc.gov/standards/mods/mods-outline-3-7.html + - http://www.loc.gov/standards/mods/v3/mods-3-7.xsd +Metadata Schema for the Description of Language Resources: + acronym: META-SHARE + field_of_science: + - humanities + - linguistics + id: metashare-metadata + identifier: + - type: local + value: fuji:m12 + - type: local + value: https://fairsharing.org/4665 + - type: homepage + value: http://www.meta-share.org/p/93/Documentation#model + - type: namespace + value: http://www.ilsp.gr/META-XMLSchema + - type: namespace + value: http://w3id.org/meta-share/meta-share/ + subject_areas: + - Humanities + - Linguistics + urls: + - http://www.meta-share.org/p/93/Documentation#model + - http://www.ilsp.gr/META-XMLSchema + - http://w3id.org/meta-share/meta-share/ +NeXML: + acronym: + field_of_science: + - biological sciences + - natural sciences + id: nexml + identifier: + - type: local + value: fuji:m45 + - type: local + value: https://doi.org/10.25504/FAIRsharing.knrb06 + - type: homepage + value: http://www.nexusformat.org/ + - type: namespace + value: http://www.nexml.org/2009 + - type: schema + value: http://www.nexml.org/2009 ../xsd/nexml.xsd + subject_areas: + - Biology + urls: + - http://download.nexusformat.org/doc/html/ref_doc.html + - http://www.nexusformat.org/ + - http://www.nexml.org/2009 + - http://www.nexml.org/2009 ../xsd/nexml.xsd +NeXus: + acronym: + field_of_science: + - crystallography + - engineering and technology + - materials engineering + - chemical sciences + - natural sciences + id: nexus + identifier: + - type: local + value: msc:m25 + - type: local + value: https://doi.org/10.25504/FAIRsharing.eq2pdx + - type: homepage + value: http://www.nexusformat.org/ + subject_areas: + - Chemistry + - Crystallography + - Materials engineering + urls: + - http://download.nexusformat.org/doc/html/ref_doc.html + - http://www.nexusformat.org/ +NetCDF Attribute Convention for Dataset Discovery: + acronym: + field_of_science: [] + id: netcdf-attribute-convention-for-dataset-discovery + identifier: + - type: local + value: msc:m89 + - type: homepage + value: https://wiki.esipfed.org/Category:Attribute_Conventions_Dataset_Discovery + subject_areas: + urls: + - https://wiki.esipfed.org/Category:Attribute_Conventions_Dataset_Discovery +OAI-ORE (Open Archives Initiative Object Reuse and Exchange): + acronym: OAI-ORE + field_of_science: + - anthropology + - history + - sciences + - social sciences + - humanities + id: oai-ore-open-archives-initiative-object-reuse-and-exchange + identifier: + - type: local + value: msc:m26 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3mtaee + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/oai-ore-open-archives-initiative-object-reuse-and-exchange + - type: homepage + value: http://www.openarchives.org/ore/toc + - type: namespace + value: http://www.openarchives.org/ore/terms/ + subject_areas: + - Anthropology + - History + - Multidisciplinary + urls: + - http://www.openarchives.org/ore/ + - http://www.openarchives.org/ore/toc + - http://www.openarchives.org/ore/terms/ +OAI-RDF Schema: + acronym: oai-rdf + field_of_science: [] + id: oai-rdf-schema + identifier: + - type: local + value: fuji:m38 + - type: schema + value: http://www.openarchives.org/OAI/2.0/rdf.xsd + - type: namespace + value: http://www.openarchives.org/OAI/2.0/rdf/ + - type: namespace + value: https://api.aiscr.cz/schema/oai_rdf/ + - type: homepage + value: http://www.openarchives.org/OAI/2.0/rdf/ + subject_areas: + urls: + - http://www.openarchives.org/OAI/2.0/rdf.xsd + - http://www.openarchives.org/OAI/2.0/rdf/ + - https://api.aiscr.cz/schema/oai_rdf/ + - http://www.openarchives.org/OAI/2.0/rdf/ +OCLC PICA XML: + acronym: pica + field_of_science: [] + id: pica-metadata-schema + identifier: + - type: local + value: fuji:m37 + - type: local + value: https://fairsharing.org/4688 + - type: namespace + value: info:srw/schema/5/picaXML-v1.0 + - type: namespace + value: http://www.oclcpica.org/xmlns/ppxml-1.0 + - type: schema + value: http://www.oclcpica.org/xml/picaplus.xsd + - type: homepage + value: http://www.oclcpica.org + subject_areas: + urls: + - info:srw/schema/5/picaXML-v1.0 + - http://www.oclcpica.org/xmlns/ppxml-1.0 + - http://www.oclcpica.org/xml/picaplus.xsd + - http://www.oclcpica.org +ODAM Structural Metadata: + acronym: + field_of_science: [] + id: odam-datapackage + identifier: + - type: local + value: 10.25504/FAIRsharing.ld9wne + - type: homepage + value: + subject_areas: + - biochemistry + - molecular-biology + - metabolic-biochemistry + - biomaterials + - bioengineering + urls: + - https://inrae.github.io/ODAM/data-preparation/url +OLAC metadata: + acronym: OLAC + field_of_science: + - humanities + - linguistics + id: olac-metadata + identifier: + - type: local + value: fuji:m14 + - type: local + value: https://doi.org/10.25504/FAIRsharing.17fbae + - type: namespace + value: http://www.language-archives.org/OLAC/1.1/ + - type: schema + value: http://www.language-archives.org/OLAC/1.1/olac.xsd + - type: homepage + value: http://www.language-archives.org/OLAC + subject_areas: + - Humanities + - Linguistics + urls: + - http://www.language-archives.org/OLAC/1.1/ + - http://www.language-archives.org/OLAC/1.1/olac.xsd + - http://www.language-archives.org/OLAC +OME-TIFF (Open Microscopy Environment TIFF): + acronym: + field_of_science: + - botany + - physiology + - agricultural sciences + - medical and health sciences + - veterinary sciences + - plant protection + - zoology + - cell biology + - natural sciences + id: ome-tiff-open-microscopy-environment-tiff + identifier: + - type: local + value: msc:m73 + - type: local + value: https://doi.org/10.25504/FAIRsharing.cq8tg2 + - type: homepage + value: http://www.openmicroscopy.org/site/support/file-formats/ome-tiff + subject_areas: + - Animal diseases + - Cell biology + - Physiology + - Plant diseases + - Plant physiology + - Zoology + urls: + - http://www.openmicroscopy.org/site/support/file-formats/ome-tiff +OME-XML (Open Microscopy Environment XML): + acronym: + field_of_science: + - botany + - physiology + - agricultural sciences + - medical and health sciences + - veterinary sciences + - plant protection + - zoology + - cell biology + - natural sciences + id: ome-xml-open-microscopy-environment-xml + identifier: + - type: local + value: msc:m29 + - type: local + value: https://doi.org/10.25504/FAIRsharing.zk8p4g + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/ome-xml-open-microscopy-environment-xml + - type: homepage + value: http://www.openmicroscopy.org/site/support/file-formats + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2016-06 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2015-01 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2013-06 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2012-06 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2011-06 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2010-04 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2010-06 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2009-09 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2008-09 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2008-02 + - type: namespace + value: http://www.openmicroscopy.org/Schemas/OME/2007-06 + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2013-06/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2012-06/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2011-06/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2010-04/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2010-06/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2009-09/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2008-09/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2008-02/index.html + - type: schema + value: http://www.openmicroscopy.org/Schemas/OME/2007-06/index.html + subject_areas: + - Animal diseases + - Cell biology + - Physiology + - Plant diseases + - Plant physiology + - Zoology + urls: + - http://www.openmicroscopy.org/Schemas/ + - http://www.openmicroscopy.org/site/support/file-formats + - http://www.openmicroscopy.org/Schemas/OME/2016-06 + - http://www.openmicroscopy.org/Schemas/OME/2015-01 + - http://www.openmicroscopy.org/Schemas/OME/2013-06 + - http://www.openmicroscopy.org/Schemas/OME/2012-06 + - http://www.openmicroscopy.org/Schemas/OME/2011-06 + - http://www.openmicroscopy.org/Schemas/OME/2010-04 + - http://www.openmicroscopy.org/Schemas/OME/2010-06 + - http://www.openmicroscopy.org/Schemas/OME/2009-09 + - http://www.openmicroscopy.org/Schemas/OME/2008-09 + - http://www.openmicroscopy.org/Schemas/OME/2008-02 + - http://www.openmicroscopy.org/Schemas/OME/2007-06 + - http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd + - http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd + - http://www.openmicroscopy.org/Schemas/OME/2013-06/index.html + - http://www.openmicroscopy.org/Schemas/OME/2012-06/index.html + - http://www.openmicroscopy.org/Schemas/OME/2011-06/index.html + - http://www.openmicroscopy.org/Schemas/OME/2010-04/index.html + - http://www.openmicroscopy.org/Schemas/OME/2010-06/index.html + - http://www.openmicroscopy.org/Schemas/OME/2009-09/index.html + - http://www.openmicroscopy.org/Schemas/OME/2008-09/index.html + - http://www.openmicroscopy.org/Schemas/OME/2008-02/index.html + - http://www.openmicroscopy.org/Schemas/OME/2007-06/index.html +ONIX for Books Product Information Message: + acronym: onix + field_of_science: + - library sciences + - humanities + id: onix-metadata-schema + identifier: + - type: local + value: fuji:m42 + - type: local + value: https://fairsharing.org/4683 + - type: homepage + value: https://www.editeur.org/8/ONIX/ + - type: namespace + value: http://www.editeur.org/onix/2.1/short + - type: schema + value: http://www.editeur.org/onix/2.1/short/ONIX_BookProduct_Release2.1_short + subject_areas: + - Bibliographic standards + - Information/library standards + urls: + - https://www.editeur.org/8/ONIX/ + - https://www.editeur.org/files/ONIX%203/APPNOTE%20Describing%20e-books%20in%20ONIX.pdf + - http://www.editeur.org/onix/2.1/short + - http://www.editeur.org/onix/2.1/short/ONIX_BookProduct_Release2.1_short +Observ-OM: + acronym: + field_of_science: + - biological sciences + - natural sciences + id: observ-om + identifier: + - type: local + value: msc:m27 + - type: local + value: https://fairsharing.org/4682 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/observ-om + - type: homepage + value: http://www.molgenis.org/wiki/ObservStart + subject_areas: + - Biology + urls: + - http://www.molgenis.org/wiki/ObservStart +Observations and Measurements: + acronym: + field_of_science: + - geology + - engineering and technology + - remote sensing + - meteorology + - chemical sciences + - natural sciences + id: observations-and-measurements + identifier: + - type: local + value: msc:m28 + - type: local + value: https://doi.org/10.25504/FAIRsharing.4ehmy9 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/observations-and-measurements + - type: homepage + value: http://www.opengeospatial.org/standards/om + - type: namespace + value: http://schemas.opengis.net/om/2.0/ + - type: schema + value: https://schemas.opengis.net/om/2.0/observation.xsd + - type: schema + value: https://schemas.opengis.net/om/1.0.0/observation.xsd + - type: namespace + value: http://www.opengis.net/om/1.0 + subject_areas: + - Chemistry + - Geology + - Meteorology + - Remote sensing + urls: + - http://portal.opengeospatial.org/files/?artifact_id=41579 + - http://www.opengeospatial.org/standards/om + - http://schemas.opengis.net/om/2.0/ + - https://schemas.opengis.net/om/2.0/observation.xsd + - https://schemas.opengis.net/om/1.0.0/observation.xsd + - http://www.opengis.net/om/1.0 +Open Archive Initiative Dublin Core (OAI DC): + acronym: oai_dc + field_of_science: + - sciences + id: oai-dublin-core-schema + identifier: + - type: local + value: fuji:m44 + - type: local + value: https://doi.org/10.25504/FAIRsharing.0417cf + - type: namespace + value: https://resources.bepress.com/OAI/2.0/qualified-dublin-core/ + - type: schema + value: http://www.openarchives.org/OAI/2.0/oai_dc.xsd + - type: namespace + value: http://www.openarchives.org/OAI/2.0/oai_dc/ + - type: namespace + value: http://www.openarchives.org/OAI/2.0/oai_dc + - type: homepage + value: http://www.openarchives.org/OAI/openarchivesprotocol.html#dublincore + subject_areas: + - Multidisciplinary + urls: + - https://resources.bepress.com/OAI/2.0/qualified-dublin-core/ + - http://www.openarchives.org/OAI/2.0/oai_dc.xsd + - http://www.openarchives.org/OAI/2.0/oai_dc/ + - http://www.openarchives.org/OAI/2.0/oai_dc + - http://www.openarchives.org/OAI/openarchivesprotocol.html#dublincore +OpenAIRE Guidelines: + acronym: OpenAIRE_G + field_of_science: + - sciences + id: openaire-guidelines + identifier: + - type: local + value: msc:m92 + - type: local + value: https://doi.org/10.25504/FAIRsharing.123197 + - type: homepage + value: https://guidelines.openaire.eu/ + - type: schema + value: https://www.openaire.eu/schema/repo-lit/4.0/openaire.xsd + - type: namespace + value: http://namespace.openaire.eu/schema/oaire/ + - type: namespace + value: oai_openaire + - type: namespace + value: https://openaire.eu + subject_areas: + - Multidisciplinary + urls: + - https://guidelines.openaire.eu/ + - https://www.openaire.eu/schema/repo-lit/4.0/openaire.xsd + - http://namespace.openaire.eu/schema/oaire/ + - oai_openaire + - https://openaire.eu +OpenAIRE Research Graph: + acronym: OpenAIRE_RG + field_of_science: + - sciences + id: openaire-research-graph + identifier: + - type: local + value: fuji:m20 + - type: local + value: https://fairsharing.org/4684 + - type: namespace + value: http://namespace.openaire.eu/oaf + - type: schema + value: https://www.openaire.eu/schema/1.0/oaf-1.0.xsd + - type: homepage + value: https://graph.openaire.eu/ + subject_areas: + - Multidisciplinary + urls: + - http://namespace.openaire.eu/oaf + - https://www.openaire.eu/schema/latest/doc/oaf.html + - https://www.openaire.eu/schema/1.0/oaf-1.0.xsd + - https://graph.openaire.eu/ +OpenSearch: + acronym: + field_of_science: [] + id: opensearch + identifier: + - type: local + value: fuji:m2 + - type: local + value: https://fairsharing.org/4685 + - type: namespace + value: http://a9.com/-/spec/opensearch/1.1/ + - type: homepage + value: https://github.com/dewitt/opensearch + subject_areas: + urls: + - http://a9.com/-/spec/opensearch/1.1/ + - https://github.com/dewitt/opensearch +PDBx/mmCIF (Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework): + acronym: + field_of_science: + - computer and information sciences + - physical sciences + - biological sciences + - crystallography + - chemical sciences + - molecular biology + - natural sciences + id: pdbx-mmcif + identifier: + - type: local + value: msc:m30 + - type: local + value: https://doi.org/10.25504/FAIRsharing.fd28en + - type: homepage + value: http://mmcif.wwpdb.org/ + subject_areas: + - Biology + - Chemistry + - Computer applications + - Crystallography + - Molecular biology + - Physics + urls: + - http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Index/ + - http://mmcif.wwpdb.org/ +PREMIS: + acronym: premis + field_of_science: + - sciences + id: premis + identifier: + - type: local + value: msc:m31 + - type: local + value: https://doi.org/10.25504/FAIRsharing.27a0f4 + - type: homepage + value: http://www.loc.gov/standards/premis/ + - type: namespace + value: http://www.loc.gov/standards/premis + - type: schema + value: https://www.loc.gov/standards/premis/v3/premis-v3-0.xsd + - type: namespace + value: http://www.loc.gov/premis/v3 + - type: schema + value: https://www.loc.gov/standards/premis/v2/premis-v2-2.xsd + - type: namespace + value: info:lc/xmlns/premis-v2 + - type: schema + value: https://www.loc.gov/standards/premis/v2/premis-v2-3.xsd + - type: schema + value: https://www.loc.gov/standards/premis/v1/PREMIS-v1-1.xsd + - type: namespace + value: http://www.loc.gov/standards/premis/v1 + subject_areas: + - Multidisciplinary + urls: + - http://www.loc.gov/standards/premis/v3/premis-3-0-final.pdf + - http://www.loc.gov/standards/premis/ + - http://www.loc.gov/standards/premis + - https://www.loc.gov/standards/premis/v3/premis-v3-0.xsd + - http://www.loc.gov/premis/v3 + - https://www.loc.gov/standards/premis/v2/premis-v2-2.xsd + - info:lc/xmlns/premis-v2 + - https://www.loc.gov/standards/premis/v2/premis-v2-3.xsd + - https://www.loc.gov/standards/premis/v1/PREMIS-v1-1.xsd + - http://www.loc.gov/standards/premis/v1 +PRISM Publishing Requirements for Industry Standard Metadata: + acronym: PRISM + field_of_science: [] + id: prism-publishing-industry-standard-metadata + identifier: + - type: local + value: fuji:m27 + - type: local + value: https://fairsharing.org/4689 + - type: homepage + value: https://www.w3.org/Submission/prism + - type: namespace + value: http://prismstandard.org/namespaces/pam/0.0/ + - type: namespace + value: http://prismstandard.org/namespaces/pam/1.2/ + - type: namespace + value: http://prismstandard.org/namespaces/pam/2.0/ + - type: namespace + value: http://prismstandard.org/namespaces/pam/2.1/ + - type: namespace + value: http://prismstandard.org/namespaces/pam/3.0/ + - type: namespace + value: http://prismstandard.org/namespaces/basic/1.2/ + - type: namespace + value: http://prismstandard.org/namespaces/basic/2.0/ + - type: namespace + value: http://prismstandard.org/namespaces/basic/1.0/ + - type: namespace + value: http://prismstandard.org/namespaces/basic/2.1/ + - type: namespace + value: http://prismstandard.org/namespaces/basic/3.0/ + - type: namespace + value: http://prismstandard.org/namespaces/pim/1.2/ + subject_areas: + urls: + - https://www.w3.org/Submission/prism + - http://prismstandard.org/namespaces/pam/0.0/ + - http://prismstandard.org/namespaces/pam/1.2/ + - http://prismstandard.org/namespaces/pam/2.0/ + - http://prismstandard.org/namespaces/pam/2.1/ + - http://prismstandard.org/namespaces/pam/3.0/ + - http://prismstandard.org/namespaces/basic/1.2/ + - http://prismstandard.org/namespaces/basic/2.0/ + - http://prismstandard.org/namespaces/basic/1.0/ + - http://prismstandard.org/namespaces/basic/2.1/ + - http://prismstandard.org/namespaces/basic/3.0/ + - http://prismstandard.org/namespaces/pim/1.2/ +PROV: + acronym: + field_of_science: + - sciences + id: prov + identifier: + - type: local + value: msc:m33 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/prov + - type: local + value: https://doi.org/10.25504/FAIRsharing.fe7cda + - type: homepage + value: http://www.w3.org/2001/sw/wiki/PROV + - type: schema + value: http://www.w3.org/ns/prov.xsd + - type: namespace + value: http://www.w3.org/ns/prov# + subject_areas: + - Multidisciplinary + urls: + - http://www.w3.org/TR/prov-overview/ + - http://www.w3.org/2001/sw/wiki/PROV + - http://www.w3.org/ns/prov.xsd + - http://www.w3.org/ns/prov# +Protocol Data Element Definitions: + acronym: + field_of_science: + - medical and health sciences + - clinical medicine + id: protocol-data-element-definitions + identifier: + - type: local + value: msc:m32 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/protocol-data-element-definitions + - type: local + value: https://doi.org/10.25504/FAIRsharing.7e962d + - type: homepage + value: http://clinicaltrials.gov/ct2/manage-recs/resources + - type: schema + value: https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/prs + - type: schema + value: https://prsinfo.clinicaltrials.gov/RRSUploadSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/rrs + subject_areas: + - Clinical medicine + urls: + - http://prsinfo.clinicaltrials.gov/definitions.html + - http://clinicaltrials.gov/ct2/manage-recs/resources + - https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd + - http://clinicaltrials.gov/prs + - https://prsinfo.clinicaltrials.gov/RRSUploadSchema.xsd + - http://clinicaltrials.gov/rrs +QuDEx (Qualitative Data Exchange Format): + acronym: + field_of_science: + - sciences + id: qudex-qualitative-data-exchange-format + identifier: + - type: local + value: msc:m34 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/qudex-qualitative-data-exchange-format + - type: local + value: https://doi.org/10.25504/FAIRsharing.d42cb9 + - type: homepage + value: http://www.data-archive.ac.uk/create-manage/projects/qudex?index=1 + - type: schema + value: https://dam.data-archive.ac.uk/standards/qudex_v03_01.xsd + - type: namespace + value: http://www.data-archive.ac.uk/dext/schema/draft + subject_areas: + - Multidisciplinary + urls: + - http://data-archive.ac.uk/create-manage/projects/qudex?index=1 + - http://www.data-archive.ac.uk/create-manage/projects/qudex?index=1 + - https://dam.data-archive.ac.uk/standards/qudex_v03_01.xsd + - http://www.data-archive.ac.uk/dext/schema/draft +QuakeML: + acronym: QuakeML + field_of_science: + - earth and related environmental sciences + - geophysics + - natural sciences + id: quakeml + identifier: + - type: local + value: fuji:m9 + - type: local + value: https://fairsharing.org/1444 + - type: namespace + value: http://quakeml.org/xmlns/quakeml/2.0 + - type: namespace + value: http://quakeml.org/xmlns/quakeml/1.2 + - type: namespace + value: http://quakeml.org/xmlns/quakeml/1.1 + - type: namespace + value: http://quakeml.org/xmlns/quakeml/1.0.1 + - type: namespace + value: http://quakeml.org/xmlns/quakeml/1.0 + - type: homepage + value: https://quake.ethz.ch/quakeml + subject_areas: + - Earth sciences + - Geophysics + urls: + - http://quakeml.org/xmlns/quakeml/2.0 + - http://quakeml.org/xmlns/quakeml/1.2 + - http://quakeml.org/xmlns/quakeml/1.1 + - http://quakeml.org/xmlns/quakeml/1.0.1 + - http://quakeml.org/xmlns/quakeml/1.0 + - https://quake.ethz.ch/quakeml + - http://www.quakeml.org/ +Qualified Dublin Core: + acronym: QDC + field_of_science: + - sciences + id: dublin-core-qualified + identifier: + - type: local + value: fuji:m22 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: homepage + value: https://www.dublincore.org/specifications/dublin-core/dcmes-qualifiers/ + - type: namespace + value: urn:dc:qdc:container + - type: namespace + value: figshare:oai:qdc + - type: namespace + value: http://naca.central.cranfield.ac.uk/ethos-oai/2.0/ + - type: namespace + value: http://ora.ox.ac.uk/oai-pmh/metadata-formats/solo_dc + - type: schema + value: https://cocoon.huma-num.fr/schemas/dcq.xsd + - type: namespace + value: http://crdo.risc.cnrs.fr/schemas/dcq/ + - type: namespace + value: http://oai.base-search.net/base_dc/ + - type: namespace + value: http://oai.base-search.net/base_dc + - type: schema + value: http://oai.base-search.net/base_dc/base_dc.xsd + subject_areas: + - Multidisciplinary + urls: + - https://www.dublincore.org/specifications/dublin-core/dcmes-qualifiers/ + - urn:dc:qdc:container + - figshare:oai:qdc + - http://naca.central.cranfield.ac.uk/ethos-oai/2.0/ + - http://ora.ox.ac.uk/oai-pmh/metadata-formats/solo_dc + - https://cocoon.huma-num.fr/schemas/dcq.xsd + - http://crdo.risc.cnrs.fr/schemas/dcq/ + - http://oai.base-search.net/base_dc/ + - http://oai.base-search.net/base_dc + - http://oai.base-search.net/base_dc/base_dc.xsd +RDF Data Cube Vocabulary: + acronym: + field_of_science: + - statistics and probability + - natural sciences + id: rdf-data-cube-vocabulary + identifier: + - type: local + value: msc:m35 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/rdf-data-cube-vocabulary + - type: local + value: https://doi.org/10.25504/FAIRsharing.c3b573 + - type: homepage + value: http://www.w3.org/TR/vocab-data-cube/ + - type: namespace + value: http://purl.org/linked-data/cube# + subject_areas: + - Statistics + urls: + - http://www.w3.org/TR/vocab-data-cube/ + - http://purl.org/linked-data/cube# +RIF-CS (Registry Interchange Format – Collections and Services): + acronym: RIF-CS + field_of_science: + - sciences + id: rif-cs-registry-interchange-format-collections-and-services + identifier: + - type: local + value: msc:m98 + - type: local + value: https://doi.org/10.25504/FAIRsharing.reybx2 + - type: homepage + value: https://www.ands.org.au/online-services/rif-cs-schema + - type: schema + value: http://services.ands.org.au/documentation/rifcs/schema/registryObjects.xsd + - type: namespace + value: http://ands.org.au/standards/rif-cs/registryObjects + - type: namespace + value: https://ands.org.au/standards/rif-cs/registryObjects + subject_areas: + - Multidisciplinary + urls: + - https://www.ands.org.au/online-services/rif-cs-schema + - http://services.ands.org.au/documentation/rifcs/schemadocs/registryObjects.html + - http://services.ands.org.au/documentation/rifcs/schema/registryObjects.xsd + - http://ands.org.au/standards/rif-cs/registryObjects + - https://ands.org.au/standards/rif-cs/registryObjects +RIOXX Metadata Application Profile: + acronym: rioxx + field_of_science: + - sciences + id: rioxx-metadata-application-profile + identifier: + - type: local + value: fuji:m5 + - type: local + value: https://fairsharing.org/4690 + - type: namespace + value: http://www.rioxx.net/schema/v2.0/rioxx/ + - type: homepage + value: https://www.rioxx.net/ + - type: namespace + value: https://www.rioxx.net/schema/v2.0/rioxxterms/ + - type: namespace + value: http://docs.rioxx.net/schema/v1.0/ + subject_areas: + - Multidisciplinary + urls: + - http://www.rioxx.net/schema/v2.0/rioxx/ + - https://www.rioxx.net/ + - https://www.rioxx.net/schema/v2.0/rioxxterms/ + - http://docs.rioxx.net/schema/v1.0/ +RO-Crate: + acronym: + field_of_science: + - sciences + id: ro-crate + identifier: + - type: local + value: https://doi.org/10.25504/FAIRsharing.wUoZKE + - type: local + value: msc:m102 + - type: homepage + value: https://w3id.org/ro/crate + - type: namespace + value: https://w3id.org/ro/crate/1.1/context + - type: namespace + value: https://w3id.org/ro/crate/1.0/context + - type: namespace + value: https://w3id.org/ro/crate/0.2/context + subject_areas: + - Multidisciplinary + urls: + - https://w3id.org/ro/crate/1.1 + - https://w3id.org/ro/crate + - https://w3id.org/ro/crate/1.1/context + - https://w3id.org/ro/crate/1.0/context + - https://w3id.org/ro/crate/0.2/context +Resource Metadata for the Virtual Observatory: + acronym: + field_of_science: + - natural sciences + - astronomy + id: resource-metadata-virtual-observatory + identifier: + - type: local + value: msc:m74 + - type: local + value: https://doi.org/10.25504/FAIRsharing.qSULus + - type: homepage + value: http://www.ivoa.net/documents/latest/RM.html + subject_areas: + - Astronomy + urls: + - http://www.ivoa.net/documents/latest/RM.html +SDAC (Standard for Documentation of Astronomical Catalogues): + acronym: + field_of_science: + - astrophysics + - natural sciences + - astronomy + id: sdac + identifier: + - type: local + value: msc:m37 + - type: local + value: https://doi.org/10.25504/FAIRsharing.zcjkc7 + - type: homepage + value: http://cds.u-strasbg.fr/doc/catstd.htx + subject_areas: + - Astronomy + - Astrophysics + urls: + - http://cds.u-strasbg.fr/doc/catstd.pdf + - http://cds.u-strasbg.fr/doc/catstd.htx +SDMX (Statistical Data and Metadata Exchange): + acronym: + field_of_science: + - political sciences + - social geography + - demography + - statistics and probability + - economics + - social sciences + - natural sciences + id: sdmx-statistical-data-and-metadata-exchange + identifier: + - type: local + value: msc:m38 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/sdmx-statistical-data-and-metadata-exchange + - type: local + value: https://doi.org/10.25504/FAIRsharing.cea9zc + - type: homepage + value: http://sdmx.org + - type: namespace + value: http://www.sdmx.org/resources/sdmxml/schemas/v3_0/common + - type: namespace + value: http://www.sdmx.org/resources/sdmxml/schemas/v3_0/registry + - type: namespace + value: http://www.sdmx.org/resources/sdmxml/schemas/v3_0/structure + - type: namespace + value: http://www.sdmx.org/resources/sdmxml/schemas/v3_0/message + - type: namespace + value: http://www.sdmx.org/resources/sdmxml/schemas/v3_0/data + - type: namespace + value: http://www.sdmx.org/resources/sdmxml/ + subject_areas: + - Demography + - Economics + - Human geography + - Social policy + - Statistics + urls: + - http://sdmx.org/?page_id=5008 + - http://sdmx.org + - http://www.sdmx.org/resources/sdmxml/schemas/v3_0/common + - http://www.sdmx.org/resources/sdmxml/schemas/v3_0/registry + - http://www.sdmx.org/resources/sdmxml/schemas/v3_0/structure + - http://www.sdmx.org/resources/sdmxml/schemas/v3_0/message + - http://www.sdmx.org/resources/sdmxml/schemas/v3_0/data + - http://www.sdmx.org/resources/sdmxml/ +SNRNASM ISA-Tab: + acronym: + field_of_science: + - biochemistry + - cell biology + - natural sciences + id: snrnasm-isa-tab + identifier: + - type: local + value: msc:m76 + - type: homepage + value: http://snrnasm.bio.unc.edu + subject_areas: + - Biochemistry + - Cell biology + urls: + - http://snrnasm.bio.unc.edu +SPASE Data Model: + acronym: + field_of_science: + - natural sciences + - astronomy + id: spase-data-model + identifier: + - type: local + value: msc:m39 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/spase-data-model + - type: local + value: https://doi.org/10.25504/FAIRsharing.f5d440 + - type: homepage + value: http://www.spase-group.org/data/ + - type: namespace + value: http://www.spase-group.org/data/schema + - type: schema + value: https://spase-group.org/data/schema/spase-1.0.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-1.1.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-1.2.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-1.2.1.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-1.2.2.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-1.3.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.0.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.1.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.1.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.2.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.3.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.4.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.6.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.8.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.2.9.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.3.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.3.1.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.3.2.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.4.0.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.4.1.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.4.2.xsd + - type: schema + value: https://spase-group.org/data/schema/spase-2.5.0.xsd + subject_areas: + - Astronomical systems + - Astronomy + - Sun + urls: + - http://www.spase-group.org/docs/schema/ + - http://www.spase-group.org/data/ + - http://www.spase-group.org/data/schema + - https://spase-group.org/data/schema/spase-1.0.0.xsd + - https://spase-group.org/data/schema/spase-1.1.0.xsd + - https://spase-group.org/data/schema/spase-1.2.0.xsd + - https://spase-group.org/data/schema/spase-1.2.1.xsd + - https://spase-group.org/data/schema/spase-1.2.2.xsd + - https://spase-group.org/data/schema/spase-1.3.0.xsd + - https://spase-group.org/data/schema/spase-2.0.0.xsd + - https://spase-group.org/data/schema/spase-2.1.0.xsd + - https://spase-group.org/data/schema/spase-2.2.0.xsd + - https://spase-group.org/data/schema/spase-2.2.1.xsd + - https://spase-group.org/data/schema/spase-2.2.2.xsd + - https://spase-group.org/data/schema/spase-2.2.3.xsd + - https://spase-group.org/data/schema/spase-2.2.4.xsd + - https://spase-group.org/data/schema/spase-2.2.6.xsd + - https://spase-group.org/data/schema/spase-2.2.8.xsd + - https://spase-group.org/data/schema/spase-2.2.9.xsd + - https://spase-group.org/data/schema/spase-2.3.0.xsd + - https://spase-group.org/data/schema/spase-2.3.1.xsd + - https://spase-group.org/data/schema/spase-2.3.2.xsd + - https://spase-group.org/data/schema/spase-2.4.0.xsd + - https://spase-group.org/data/schema/spase-2.4.1.xsd + - https://spase-group.org/data/schema/spase-2.4.2.xsd + - https://spase-group.org/data/schema/spase-2.5.0.xsd + - http://www.spase-group.org/data/model/spase-2_2_2.pdf + - http://www.spase-group.org/data/model/spase-2_2_3.pdf + - http://www.spase-group.org/data/model/spase-2_2_4.pdf + - http://www.spase-group.org/data/model/spase-2_2_5.pdf + - http://www.spase-group.org/data/model/spase-2_2_6.pdf + - http://www.spase-group.org/data/model/spase-2_2_7.pdf + - http://www.spase-group.org/data/model/spase-2_2_9.pdf + - http://www.spase-group.org/data/model/spase-2_2_8.pdf +Schema.org: + acronym: schemaorg + field_of_science: + - sciences + id: schemaorg + identifier: + - type: local + value: https://doi.org/10.25504/FAIRsharing.hzdzq8 + - type: local + value: msc:m101 + - type: namespace + value: https://schema.org + - type: namespace + value: http://schema.org + - type: homepage + value: https://schema.org/docs/schemas.html + subject_areas: + - Multidisciplinary + urls: + - https://schema.org + - http://schema.org + - https://schema.org/docs/documents.html + - https://schema.org/docs/schemas.html +Shoreline Metadata Profile: + acronym: + field_of_science: + - oceanography + - natural sciences + - hydrology + id: shoreline-metadata-profile + identifier: + - type: local + value: msc:m75 + - type: local + value: https://doi.org/10.25504/FAIRsharing.22041b + - type: homepage + value: http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/shoreline-metadata/ + subject_areas: + - Hydrology + - Oceanography + urls: + - http://www.fgdc.gov/standards/projects/FGDC-standards-projects/metadata/shoreline-metadata/ +TEI (Text Encoding Initiative) Guidelines: + acronym: TEI + field_of_science: + - humanities + - languages and literature + - history + id: tei-text-encoding-initiative-guidelines + identifier: + - type: local + value: msc:m99 + - type: local + value: https://doi.org/10.25504/FAIRsharing.87b86e + - type: homepage + value: http://www.tei-c.org/Guidelines/P5/ + - type: namespace + value: http://www.tei-c.org/ns/1.0 + subject_areas: + - History + - Languages + urls: + - http://www.tei-c.org/Guidelines/P5/ + - https://www.tei-c.org/release/doc/tei-p5-doc/en/html/index.html + - http://www.tei-c.org/ns/1.0 +TIDCC (Towards an International Data Commons for Crystallography): + acronym: + field_of_science: + - crystallography + - natural sciences + id: tidcc-towards-international-data-commons-crystallography + identifier: + - type: local + value: msc:m78 + - type: local + value: https://fairsharing.org/208 + - type: homepage + value: http://wiki.ecrystals.chem.soton.ac.uk/images/9/9d/ECrystals-WP4-PM-Final.pdf + subject_areas: + - Crystallography + urls: + - http://wiki.ecrystals.chem.soton.ac.uk/images/9/9d/ECrystals-WP4-PM-Final.pdf +Tabular Data Package: + acronym: + field_of_science: + - sciences + id: tabular-data-package + identifier: + - type: local + value: msc:m77 + - type: local + value: https://doi.org/10.25504/FAIRsharing.082881 + - type: homepage + value: http://frictionlessdata.io/guides/tabular-data-package/ + subject_areas: + - Multidisciplinary + urls: + - http://frictionlessdata.io/guides/tabular-data-package/ +The Atom Syndication Format: + acronym: ATOM + field_of_science: + - sciences + id: atom-syndication-format + identifier: + - type: local + value: fuji:m13 + - type: local + value: https://fairsharing.org/4648 + - type: namespace + value: https://www.w3.org/2005/Atom + - type: namespace + value: http://www.w3.org/2005/Atom + - type: homepage + value: https://datatracker.ietf.org/wg/atompub/about/ + subject_areas: + - Multidisciplinary + urls: + - https://www.w3.org/2005/Atom + - http://www.w3.org/2005/Atom + - https://datatracker.ietf.org/wg/atompub/about/ + - https://datatracker.ietf.org/doc/html/rfc4287 +The Open Graph protocol metadata format: + acronym: OpenGraph + field_of_science: [] + id: opengraph + identifier: + - type: local + value: fuji:m46 + - type: homepage + value: https://ogp.me + - type: namespace + value: https://ogp.me/ns# + subject_areas: + urls: + - https://ogp.me + - https://ogp.me/ns# +The OpenURL ContextObject Format: + acronym: CTX + field_of_science: + - sciences + id: openurl-contextobject + identifier: + - type: local + value: fuji:m7 + - type: local + value: https://fairsharing.org/4686 + - type: namespace + value: info:ofi/fmt:xml:xsd:ctx + - type: namespace + value: info:ofi/fmt:kev:mtx:ctx + - type: homepage + value: https://www.oclc.org/research/activities/registry.html + subject_areas: + - Multidisciplinary + urls: + - info:ofi/fmt:xml:xsd:ctx + - info:ofi/fmt:kev:mtx:ctx + - https://groups.niso.org/apps/group_public/download.php/14833/z39_88_2004_r2010.pdf + - https://www.oclc.org/research/activities/registry.html +UK AGMAP (Academic Geospatial Metadata Application Profile): + acronym: + field_of_science: + - physical geography + - natural sciences + - cartography + id: uk-agmap-academic-geospatial-metadata-application-profile + identifier: + - type: local + value: msc:m79 + - type: homepage + value: http://www.gogeo.ac.uk/gogeo/metadata/agmap.htm + subject_areas: + - Cartography + - Geography + - Topography + urls: + - http://www.gogeo.ac.uk/gogeo/metadata/agmap.htm +UK Gemini: + acronym: + field_of_science: + - physical geography + - natural sciences + - cartography + id: uk-gemini + identifier: + - type: local + value: msc:m80 + - type: local + value: https://doi.org/10.25504/FAIRsharing.b49fab + - type: homepage + value: http://www.agi.org.uk/uk-gemini/ + subject_areas: + - Cartography + - Geography + - Topography + urls: + - http://www.agi.org.uk/uk-gemini/ +UKEOF: + acronym: + field_of_science: + - ecology + - geology + - biological sciences + - engineering and technology + - climatology + - soil sciences + - remote sensing + - meteorology + - natural sciences + - hydrology + id: ukeof + identifier: + - type: local + value: msc:m40 + - type: local + value: https://doi.org/10.25504/FAIRsharing.9xytp6 + - type: homepage + value: http://www.ukeof.org.uk/ + - type: schema + value: https://cataloguestaging.ukeof.org.uk/schema/ukeof.1.0.0.xsd + - type: schema + value: https://www.ukeof.org.uk/schema/1/UKEOF_v1.0.xsd + - type: namespace + value: http://www.ukeof.org.uk/schema/1 + subject_areas: + - Biogeography + - Biological diversity + - Climatology + - Ecology + - Geology + - Hydrology + - Meteorology + - Remote sensing + - Soil sciences + urls: + - http://schema.ukeof.org.uk/ + - http://www.ukeof.org.uk/ + - https://cataloguestaging.ukeof.org.uk/schema/ukeof.1.0.0.xsd + - https://www.ukeof.org.uk/schema/1/UKEOF_v1.0.xsd + - http://www.ukeof.org.uk/schema/1 +USGIN (US Geoscience Information Network) Metadata Profile: + acronym: + field_of_science: + - earth and related environmental sciences + - natural sciences + id: usgin-iso-profile + identifier: + - type: local + value: msc:m81 + - type: local + value: https://doi.org/10.25504/FAIRsharing.c82136 + - type: homepage + value: http://repository.stategeothermaldata.org/repository/resource/98ddf901b9782a25982e01af3b0bda50/ + subject_areas: + - Earth sciences + urls: + - http://repository.stategeothermaldata.org/repository/resource/98ddf901b9782a25982e01af3b0bda50/ + - http://usgin.github.io/usginspecs/USGIN_ISO_Metadata.htm +VarioML: + acronym: + field_of_science: + - genetics + - natural sciences + id: varioml + identifier: + - type: local + value: msc:m82 + - type: local + value: https://doi.org/10.25504/FAIRsharing.pxvkt0 + - type: homepage + value: http://www.ncbi.nlm.nih.gov/pubmed/23031277 + - type: namespace + value: http://varioml.org/xml/1.0 + subject_areas: + - Genetics + urls: + - http://www.ncbi.nlm.nih.gov/pubmed/23031277 + - http://varioml.org/xml/1.0 +WMO Core Metadata Profile: + acronym: + field_of_science: + - natural sciences + - meteorology + id: wmo-core-metadata-profile + identifier: + - type: local + value: msc:m84 + - type: local + value: https://doi.org/10.25504/FAIRsharing.5e7bdc + - type: homepage + value: https://wis.wmo.int/2012/metadata/ + subject_areas: + - Meteorology + urls: + - https://wis.wmo.int/2012/metadata/ +WaterML: + acronym: + field_of_science: + - natural sciences + - hydrology + id: waterml + identifier: + - type: local + value: msc:m83 + - type: local + value: https://doi.org/10.25504/FAIRsharing.e07e1b + - type: homepage + value: http://www.opengeospatial.org/standards/waterml + - type: schema + value: https://schemas.opengis.net/waterml/2.0/waterml2.xsd + - type: namespace + value: http://www.opengis.net/waterml/2.0 + subject_areas: + - Hydrology + urls: + - http://www.opengeospatial.org/standards/waterml + - https://schemas.opengis.net/waterml/2.0/waterml2.xsd + - http://www.opengis.net/waterml/2.0 +XOAI, a DSPACE Metadata Format: + acronym: XOAI + field_of_science: [] + id: xoai-metadata-format + identifier: + - type: local + value: fuji:m6 + - type: homepage + value: https://github.com/DSpace/xoai + - type: namespace + value: http://www.lyncode.com/xoai + subject_areas: + urls: + - https://github.com/DSpace/xoai + - http://www.lyncode.com/xoai +XmetaDiss: + acronym: xmetadiss + field_of_science: + - library sciences + - sciences + - humanities + id: xmetadiss-schema + identifier: + - type: local + value: fuji:m43 + - type: schema + value: https://d-nb.info/standards/schema/xmetadissplus.xsd + - type: namespace + value: http://www.d-nb.de/standards/xmetadissplus/ + - type: namespace + value: http://www.d-nb.de/standards/xMetaDiss/ + - type: homepage + value: http://www.d-nb.de/standards/xMetaDiss/ + subject_areas: + - Multidisciplinary + - Bibliographic standards + - Information/library standards + urls: + - https://d-nb.info/standards/schema/xmetadissplus.xsd + - http://www.d-nb.de/standards/xmetadissplus/ + - http://www.d-nb.de/standards/xMetaDiss/ + - http://www.d-nb.de/standards/xMetaDiss/ + - https://d-nb.info/1260521133/34 +da|ra Metadata Schema: + acronym: da|ra + field_of_science: + - sociology + - social sciences + - political sciences + id: dara-metadata-schema + identifier: + - type: local + value: fuji:m10 + - type: local + value: https://fairsharing.org/4651 + - type: namespace + value: http://da-ra.de/schema/kernel-4 + - type: schema + value: http://da-ra.de/dara/schemadefinitions/dara.xsd + - type: schema + value: dara_v2.2.1_de_en_19112012.xsd + - type: schema + value: http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd + - type: homepage + value: https://www.da-ra.de/downloads#metadata + subject_areas: + - Social policy + - Sociology + urls: + - http://da-ra.de/schema/kernel-4 + - http://da-ra.de/dara/schemadefinitions/dara.xsd + - dara_v2.2.1_de_en_19112012.xsd + - http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd + - https://www.da-ra.de/downloads#version-3-0 + - https://www.da-ra.de/downloads#metadata +eBank UK Metadata Application Profile: + acronym: + field_of_science: + - crystallography + - natural sciences + id: ebank-uk-metadata-application-profile + identifier: + - type: local + value: msc:m57 + - type: local + value: https://doi.org/10.25504/FAIRsharing.ad4856 + - type: homepage + value: http://ecrystals.chem.soton.ac.uk + - type: schema + value: http://naca.central.cranfield.ac.uk/ethos-oai/2.0/uketd_dc.xsd + - type: namespace + value: http://naca.central.cranfield.ac.uk/ethos-oai/uketd_dc/ + subject_areas: + - Crystallography + urls: + - http://ecrystals.chem.soton.ac.uk + - http://naca.central.cranfield.ac.uk/ethos-oai/2.0/uketd_dc.xsd + - http://naca.central.cranfield.ac.uk/ethos-oai/uketd_dc/ +isaconfig-diXa: + acronym: + field_of_science: + - medical and health sciences + - toxicology + - genetics + - natural sciences + id: isaconfig-dixa + identifier: + - type: local + value: msc:m68 + - type: homepage + value: https://bitbucket.org/kanterae/isaconfig-dixa + subject_areas: + - Genetics + - Toxicology + urls: + - https://bitbucket.org/kanterae/isaconfig-dixa +museumdat: + acronym: museumdat + field_of_science: + - humanities + id: museumdat-schema + identifier: + - type: local + value: fuji:m31 + - type: local + value: https://fairsharing.org/4671 + - type: schema + value: http://museum.zib.de/museumdat/museumdat-v1.0.xsd + - type: homepage + value: http://museum.zib.de/museumdat/ + subject_areas: + - Humanities + - Cultural heritage + urls: + - http://museum.zib.de/museumdat/museumdat-v1.0.xsd + - http://museum.zib.de/museumdat/ +'null': + acronym: scholix + field_of_science: [] + id: scholix-metadata-schema + identifier: + - type: local + value: fuji:m28 + - type: local + value: https://doi.org/10.25504/FAIRsharing.B0d5Kn + - type: homepage + value: http://www.scholix.org/schema + - type: namespace + value: http://www.scholix.org + - type: schema + value: https://github.com/scholix/schema/blob/master/xsd/v3/schema.xsd + - type: schema + value: https://github.com/scholix/schema/blob/master/xsd/v1/scholix.xsd + subject_areas: + urls: + - http://www.scholix.org/schema + - http://www.scholix.org + - https://github.com/scholix/schema/blob/master/xsd/v3/schema.xsd + - https://github.com/scholix/schema/blob/master/xsd/v1/scholix.xsd +xepicur: + acronym: epicur + field_of_science: [] + id: epicur-metadata-schema + identifier: + - type: local + value: fuji:m21 + - type: local + value: https://fairsharing.org/4659 + - type: namespace + value: urn:nbn:de:1111-2004033116 + - type: schema + value: https://files.dnb.de/Web/xepicur.xsd + - type: homepage + value: https://wiki.dnb.de/display/URNSERVDOK/xepicur+-+XML-Datentransferformat+zur+Verwaltung+von+URN + subject_areas: + urls: + - urn:nbn:de:1111-2004033116 + - ' https://files.dnb.de/Web/xepicur.xsd' + - https://wiki.dnb.de/display/URNSERVDOK/xepicur+-+XML-Datentransferformat+zur+Verwaltung+von+URN diff --git a/fuji_server/data/metadata_standards_uris.json b/fuji_server/data/metadata_standards_uris.json deleted file mode 100644 index 1419e1d5..00000000 --- a/fuji_server/data/metadata_standards_uris.json +++ /dev/null @@ -1,40040 +0,0 @@ -{ - " http://schemas.seadatanet.org/StandardsSoftware/Metadata-formats/SDN2_CSR_ISO19139_5.0.0.xsd": { - "acronym": "CSR", - "field_of_science": [ - "glaciology", - "climatology", - "oceanography", - "meteorology", - "earth and related environmental sciences", - "natural sciences", - "hydrology" - ], - "id": "cruise-summary-reports", - "identifier": [ - { - "type": "local", - "value": "msc:m52" - }, - { - "type": "local", - "value": "https://doi.org/10.25504/FAIRsharing.e36460" - }, - { - "type": "homepage", - "value": "http://www.seadatanet.org/Metadata/CSR" - }, - { - "type": "namespace", - "value": "http://www.seadatanet.org" - }, - { - "type": "schema", - "value": "http://schemas.seadatanet.org/Standards-Software/Metadata-formats/SDN_CSR_ISO19139_5.2.0.xsd" - }, - { - "type": "schema", - "value": "http://schemas.seadatanet.org/StandardsSoftware/Metadata-formats/SDN2_CSR_ISO19139_5.0.0.xsd" - } - ], - "subject_areas": [ - "Climatology", - "Earth sciences", - "Glaciology", - "Hydrology", - "Meteorology", - "Oceanography" - ], - "title": "Cruise Summary Reports" - }, - " https://files.dnb.de/Web/xepicur.xsd": { - "acronym": "epicur", - "field_of_science": [], - "id": "epicur-metadata-schema", - "identifier": [ - { - "type": "local", - "value": "fuji:m21" - }, - { - "type": "local", - "value": "https://fairsharing.org/4659" - }, - { - "type": "namespace", - "value": "urn:nbn:de:1111-2004033116" - }, - { - "type": "schema", - "value": "https://files.dnb.de/Web/xepicur.xsd" - }, - { - "type": "homepage", - "value": "https://wiki.dnb.de/display/URNSERVDOK/xepicur+-+XML-Datentransferformat+zur+Verwaltung+von+URN" - } - ], - "subject_areas": null, - "title": "xepicur" - }, - "EDMED_sdn_V1.2.xsd": { - "acronym": null, - "field_of_science": [ - "ecology", - "glaciology", - "environmental sciences", - "climatology", - "oceanography", - "soil sciences", - "hydrogeology", - "meteorology", - "natural sciences", - "hydrology" - ], - "id": "edmed-metadata-profile", - "identifier": [ - { - "type": "local", - "value": "msc:m58" - }, - { - "type": "local", - "value": "https://doi.org/10.25504/FAIRsharing.ed7f20" - }, - { - "type": "homepage", - "value": "https://www.bodc.ac.uk/data/information_and_inventories/edmed/" - }, - { - "type": "schema", - "value": "EDMED_sdn_V1.2.xsd" - } - ], - "subject_areas": [ - "Climatology", - "Ecology", - "Environmental sciences", - "Glaciology", - "Hydrogeology", - "Hydrology", - "Meteorology", - "Oceanography", - "Soil sciences" - ], - "title": "EDMED Metadata Profile" - }, - "dara_v2.2.1_de_en_19112012.xsd": { - "acronym": "da|ra", - "field_of_science": [ - "sociology", - "social sciences", - "political sciences" - ], - "id": "dara-metadata-schema", - "identifier": [ - { - "type": "local", - "value": "fuji:m10" - }, - { - "type": "local", - "value": "https://fairsharing.org/4651" - }, - { - "type": "namespace", - "value": "http://da-ra.de/schema/kernel-4" - }, - { - "type": "schema", - "value": "http://da-ra.de/dara/schemadefinitions/dara.xsd" - }, - { - "type": "schema", - "value": "dara_v2.2.1_de_en_19112012.xsd" - }, - { - "type": "schema", - "value": "http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd" - }, - { - "type": "homepage", - "value": "https://www.da-ra.de/downloads#metadata" - } - ], - "subject_areas": [ - "Social policy", - "Sociology" - ], - "title": "da|ra Metadata Schema" - }, - "ddi:codebook:2_5": { - "acronym": "DDI", - "field_of_science": [ - "political sciences", - "public health", - "social geography", - "history", - "demography", - "medical and health sciences", - "sociology", - "statistics and probability", - "economics", - "law", - "social sciences", - "humanities", - "natural sciences" - ], - "id": "ddi-data-documentation-initiative", - "identifier": [ - { - "type": "local", - "value": "msc:m13" - }, - { - "type": "local", - "value": "https://doi.org/10.25504/FAIRsharing.1t5ws6" - }, - { - "type": "local", - "value": "https://doi.org/10.25504/FAIRsharing.EZCpPd" - }, - { - "type": "local", - "value": "http://www.dcc.ac.uk/resources/metadata-standards/ddi-data-documentation-initiative" - }, - { - "type": "homepage", - "value": "http://www.ddialliance.org/" - }, - { - "type": "namespace", - "value": "http://www.icpsr.umich.edu/DDI" - }, - { - "type": "schema", - "value": "http://www.ddialliance.org/DDI/schema/ddi3.1/dataset.xsd" - 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} - ], - "subject_areas": [ - "Humanities", - "Cultural heritage" - ], - "title": "LIDO, Lightweight Information Describing Objects" - }, - "www.lido-schema.org/schema/v1.1/lido-v1.1.xsd": { - "acronym": "LIDO", - "field_of_science": [ - "humanities" - ], - "id": "lido-lightweight-information-describing-objects", - "identifier": [ - { - "type": "local", - "value": "fuji:m18" - }, - { - "type": "local", - "value": "https://doi.org/10.25504/FAIRsharing.73558b" - }, - { - "type": "schema", - "value": "www.lido-schema.org/schema/latest/lido.xsd" - }, - { - "type": "schema", - "value": "www.lido-schema.org/schema/v1.1/lido-v1.1.xsd" - }, - { - "type": "schema", - "value": "http://www.lido-schema.org/schema/v1.0/lido-v1.0.xsd" - }, - { - "type": "schema", - "value": "http://lido-schema.org/schema/v1.1/lido-v1.1.xsd" - }, - { - "type": "namespace", - "value": "http://www.lido-schema.org" - }, - { - "type": "homepage", - "value": "http://www.lido-schema.org" - } - ], - "subject_areas": [ - "Humanities", - "Cultural heritage" - ], - "title": "LIDO, Lightweight Information Describing Objects" - } -} diff --git a/fuji_server/data/metadata_standards_uris.yaml b/fuji_server/data/metadata_standards_uris.yaml new file mode 100644 index 00000000..21e38ef3 --- /dev/null +++ b/fuji_server/data/metadata_standards_uris.yaml @@ -0,0 +1,23639 @@ +' http://schemas.seadatanet.org/StandardsSoftware/Metadata-formats/SDN2_CSR_ISO19139_5.0.0.xsd': + acronym: CSR + field_of_science: + - glaciology + - climatology + - oceanography + - meteorology + - earth and related environmental sciences + - natural sciences + - hydrology + id: cruise-summary-reports + identifier: + - type: local + value: msc:m52 + - type: local + value: https://doi.org/10.25504/FAIRsharing.e36460 + - type: homepage + value: http://www.seadatanet.org/Metadata/CSR + - type: namespace + value: http://www.seadatanet.org + - type: schema + value: http://schemas.seadatanet.org/Standards-Software/Metadata-formats/SDN_CSR_ISO19139_5.2.0.xsd + - type: schema + value: http://schemas.seadatanet.org/StandardsSoftware/Metadata-formats/SDN2_CSR_ISO19139_5.0.0.xsd + subject_areas: + - Climatology + - Earth sciences + - Glaciology + - Hydrology + - Meteorology + - Oceanography + title: Cruise Summary Reports +' https://files.dnb.de/Web/xepicur.xsd': + acronym: epicur + field_of_science: [] + id: epicur-metadata-schema + identifier: + - type: local + value: fuji:m21 + - type: local + value: https://fairsharing.org/4659 + - type: namespace + value: urn:nbn:de:1111-2004033116 + - type: schema + value: https://files.dnb.de/Web/xepicur.xsd + - type: homepage + value: https://wiki.dnb.de/display/URNSERVDOK/xepicur+-+XML-Datentransferformat+zur+Verwaltung+von+URN + subject_areas: + title: xepicur +EDMED_sdn_V1.2.xsd: + acronym: + field_of_science: + - ecology + - glaciology + - environmental sciences + - climatology + - oceanography + - soil sciences + - hydrogeology + - meteorology + - natural sciences + - hydrology + id: edmed-metadata-profile + identifier: + - type: local + value: msc:m58 + - type: local + value: https://doi.org/10.25504/FAIRsharing.ed7f20 + - type: homepage + value: https://www.bodc.ac.uk/data/information_and_inventories/edmed/ + - type: schema + value: EDMED_sdn_V1.2.xsd + subject_areas: + - Climatology + - Ecology + - Environmental sciences + - Glaciology + - Hydrogeology + - Hydrology + - Meteorology + - Oceanography + - Soil sciences + title: EDMED Metadata Profile +dara_v2.2.1_de_en_19112012.xsd: + acronym: da|ra + field_of_science: + - sociology + - social sciences + - political sciences + id: dara-metadata-schema + identifier: + - type: local + value: fuji:m10 + - type: local + value: https://fairsharing.org/4651 + - type: namespace + value: http://da-ra.de/schema/kernel-4 + - type: schema + value: http://da-ra.de/dara/schemadefinitions/dara.xsd + - type: schema + value: dara_v2.2.1_de_en_19112012.xsd + - type: schema + value: http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd + - type: homepage + value: https://www.da-ra.de/downloads#metadata + subject_areas: + - Social policy + - Sociology + title: da|ra Metadata Schema +ddi:codebook:2_5: + acronym: DDI + field_of_science: + - political sciences + - public health + - social geography + - history + - demography + - medical and health sciences + - sociology + - statistics and probability + - economics + - law + - social sciences + - humanities + - natural sciences + id: ddi-data-documentation-initiative + identifier: + - type: local + value: msc:m13 + - type: local + value: https://doi.org/10.25504/FAIRsharing.1t5ws6 + - type: local + value: https://doi.org/10.25504/FAIRsharing.EZCpPd + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/ddi-data-documentation-initiative + - type: homepage + value: http://www.ddialliance.org/ + - type: namespace + value: http://www.icpsr.umich.edu/DDI + - type: schema + value: http://www.ddialliance.org/DDI/schema/ddi3.1/dataset.xsd + - type: namespace + value: ddi:codebook:2_5 + - type: namespace + value: ddi:dataset:3_3 + - type: namespace + value: ddi:dataset:3_2 + - 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History + - Human geography + - Land use + - Law + - Politics + - Social policy + - Sociology + - Statistics + title: DDI (Data Documentation Initiative) +ddi:dataset:3_0: + acronym: DDI + field_of_science: + - political sciences + - public health + - social geography + - history + - demography + - medical and health sciences + - sociology + - statistics and probability + - economics + - law + - social sciences + - humanities + - natural sciences + id: ddi-data-documentation-initiative + identifier: + - type: local + value: msc:m13 + - type: local + value: https://doi.org/10.25504/FAIRsharing.1t5ws6 + - type: local + value: https://doi.org/10.25504/FAIRsharing.EZCpPd + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/ddi-data-documentation-initiative + - type: homepage + value: http://www.ddialliance.org/ + - type: namespace + value: http://www.icpsr.umich.edu/DDI + - type: schema + value: http://www.ddialliance.org/DDI/schema/ddi3.1/dataset.xsd + - type: namespace + value: ddi:codebook:2_5 + - 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Demography + - Economics + - Health policy + - History + - Human geography + - Land use + - Law + - Politics + - Social policy + - Sociology + - Statistics + title: DDI (Data Documentation Initiative) +ddi:dataset:3_1: + acronym: DDI + field_of_science: + - political sciences + - public health + - social geography + - history + - demography + - medical and health sciences + - sociology + - statistics and probability + - economics + - law + - social sciences + - humanities + - natural sciences + id: ddi-data-documentation-initiative + identifier: + - type: local + value: msc:m13 + - type: local + value: https://doi.org/10.25504/FAIRsharing.1t5ws6 + - type: local + value: https://doi.org/10.25504/FAIRsharing.EZCpPd + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/ddi-data-documentation-initiative + - type: homepage + value: http://www.ddialliance.org/ + - type: namespace + value: http://www.icpsr.umich.edu/DDI + - type: schema + value: http://www.ddialliance.org/DDI/schema/ddi3.1/dataset.xsd + - 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Demography + - Economics + - Health policy + - History + - Human geography + - Land use + - Law + - Politics + - Social policy + - Sociology + - Statistics + title: DDI (Data Documentation Initiative) +eml://ecoinformatics.org/eml-2.0.0: + acronym: EML + field_of_science: + - ecology + - botany + - biological sciences + - zoology + - natural sciences + id: eml-ecological-metadata-language + identifier: + - type: local + value: msc:m16 + - type: local + value: https://doi.org/10.25504/FAIRsharing.r3vtvx + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/eml-ecological-metadata-language + - type: homepage + value: https://eml.ecoinformatics.org/ + - type: namespace + value: eml://eml.ecoinformatics.org/eml-2.0.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.0.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.0.1 + - type: namespace + value: eml://ecoinformatics.org/eml-2.1.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.1.1 + - 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Livestock + title: AgMES (Agricultural Metadata Element Set) +http://amf.openlib.org: + acronym: AMF + field_of_science: + - sciences + id: amf-academic-metadata-format + identifier: + - type: local + value: fuji:m25 + - type: local + value: https://fairsharing.org/4646 + - type: namespace + value: http://amf.openlib.org + - type: homepage + value: http://amf.openlib.org + - type: schema + value: http://amf.openlib.org/2001/amf.xsd + subject_areas: + - Multidisciplinary + title: Academic Metadata Format +http://amf.openlib.org/2001/amf.xsd: + acronym: AMF + field_of_science: + - sciences + id: amf-academic-metadata-format + identifier: + - type: local + value: fuji:m25 + - type: local + value: https://fairsharing.org/4646 + - type: namespace + value: http://amf.openlib.org + - type: homepage + value: http://amf.openlib.org + - type: schema + value: http://amf.openlib.org/2001/amf.xsd + subject_areas: + - Multidisciplinary + title: Academic Metadata Format +http://ands.org.au/standards/rif-cs/registryObjects: + acronym: RIF-CS + field_of_science: + - sciences + id: rif-cs-registry-interchange-format-collections-and-services + identifier: + - type: local + value: msc:m98 + - type: local + value: https://doi.org/10.25504/FAIRsharing.reybx2 + - type: homepage + value: https://www.ands.org.au/online-services/rif-cs-schema + - type: schema + value: http://services.ands.org.au/documentation/rifcs/schema/registryObjects.xsd + - type: namespace + value: http://ands.org.au/standards/rif-cs/registryObjects + - type: namespace + value: https://ands.org.au/standards/rif-cs/registryObjects + subject_areas: + - Multidisciplinary + title: RIF-CS (Registry Interchange Format – Collections and Services) +http://ariadne-registry.dcu.gr/: + acronym: ACDM + field_of_science: + - humanities + - archaeology + id: ariadne-dataset-catalogue-model + identifier: + - type: local + value: fuji:m19 + - type: local + value: https://fairsharing.org/4647 + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - 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type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - type: namespace + value: http://registry.ariadne-infrastructure.eu/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/ + - type: namespace + value: http://ariadne-registry.dcu.gr/schema-definition + - type: homepage + value: http://ariadne-registry.dcu.gr/ + subject_areas: + - Archaeology + title: ARIADNE Dataset Catalogue Model (ACDM) +http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd: + acronym: ACDM + field_of_science: + - humanities + - archaeology + id: ariadne-dataset-catalogue-model + identifier: + - type: local + value: fuji:m19 + - type: local + value: https://fairsharing.org/4647 + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - type: namespace + value: http://registry.ariadne-infrastructure.eu/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/ + - type: namespace + value: http://ariadne-registry.dcu.gr/schema-definition + - type: homepage + value: http://ariadne-registry.dcu.gr/ + subject_areas: + - Archaeology + title: ARIADNE Dataset Catalogue Model (ACDM) +http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd: + acronym: ACDM + field_of_science: + - humanities + - archaeology + id: ariadne-dataset-catalogue-model + identifier: + - type: local + value: fuji:m19 + - type: local + value: https://fairsharing.org/4647 + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - type: namespace + value: http://registry.ariadne-infrastructure.eu/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/ + - type: namespace + value: http://ariadne-registry.dcu.gr/schema-definition + - type: homepage + value: http://ariadne-registry.dcu.gr/ + subject_areas: + - Archaeology + title: ARIADNE Dataset Catalogue Model (ACDM) +http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd: + acronym: ACDM + field_of_science: + - humanities + - archaeology + id: ariadne-dataset-catalogue-model + identifier: + - type: local + value: fuji:m19 + - type: local + value: https://fairsharing.org/4647 + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - type: namespace + value: http://registry.ariadne-infrastructure.eu/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/ + - type: namespace + value: http://ariadne-registry.dcu.gr/schema-definition + - type: homepage + value: http://ariadne-registry.dcu.gr/ + subject_areas: + - Archaeology + title: ARIADNE Dataset Catalogue Model (ACDM) +http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd: + acronym: ACDM + field_of_science: + - humanities + - archaeology + id: ariadne-dataset-catalogue-model + identifier: + - type: local + value: fuji:m19 + - type: local + value: https://fairsharing.org/4647 + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - type: namespace + value: http://registry.ariadne-infrastructure.eu/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/ + - type: namespace + value: http://ariadne-registry.dcu.gr/schema-definition + - type: homepage + value: http://ariadne-registry.dcu.gr/ + subject_areas: + - Archaeology + title: ARIADNE Dataset Catalogue Model (ACDM) +http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd: + acronym: ACDM + field_of_science: + - humanities + - archaeology + id: ariadne-dataset-catalogue-model + identifier: + - type: local + value: fuji:m19 + - type: local + value: https://fairsharing.org/4647 + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.7/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.8/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/6.9/acdm.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema_definition/sample_ariadne_xml.xsd + - type: schema + value: http://ariadne-registry.dcu.gr/schema-definition/sample_ariadne_xml.xsd + - type: namespace + value: http://registry.ariadne-infrastructure.eu/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/cat/1.1/ + - type: namespace + value: https://www.ariadne-infrastructure.eu/resource/ao/ + - type: namespace + value: http://ariadne-registry.dcu.gr/schema-definition + - type: homepage + value: http://ariadne-registry.dcu.gr/ + subject_areas: + - Archaeology + title: ARIADNE Dataset Catalogue Model (ACDM) +http://bluenet3.antcrc.utas.edu.au/mcp: + acronym: ISO19115 + field_of_science: + - geology + - glaciology + - climatology + - oceanography + - physical geography + - hydrogeology + - meteorology + - earth and related environmental sciences + - natural sciences + - cartography + - hydrology + id: iso-19115 + identifier: + - type: local + value: msc:m22 + - type: local + value: https://doi.org/10.25504/FAIRsharing.t7mby9 + - type: homepage + value: http://www.iso.org/iso/catalogue_detail.htm?csnumber=53798 + - type: namespace + value: http://www.isotc211.org/2005/gmd/gmd.xsd + - type: namespace + value: http://www.isotc211.org/2005/gmd + - type: namespace + value: http://standards.iso.org/iso/19115/-3/mds/2.0 + - type: namespace + value: http://standards.iso.org/iso/19115/-3/mds/1.0 + - type: namespace + value: http://standards.iso.org/iso/19115/-3/mdb/2.0 + - type: namespace + value: http://bluenet3.antcrc.utas.edu.au/mcp + subject_areas: + - Cartography + - Climatology + - Earth sciences + - Geography + - Geology + - Glaciology + - Hydrogeology + - Hydrology + - Meteorology + - Oceanography + - Topography + title: ISO 19115 +http://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/profiles/clarin.eu:cr1:p_1290431694484/xsd: + acronym: CMDI + field_of_science: + - humanities + - linguistics + - languages and literature + id: cmd-component-metadata + identifier: + - type: local + value: fuji:m6 + - type: local + value: https://doi.org/10.25504/FAIRsharing.2e0599 + - type: namespace + value: http://www.clarin.eu/cmd/ + - type: namespace + value: https://www.clarin.eu/cmd/1 + - type: homepage + value: https://www.clarin.eu/content/component-metadata + - type: namespace + value: http://www.clarin.eu/cmd/1 + - type: schema + value: http://infra.clarin.eu/CMDI/1.x/xsd/cmd-envelop.xsd + - type: schema + value: http://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/profiles/clarin.eu:cr1:p_1290431694484/xsd + - type: schema + value: https://infra.clarin.eu/CMDI/1.x/xsd/cmd-envelop.xsd + - type: schema + value: http://www.clarin.eu/cmd/1/profiles/clarin.eu:cr1:p_1290431694484 + - type: schema + value: https://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/1.x/profiles/clarin.eu:cr1:p_1290431694484/xsd + subject_areas: + - Linguistics + - Languages + title: Component MetaData Specification (CMDI) +http://cds.u-strasbg.fr/doc/catstd.htx: + acronym: + field_of_science: + - astrophysics + - natural sciences + - astronomy + id: sdac + identifier: + - type: local + value: msc:m37 + - type: local + value: https://doi.org/10.25504/FAIRsharing.zcjkc7 + - type: homepage + value: http://cds.u-strasbg.fr/doc/catstd.htx + subject_areas: + - Astronomy + - Astrophysics + title: SDAC (Standard for Documentation of Astronomical Catalogues) +http://cds.u-strasbg.fr/doc/catstd.pdf: + acronym: + field_of_science: + - astrophysics + - natural sciences + - astronomy + id: sdac + identifier: + - type: local + value: msc:m37 + - type: local + value: https://doi.org/10.25504/FAIRsharing.zcjkc7 + - type: homepage + value: http://cds.u-strasbg.fr/doc/catstd.htx + subject_areas: + - Astronomy + - Astrophysics + title: SDAC (Standard for Documentation of Astronomical Catalogues) +http://cfconventions.org/: + acronym: CF + field_of_science: + - climatology + - oceanography + - natural sciences + - meteorology + id: cf-climate-and-forecast-metadata-conventions + identifier: + - type: local + value: msc:m5 + - type: local + value: https://doi.org/10.25504/FAIRsharing.f8cd83 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/cf-climate-and-forecast-metadata-conventions + - type: homepage + value: http://cfconventions.org/ + subject_areas: + - Climatology + - Meteorology + - Oceanography + title: CF (Climate and Forecast) Metadata Conventions +http://cfconventions.org/documents.html: + acronym: CF + field_of_science: + - climatology + - oceanography + - natural sciences + - meteorology + id: cf-climate-and-forecast-metadata-conventions + identifier: + - type: local + value: msc:m5 + - type: local + value: https://doi.org/10.25504/FAIRsharing.f8cd83 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/cf-climate-and-forecast-metadata-conventions + - type: homepage + value: http://cfconventions.org/ + subject_areas: + - Climatology + - Meteorology + - Oceanography + title: CF (Climate and Forecast) Metadata Conventions +http://clarin-pl.eu/ns/experimental/bibtex: + acronym: BibTeX + field_of_science: [] + id: bibtex-format + identifier: + - type: local + value: fuji:m34 + - type: local + value: https://doi.org/10.25504/FAIRsharing.bdf2fe + - type: homepage + value: http://www.bibtex.org/ + - type: namespace + value: http://clarin-pl.eu/ns/experimental/bibtex + - type: namespace + value: http://lindat.mff.cuni.cz/ns/experimental/bibtex + - type: namespace + value: http://repository.clarin.dk/ns/experimental/bibtex + subject_areas: + title: BibTeX +http://clinicaltrials.gov/ct2/manage-recs/resources: + acronym: + field_of_science: + - medical and health sciences + - clinical medicine + id: protocol-data-element-definitions + identifier: + - type: local + value: msc:m32 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/protocol-data-element-definitions + - type: local + value: https://doi.org/10.25504/FAIRsharing.7e962d + - type: homepage + value: http://clinicaltrials.gov/ct2/manage-recs/resources + - type: schema + value: https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/prs + - type: schema + value: https://prsinfo.clinicaltrials.gov/RRSUploadSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/rrs + subject_areas: + - Clinical medicine + title: Protocol Data Element Definitions +http://clinicaltrials.gov/prs: + acronym: + field_of_science: + - medical and health sciences + - clinical medicine + id: protocol-data-element-definitions + identifier: + - type: local + value: msc:m32 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/protocol-data-element-definitions + - type: local + value: https://doi.org/10.25504/FAIRsharing.7e962d + - type: homepage + value: http://clinicaltrials.gov/ct2/manage-recs/resources + - type: schema + value: https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/prs + - type: schema + value: https://prsinfo.clinicaltrials.gov/RRSUploadSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/rrs + subject_areas: + - Clinical medicine + title: Protocol Data Element Definitions +http://clinicaltrials.gov/rrs: + acronym: + field_of_science: + - medical and health sciences + - clinical medicine + id: protocol-data-element-definitions + identifier: + - type: local + value: msc:m32 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/protocol-data-element-definitions + - type: local + value: https://doi.org/10.25504/FAIRsharing.7e962d + - type: homepage + value: http://clinicaltrials.gov/ct2/manage-recs/resources + - type: schema + value: https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/prs + - type: schema + value: https://prsinfo.clinicaltrials.gov/RRSUploadSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/rrs + subject_areas: + - Clinical medicine + title: Protocol Data Element Definitions +http://code.google.com/p/applecore/wiki/Introduction: + acronym: aDwC + field_of_science: + - natural sciences + - botany + id: apple-core + identifier: + - type: local + value: msc:m47 + - type: local + value: https://fairsharing.org/726 + - type: homepage + value: http://code.google.com/p/applecore/wiki/Introduction + subject_areas: + - Botany + title: Apple Core +http://code.google.com/p/darwincore-germplasm/: + acronym: + field_of_science: + - natural sciences + - botany + id: dwc-germplasm + identifier: + - type: local + value: msc:m56 + - type: local + value: https://doi.org/10.25504/FAIRsharing.hgsFLe + - type: homepage + value: http://code.google.com/p/darwincore-germplasm/ + - type: namespace + value: http://purl.org/germplasm# + - type: namespace + value: http://purl.org/germplasm/germplasmTerm# + subject_areas: + - Botany + title: DwC Germplasm +http://crdo.risc.cnrs.fr/schemas/dcq/: + acronym: QDC + field_of_science: + - sciences + id: dublin-core-qualified + identifier: + - type: local + value: fuji:m22 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: homepage + value: https://www.dublincore.org/specifications/dublin-core/dcmes-qualifiers/ + - type: namespace + value: urn:dc:qdc:container + - type: namespace + value: figshare:oai:qdc + - type: namespace + value: http://naca.central.cranfield.ac.uk/ethos-oai/2.0/ + - type: namespace + value: http://ora.ox.ac.uk/oai-pmh/metadata-formats/solo_dc + - type: schema + value: https://cocoon.huma-num.fr/schemas/dcq.xsd + - type: namespace + value: http://crdo.risc.cnrs.fr/schemas/dcq/ + - type: namespace + value: http://oai.base-search.net/base_dc/ + - type: namespace + value: http://oai.base-search.net/base_dc + - type: schema + value: http://oai.base-search.net/base_dc/base_dc.xsd + subject_areas: + - Multidisciplinary + title: Qualified Dublin Core +http://da-ra.de/dara/schemadefinitions/dara.xsd: + acronym: da|ra + field_of_science: + - sociology + - social sciences + - political sciences + id: dara-metadata-schema + identifier: + - type: local + value: fuji:m10 + - type: local + value: https://fairsharing.org/4651 + - type: namespace + value: http://da-ra.de/schema/kernel-4 + - type: schema + value: http://da-ra.de/dara/schemadefinitions/dara.xsd + - type: schema + value: dara_v2.2.1_de_en_19112012.xsd + - type: schema + value: http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd + - type: homepage + value: https://www.da-ra.de/downloads#metadata + subject_areas: + - Social policy + - Sociology + title: da|ra Metadata Schema +http://da-ra.de/schema/kernel-4: + acronym: da|ra + field_of_science: + - sociology + - social sciences + - political sciences + id: dara-metadata-schema + identifier: + - type: local + value: fuji:m10 + - type: local + value: https://fairsharing.org/4651 + - type: namespace + value: http://da-ra.de/schema/kernel-4 + - type: schema + value: http://da-ra.de/dara/schemadefinitions/dara.xsd + - type: schema + value: dara_v2.2.1_de_en_19112012.xsd + - type: schema + value: http://www.da-ra.de/fileadmin/media/da-ra.de/Technik/dara_v3.1_de_en_18112014.xsd + - type: homepage + value: https://www.da-ra.de/downloads#metadata + subject_areas: + - Social policy + - Sociology + title: da|ra Metadata Schema +http://data-archive.ac.uk/create-manage/projects/qudex?index=1: + acronym: + field_of_science: + - sciences + id: qudex-qualitative-data-exchange-format + identifier: + - type: local + value: msc:m34 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/qudex-qualitative-data-exchange-format + - type: local + value: https://doi.org/10.25504/FAIRsharing.d42cb9 + - type: homepage + value: http://www.data-archive.ac.uk/create-manage/projects/qudex?index=1 + - type: schema + value: https://dam.data-archive.ac.uk/standards/qudex_v03_01.xsd + - type: namespace + value: http://www.data-archive.ac.uk/dext/schema/draft + subject_areas: + - Multidisciplinary + title: QuDEx (Qualitative Data Exchange Format) +http://datacite.org/schema/kernel: + acronym: datacite + field_of_science: + - sciences + id: datacite-metadata-schema + identifier: + - type: local + value: msc:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.me4qwe + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/datacite-metadata-schema + - type: homepage + value: http://schema.datacite.org + - type: namespace + value: http://datacite.org/schema/kernel + subject_areas: + - Multidisciplinary + title: DataCite Metadata Schema +http://datacite.org/schema/kernel-2.1: + acronym: datacite + field_of_science: + - sciences + id: datacite-metadata-schema + identifier: + - type: local + value: msc:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.me4qwe + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/datacite-metadata-schema + - type: homepage + value: http://schema.datacite.org + - type: namespace + value: http://datacite.org/schema/kernel + subject_areas: + - Multidisciplinary + title: DataCite Metadata Schema +http://datacite.org/schema/kernel-2.2: + acronym: datacite + field_of_science: + - sciences + id: datacite-metadata-schema + identifier: + - type: local + value: msc:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.me4qwe + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/datacite-metadata-schema + - type: homepage + value: http://schema.datacite.org + - type: namespace + value: http://datacite.org/schema/kernel + subject_areas: + - Multidisciplinary + title: DataCite Metadata Schema +http://datacite.org/schema/kernel-3: + acronym: datacite + field_of_science: + - sciences + id: datacite-metadata-schema + identifier: + - type: local + value: msc:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.me4qwe + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/datacite-metadata-schema + - type: homepage + value: http://schema.datacite.org + - type: namespace + value: http://datacite.org/schema/kernel + subject_areas: + - Multidisciplinary + title: DataCite Metadata Schema +http://datacite.org/schema/kernel-3.1: + acronym: datacite + field_of_science: + - sciences + id: datacite-metadata-schema + identifier: + - type: local + value: msc:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.me4qwe + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/datacite-metadata-schema + - type: homepage + value: http://schema.datacite.org + - type: namespace + value: http://datacite.org/schema/kernel + subject_areas: + - Multidisciplinary + title: DataCite Metadata Schema +http://datacite.org/schema/kernel-4: + acronym: datacite + field_of_science: + - sciences + id: datacite-metadata-schema + identifier: + - type: local + value: msc:m11 + - type: local + value: https://doi.org/10.25504/FAIRsharing.me4qwe + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/datacite-metadata-schema + - type: homepage + value: http://schema.datacite.org + - type: namespace + value: http://datacite.org/schema/kernel + subject_areas: + - Multidisciplinary + title: DataCite Metadata Schema +http://datadryad.org/metadata/: + acronym: + field_of_science: + - sciences + id: dryad-metadata-application-profile + identifier: + - type: local + value: msc:m55 + - type: homepage + value: http://wiki.datadryad.org/Metadata_Profile + - type: namespace + value: http://datadryad.org/metadata/ + - type: schema + value: http://datadryad.org/profile/v3.1/dryad.xsd + - type: schema + value: http://datadryad.org/profile/v3/dryad.xsd + - type: schema + value: http://ils.unc.edu/mrc/dryad/version1_0/dryad_1_0.xsd + subject_areas: + - Multidisciplinary + title: Dryad Metadata Application Profile +http://datadryad.org/profile/v3.1/dryad.xsd: + acronym: + field_of_science: + - sciences + id: dryad-metadata-application-profile + identifier: + - type: local + value: msc:m55 + - type: homepage + value: http://wiki.datadryad.org/Metadata_Profile + - type: namespace + value: http://datadryad.org/metadata/ + - type: schema + value: http://datadryad.org/profile/v3.1/dryad.xsd + - type: schema + value: http://datadryad.org/profile/v3/dryad.xsd + - type: schema + value: http://ils.unc.edu/mrc/dryad/version1_0/dryad_1_0.xsd + subject_areas: + - Multidisciplinary + title: Dryad Metadata Application Profile +http://datadryad.org/profile/v3/dryad.xsd: + acronym: + field_of_science: + - sciences + id: dryad-metadata-application-profile + identifier: + - type: local + value: msc:m55 + - type: homepage + value: http://wiki.datadryad.org/Metadata_Profile + - type: namespace + value: http://datadryad.org/metadata/ + - type: schema + value: http://datadryad.org/profile/v3.1/dryad.xsd + - type: schema + value: http://datadryad.org/profile/v3/dryad.xsd + - type: schema + value: http://ils.unc.edu/mrc/dryad/version1_0/dryad_1_0.xsd + subject_areas: + - Multidisciplinary + title: Dryad Metadata Application Profile +http://diglib.hab.de/rules/schema/emblem: + acronym: Emblem + field_of_science: + - humanities + id: emblem-metadata-schema + identifier: + - type: local + value: fuji:m16 + - type: local + value: https://fairsharing.org/4654 + - type: homepage + value: http://diglib.hab.de/rules/schema/emblem/ + - type: namespace + value: http://diglib.hab.de/rules/schema/emblem + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-3.xsd + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-2.xsd + subject_areas: + - Humanities + title: Emblem XML-Schema +http://diglib.hab.de/rules/schema/emblem/: + acronym: Emblem + field_of_science: + - humanities + id: emblem-metadata-schema + identifier: + - type: local + value: fuji:m16 + - type: local + value: https://fairsharing.org/4654 + - type: homepage + value: http://diglib.hab.de/rules/schema/emblem/ + - type: namespace + value: http://diglib.hab.de/rules/schema/emblem + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-3.xsd + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-2.xsd + subject_areas: + - Humanities + title: Emblem XML-Schema +http://diglib.hab.de/rules/schema/emblem/emblem-1-2.xsd: + acronym: Emblem + field_of_science: + - humanities + id: emblem-metadata-schema + identifier: + - type: local + value: fuji:m16 + - type: local + value: https://fairsharing.org/4654 + - type: homepage + value: http://diglib.hab.de/rules/schema/emblem/ + - type: namespace + value: http://diglib.hab.de/rules/schema/emblem + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-3.xsd + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-2.xsd + subject_areas: + - Humanities + title: Emblem XML-Schema +http://diglib.hab.de/rules/schema/emblem/emblem-1-3.xsd: + acronym: Emblem + field_of_science: + - humanities + id: emblem-metadata-schema + identifier: + - type: local + value: fuji:m16 + - type: local + value: https://fairsharing.org/4654 + - type: homepage + value: http://diglib.hab.de/rules/schema/emblem/ + - type: namespace + value: http://diglib.hab.de/rules/schema/emblem + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-3.xsd + - type: schema + value: http://diglib.hab.de/rules/schema/emblem/emblem-1-2.xsd + subject_areas: + - Humanities + title: Emblem XML-Schema +http://docs.fdsn.org/projects/stationxml/en/latest/: + acronym: + field_of_science: + - earth and related environmental sciences + - geophysics + - natural sciences + id: fdsn-seismograph + identifier: + - type: local + value: fuji:m8 + - type: local + value: https://fairsharing.org/1434 + - type: namespace + value: http://www.fdsn.org/xml/station/1 + - type: homepage + value: http://www.fdsn.org/xml/station/ + subject_areas: + - Earth sciences + - Geophysics + title: International Federation of Digital Seismograph Networks StationXML (FDSN StationXML) +http://docs.rioxx.net/schema/v1.0/: + acronym: rioxx + field_of_science: + - sciences + id: rioxx-metadata-application-profile + identifier: + - type: local + value: fuji:m5 + - type: local + value: https://fairsharing.org/4690 + - type: namespace + value: http://www.rioxx.net/schema/v2.0/rioxx/ + - type: homepage + value: https://www.rioxx.net/ + - type: namespace + value: https://www.rioxx.net/schema/v2.0/rioxxterms/ + - type: namespace + value: http://docs.rioxx.net/schema/v1.0/ + subject_areas: + - Multidisciplinary + title: RIOXX Metadata Application Profile +http://download.nexusformat.org/doc/html/ref_doc.html: + acronym: + field_of_science: + - crystallography + - engineering and technology + - materials engineering + - chemical sciences + - natural sciences + id: nexus + identifier: + - type: local + value: msc:m25 + - type: local + value: https://doi.org/10.25504/FAIRsharing.eq2pdx + - type: homepage + value: http://www.nexusformat.org/ + subject_areas: + - Chemistry + - Crystallography + - Materials engineering + title: NeXus +http://dublincore.org: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/dc.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/qdc/dcterms.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/schemas/xmls/simpledc20021212.xsd: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcmitype.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/simpledc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dc.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/dcmitype.xsd + - type: namespace + value: http://purl.org/dc/elements/1.1/ + - type: namespace + value: http://purl.org/dc/terms/ + - type: namespace + value: http://purl.org/dc/dcmitype/ + subject_areas: + - Multidisciplinary + title: Dublin Core +http://dublincore.org/specifications/: + acronym: DC + field_of_science: + - sciences + id: dublin-core + identifier: + - type: local + value: msc:m15 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/dublin-core + - type: homepage + value: http://dublincore.org + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/simpledc20021212.xsd + - type: schema + value: http://dublincore.org/schemas/xmls/qdc/2008/02/11/dc.xsd + - 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ecology + - botany + - biological sciences + - zoology + - natural sciences + identifier: eml-ecological-metadata-language + ids: + - type: local + value: msc:m16 + - type: local + value: https://doi.org/10.25504/FAIRsharing.r3vtvx + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/eml-ecological-metadata-language + - type: homepage + value: https://eml.ecoinformatics.org/ + - type: namespace + value: eml://eml.ecoinformatics.org/eml-2.0.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.0.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.0.1 + - type: namespace + value: eml://ecoinformatics.org/eml-2.1.0 + - type: namespace + value: eml://ecoinformatics.org/eml-2.1.1 + - type: namespace + value: https://eml.ecoinformatics.org/eml-2.2.0 + - type: namespace + value: https://eml.ecoinformatics.org/eml-2.2.1 + - type: schema + value: https://eml.ecoinformatics.org/schema/eml_xsd + subject_areas: + - Biological diversity + - Botany + - Ecology + - Zoology + title: EML (Ecological Metadata Language) +http://www.dcc.ac.uk/resources/metadata-standards/fgdccsdgm-federal-geographic-data-committee-content-standard-digital-ge: + acronym: fgdc + field_of_science: + - meteorology + - biochemistry + - climatology + - social geography + - oceanography + - physical geography + - marine biology + - social sciences + - natural sciences + - cartography + - hydrology + identifier: fgdccsdgm-federal-geographic-data-committee-content-standard-digital-ge + ids: + - type: local + value: msc:m17 + - type: local + value: https://fairsharing.org/1445 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/fgdccsdgm-federal-geographic-data-committee-content-standard-digital-ge + - type: homepage + value: http://www.fgdc.gov/metadata/geospatial-metadata-standards/ + - type: schema + value: https://www.fgdc.gov/schemas/metadata/fgdc-std-001-1998.xsd + - type: schema + value: https://www.fgdc.gov/schemas/metadata/fgdc-std-001.2-2001.xsd + - 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genetics + - natural sciences + identifier: genome-metadata + ids: + - type: local + value: msc:m19 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/genome-metadata + - type: homepage + value: http://enews.patricbrc.org/faqs/genome-metadata-faqs/ + subject_areas: + - Genetics + title: Genome Metadata +http://www.dcc.ac.uk/resources/metadata-standards/international-virtual-observatory-alliance-technical-specifications: + acronym: ivoa-reg + field_of_science: + - natural sciences + - astronomy + identifier: ivoa-registry-metdata + ids: + - type: local + value: fuji:m35 + - type: local + value: https://doi.org/10.25504/FAIRsharing.RycpEU + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/international-virtual-observatory-alliance-technical-specifications + - type: namespace + value: http://www.ivoa.net/xml/VORegistry/v1.0 + - type: namespace + value: http://www.ivoa.net/xml/RegistryInterface/v1.0 + - type: homepage + value: https://www.ivoa.net/Documents/cover/RDFVORegistry-20070920.html + subject_areas: + - Astronomy + title: IVOA Registry Interfaces +http://www.dcc.ac.uk/resources/metadata-standards/isa-tab: + acronym: + field_of_science: + - biological sciences + - biochemistry + - engineering and technology + - cell metabolism + - molecular biology + - biophysics + - cell biology + - genetics + - natural sciences + identifier: isa-tab + ids: + - type: local + value: msc:m21 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/isa-tab + - type: homepage + value: http://isatab.sourceforge.net/format.html + subject_areas: + - Biochemicals + - Biochemistry + - Biophysics + - Biotechnology + - Cell biology + - Genetics + - Metabolism + - Molecular biology + title: ISA-Tab +http://www.dcc.ac.uk/resources/metadata-standards/mibbi-minimum-information-biological-and-biomedical-investigations: + acronym: + field_of_science: + - computer and information sciences + - biological sciences + - environmental sciences + - biochemistry + - engineering and technology + - cell metabolism + - proteins + - cell biology + - genetics + - natural sciences + identifier: mibbi-minimum-information-biological-and-biomedical-investigations + ids: + - type: local + value: msc:m23 + - type: local + value: https://fairsharing.org/3518 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/mibbi-minimum-information-biological-and-biomedical-investigations + - type: homepage + value: http://mibbi.sourceforge.net/portal.shtml + subject_areas: + - Biochemistry + - Biology + - Biotechnology + - Cell biology + - Computer applications + - Environmental sciences + - Genetics + - Metabolism + - Proteins + title: MIBBI (Minimum Information for Biological and Biomedical Investigations) +http://www.dcc.ac.uk/resources/metadata-standards/midas-heritage: + acronym: MIDAS + field_of_science: + - architectural design + - humanities + - archaeology + - history + identifier: midas-heritage + ids: + - type: local + value: msc:m24 + - type: local + value: https://doi.org/10.25504/FAIRsharing.q0hgq + - 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type: namespace + value: http://www.openarchives.org/ore/terms/ + subject_areas: + - Anthropology + - History + - Multidisciplinary + title: OAI-ORE (Open Archives Initiative Object Reuse and Exchange) +http://www.dcc.ac.uk/resources/metadata-standards/observ-om: + acronym: + field_of_science: + - biological sciences + - natural sciences + identifier: observ-om + ids: + - type: local + value: msc:m27 + - type: local + value: https://fairsharing.org/4682 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/observ-om + - type: homepage + value: http://www.molgenis.org/wiki/ObservStart + subject_areas: + - Biology + title: Observ-OM +http://www.dcc.ac.uk/resources/metadata-standards/observations-and-measurements: + acronym: + field_of_science: + - geology + - engineering and technology + - remote sensing + - meteorology + - chemical sciences + - natural sciences + identifier: observations-and-measurements + ids: + - type: local + value: msc:m28 + - type: local + value: https://doi.org/10.25504/FAIRsharing.4ehmy9 + - 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Physiology + - Plant diseases + - Plant physiology + - Zoology + title: OME-XML (Open Microscopy Environment XML) +http://www.dcc.ac.uk/resources/metadata-standards/protocol-data-element-definitions: + acronym: + field_of_science: + - medical and health sciences + - clinical medicine + identifier: protocol-data-element-definitions + ids: + - type: local + value: msc:m32 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/protocol-data-element-definitions + - type: local + value: https://doi.org/10.25504/FAIRsharing.7e962d + - type: homepage + value: http://clinicaltrials.gov/ct2/manage-recs/resources + - type: schema + value: https://prsinfo.clinicaltrials.gov/ProtocolRecordSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/prs + - type: schema + value: https://prsinfo.clinicaltrials.gov/RRSUploadSchema.xsd + - type: namespace + value: http://clinicaltrials.gov/rrs + subject_areas: + - Clinical medicine + title: Protocol Data Element Definitions +http://www.dcc.ac.uk/resources/metadata-standards/prov: + acronym: + field_of_science: + - sciences + identifier: prov + ids: + - type: local + value: msc:m33 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/prov + - type: local + value: https://doi.org/10.25504/FAIRsharing.fe7cda + - type: homepage + value: http://www.w3.org/2001/sw/wiki/PROV + - type: schema + value: http://www.w3.org/ns/prov.xsd + - type: namespace + value: http://www.w3.org/ns/prov# + subject_areas: + - Multidisciplinary + title: PROV +http://www.dcc.ac.uk/resources/metadata-standards/qudex-qualitative-data-exchange-format: + acronym: + field_of_science: + - sciences + identifier: qudex-qualitative-data-exchange-format + ids: + - type: local + value: msc:m34 + - type: local + value: http://www.dcc.ac.uk/resources/metadata-standards/qudex-qualitative-data-exchange-format + - type: local + value: https://doi.org/10.25504/FAIRsharing.d42cb9 + - type: homepage + value: http://www.data-archive.ac.uk/create-manage/projects/qudex?index=1 + - type: schema + value: https://dam.data-archive.ac.uk/standards/qudex_v03_01.xsd + - 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Multidisciplinary + title: ETD-MS an Interoperability Metadata Standard for Electronic Theses and Dissertations +http://www.ndltd.org/standards/metadata/etdms/1.1/: + acronym: ETD-MS + field_of_science: + - sciences + id: etdms-metadata-schema + identifier: + - type: local + value: fuji:m17 + - type: local + value: https://fairsharing.org/4660 + - type: homepage + value: https://ndltd.org/metadata/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.1/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.0/ + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdms11.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdc.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdcterms.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.0/etdms.xsd + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1-0/ + subject_areas: + - Multidisciplinary + title: ETD-MS an Interoperability Metadata Standard for Electronic Theses and Dissertations +http://www.ndltd.org/standards/metadata/etdms/1.1/etdms11.xsd: + acronym: ETD-MS + field_of_science: + - sciences + id: etdms-metadata-schema + identifier: + - type: local + value: fuji:m17 + - type: local + value: https://fairsharing.org/4660 + - type: homepage + value: https://ndltd.org/metadata/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.1/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.0/ + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdms11.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdc.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdcterms.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.0/etdms.xsd + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1-0/ + subject_areas: + - Multidisciplinary + title: ETD-MS an Interoperability Metadata Standard for Electronic Theses and Dissertations +http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdc.xsd: + acronym: ETD-MS + field_of_science: + - sciences + id: etdms-metadata-schema + identifier: + - type: local + value: fuji:m17 + - type: local + value: https://fairsharing.org/4660 + - type: homepage + value: https://ndltd.org/metadata/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.1/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.0/ + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdms11.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdc.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdcterms.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.0/etdms.xsd + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1-0/ + subject_areas: + - Multidisciplinary + title: ETD-MS an Interoperability Metadata Standard for Electronic Theses and Dissertations +http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdcterms.xsd: + acronym: ETD-MS + field_of_science: + - sciences + id: etdms-metadata-schema + identifier: + - type: local + value: fuji:m17 + - type: local + value: https://fairsharing.org/4660 + - type: homepage + value: https://ndltd.org/metadata/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.1/ + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1.0/ + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdms11.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdc.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.1/etdmsdcterms.xsd + - type: schema + value: http://www.ndltd.org/standards/metadata/etdms/1.0/etdms.xsd + - type: namespace + value: http://www.ndltd.org/standards/metadata/etdms/1-0/ + subject_areas: + - Multidisciplinary + title: ETD-MS an Interoperability Metadata Standard for Electronic Theses and Dissertations +http://www.nexml.org/2009: + acronym: + field_of_science: + - biological sciences + - natural sciences + id: nexml + identifier: + - type: local + value: fuji:m45 + - type: local + value: https://doi.org/10.25504/FAIRsharing.knrb06 + - type: homepage + value: http://www.nexusformat.org/ + - type: namespace + value: http://www.nexml.org/2009 + - type: schema + value: http://www.nexml.org/2009 ../xsd/nexml.xsd + subject_areas: + - Biology + title: NeXML +http://www.nexml.org/2009 ../xsd/nexml.xsd: + acronym: + field_of_science: + - biological sciences + - natural sciences + id: nexml + identifier: + - type: local + value: fuji:m45 + - type: local + value: https://doi.org/10.25504/FAIRsharing.knrb06 + - type: homepage + value: http://www.nexusformat.org/ + - type: namespace + value: http://www.nexml.org/2009 + - type: schema + value: http://www.nexml.org/2009 ../xsd/nexml.xsd + subject_areas: + - 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type: schema + value: https://catalog.clarin.eu/ds/ComponentRegistry/rest/registry/1.x/profiles/clarin.eu:cr1:p_1290431694484/xsd + subject_areas: + - Linguistics + - Languages + title: Component MetaData Specification (CMDI) +https://cataloguestaging.ukeof.org.uk/schema/ukeof.1.0.0.xsd: + acronym: + field_of_science: + - ecology + - geology + - biological sciences + - engineering and technology + - climatology + - soil sciences + - remote sensing + - meteorology + - natural sciences + - hydrology + id: ukeof + identifier: + - type: local + value: msc:m40 + - type: local + value: https://doi.org/10.25504/FAIRsharing.9xytp6 + - type: homepage + value: http://www.ukeof.org.uk/ + - type: schema + value: https://cataloguestaging.ukeof.org.uk/schema/ukeof.1.0.0.xsd + - type: schema + value: https://www.ukeof.org.uk/schema/1/UKEOF_v1.0.xsd + - type: namespace + value: http://www.ukeof.org.uk/schema/1 + subject_areas: + - Biogeography + - Biological diversity + - Climatology + - Ecology + - Geology + - Hydrology + - Meteorology + - Remote sensing + - Soil sciences + title: UKEOF +https://cidoc.mini.icom.museum/working-groups/lido/lido-overview/about-lido/what-is-lido/: + acronym: LIDO + field_of_science: + - humanities + id: lido-lightweight-information-describing-objects + identifier: + - type: local + value: fuji:m18 + - type: local + value: https://doi.org/10.25504/FAIRsharing.73558b + - type: schema + value: www.lido-schema.org/schema/latest/lido.xsd + - type: schema + value: www.lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: schema + value: http://www.lido-schema.org/schema/v1.0/lido-v1.0.xsd + - type: schema + value: http://lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: namespace + value: http://www.lido-schema.org + - type: homepage + value: http://www.lido-schema.org + subject_areas: + - Humanities + - Cultural heritage + title: LIDO, Lightweight Information Describing Objects +? https://clarivate.com/products/scientific-and-academic-research/research-discovery-and-workflow-solutions/webofscience-platform/data-citation-index/ +: acronym: dci + field_of_science: + - library sciences + - humanities + id: clarivate-data-citation-index-schema + identifier: + - type: local + value: fuji:m39 + - type: namespace + value: https://clarivate.com/products/web-of-science/web-science-form/data-citation-index/ + - type: homepage + value: https://clarivate.com/products/scientific-and-academic-research/research-discovery-and-workflow-solutions/webofscience-platform/data-citation-index/ + subject_areas: + - Bibliographic standards + title: Clarivate Data Citation Index Schema +https://clarivate.com/products/web-of-science/web-science-form/data-citation-index/: + acronym: dci + field_of_science: + - library sciences + - humanities + id: clarivate-data-citation-index-schema + identifier: + - type: local + value: fuji:m39 + - type: namespace + value: https://clarivate.com/products/web-of-science/web-science-form/data-citation-index/ + - type: homepage + value: https://clarivate.com/products/scientific-and-academic-research/research-discovery-and-workflow-solutions/webofscience-platform/data-citation-index/ + subject_areas: + - Bibliographic standards + title: Clarivate Data Citation Index Schema +https://cocoon.huma-num.fr/schemas/dcq.xsd: + acronym: QDC + field_of_science: + - sciences + id: dublin-core-qualified + identifier: + - type: local + value: fuji:m22 + - type: local + value: https://doi.org/10.25504/FAIRsharing.3nx7t + - type: homepage + value: https://www.dublincore.org/specifications/dublin-core/dcmes-qualifiers/ + - type: namespace + value: urn:dc:qdc:container + - type: namespace + value: figshare:oai:qdc + - type: namespace + value: http://naca.central.cranfield.ac.uk/ethos-oai/2.0/ + - type: namespace + value: http://ora.ox.ac.uk/oai-pmh/metadata-formats/solo_dc + - type: schema + value: https://cocoon.huma-num.fr/schemas/dcq.xsd + - type: namespace + value: http://crdo.risc.cnrs.fr/schemas/dcq/ + - type: namespace + value: http://oai.base-search.net/base_dc/ + - type: namespace + value: http://oai.base-search.net/base_dc + - type: schema + value: http://oai.base-search.net/base_dc/base_dc.xsd + subject_areas: + - Multidisciplinary + title: Qualified Dublin Core +https://d-nb.info/1260521133/34: + acronym: xmetadiss + field_of_science: + - library sciences + - sciences + - humanities + id: xmetadiss-schema + identifier: + - type: local + value: fuji:m43 + - type: schema + value: https://d-nb.info/standards/schema/xmetadissplus.xsd + - type: namespace + value: http://www.d-nb.de/standards/xmetadissplus/ + - type: namespace + value: http://www.d-nb.de/standards/xMetaDiss/ + - type: homepage + value: http://www.d-nb.de/standards/xMetaDiss/ + subject_areas: + - Multidisciplinary + - Bibliographic standards + - Information/library standards + title: XmetaDiss +https://d-nb.info/standards/schema/xmetadissplus.xsd: + acronym: xmetadiss + field_of_science: + - library sciences + - sciences + - humanities + id: xmetadiss-schema + identifier: + - type: local + value: fuji:m43 + - type: schema + value: https://d-nb.info/standards/schema/xmetadissplus.xsd + - type: namespace + value: http://www.d-nb.de/standards/xmetadissplus/ + - 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sciences + id: crossref-schema + identifier: + - type: local + value: fuji:m40 + - type: local + value: https://doi.org/10.25504/FAIRsharing.bbQbSW + - type: homepage + value: http://www.crossref.org/schema + - type: namespace + value: http://www.crossref.org/schema/4.4.0 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.0.xsd + - type: schema + value: https://data.crossref.org/schemas/crossref4.3.7.xsd + - type: namespace + value: http://www.crossref.org/schema/4.3.7 + - type: namespace + value: http://www.crossref.org/schema/4.4.1 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.1.xsd + - type: namespace + value: http://www.crossref.org/schema/4.4.2 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.2.xsd + - type: namespace + value: http://www.crossref.org/schema/4.8.1 + - type: schema + value: https://data.crossref.org/schemas/crossref4.8.1.xsd + - type: namespace + value: http://www.crossref.org/schema/5.3.1 + - type: schema + value: https://data.crossref.org/schemas/crossref5.3.1.xsd + subject_areas: + - Multidisciplinary + title: Crossref Schema +https://data.crossref.org/schemas/crossref4.4.0.xsd: + acronym: crossref + field_of_science: + - sciences + id: crossref-schema + identifier: + - type: local + value: fuji:m40 + - type: local + value: https://doi.org/10.25504/FAIRsharing.bbQbSW + - type: homepage + value: http://www.crossref.org/schema + - type: namespace + value: http://www.crossref.org/schema/4.4.0 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.0.xsd + - type: schema + value: https://data.crossref.org/schemas/crossref4.3.7.xsd + - type: namespace + value: http://www.crossref.org/schema/4.3.7 + - type: namespace + value: http://www.crossref.org/schema/4.4.1 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.1.xsd + - type: namespace + value: http://www.crossref.org/schema/4.4.2 + - type: schema + value: https://data.crossref.org/schemas/crossref4.4.2.xsd + - type: namespace + value: http://www.crossref.org/schema/4.8.1 + - type: schema + value: https://data.crossref.org/schemas/crossref4.8.1.xsd + - 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Multidisciplinary + title: Crossref Schema +https://datatracker.ietf.org/doc/html/rfc4287: + acronym: ATOM + field_of_science: + - sciences + id: atom-syndication-format + identifier: + - type: local + value: fuji:m13 + - type: local + value: https://fairsharing.org/4648 + - type: namespace + value: https://www.w3.org/2005/Atom + - type: namespace + value: http://www.w3.org/2005/Atom + - type: homepage + value: https://datatracker.ietf.org/wg/atompub/about/ + subject_areas: + - Multidisciplinary + title: The Atom Syndication Format +https://datatracker.ietf.org/wg/atompub/about/: + acronym: ATOM + field_of_science: + - sciences + id: atom-syndication-format + identifier: + - type: local + value: fuji:m13 + - type: local + value: https://fairsharing.org/4648 + - type: namespace + value: https://www.w3.org/2005/Atom + - type: namespace + value: http://www.w3.org/2005/Atom + - type: homepage + value: https://datatracker.ietf.org/wg/atompub/about/ + subject_areas: + - Multidisciplinary + title: The Atom Syndication Format +https://ddialliance.org/Specification/DDI-Codebook/2.1/XMLSchema/codebook.xsd: + acronym: DDI + field_of_science: + - 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Cartography + - Climatology + - Earth sciences + - Geography + - Geology + - Glaciology + - Hydrogeology + - Hydrology + - Meteorology + - Oceanography + - Topography + title: Geography Markup Language +www.lido-schema.org/schema/latest/lido.xsd: + acronym: LIDO + field_of_science: + - humanities + id: lido-lightweight-information-describing-objects + identifier: + - type: local + value: fuji:m18 + - type: local + value: https://doi.org/10.25504/FAIRsharing.73558b + - type: schema + value: www.lido-schema.org/schema/latest/lido.xsd + - type: schema + value: www.lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: schema + value: http://www.lido-schema.org/schema/v1.0/lido-v1.0.xsd + - type: schema + value: http://lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: namespace + value: http://www.lido-schema.org + - type: homepage + value: http://www.lido-schema.org + subject_areas: + - Humanities + - Cultural heritage + title: LIDO, Lightweight Information Describing Objects +www.lido-schema.org/schema/v1.1/lido-v1.1.xsd: + acronym: LIDO + field_of_science: + - humanities + id: lido-lightweight-information-describing-objects + identifier: + - type: local + value: fuji:m18 + - type: local + value: https://doi.org/10.25504/FAIRsharing.73558b + - type: schema + value: www.lido-schema.org/schema/latest/lido.xsd + - type: schema + value: www.lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: schema + value: http://www.lido-schema.org/schema/v1.0/lido-v1.0.xsd + - type: schema + value: http://lido-schema.org/schema/v1.1/lido-v1.1.xsd + - type: namespace + value: http://www.lido-schema.org + - type: homepage + value: http://www.lido-schema.org + subject_areas: + - Humanities + - Cultural heritage + title: LIDO, Lightweight Information Describing Objects diff --git a/fuji_server/data/open_formats.json b/fuji_server/data/open_formats.json deleted file mode 100644 index 68c8f486..00000000 --- a/fuji_server/data/open_formats.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "application/CCP4-mtz-freerflag": "Generic", - "application/CCP4-mtz-map": "Generic", - "application/CCP4-mtz-observed": "Generic", - "application/CCP4-mtz-phases": "Generic", - "application/CCP4-unmerged-experimental": "Generic", - "application/dbase": "Generic", - "application/dbf": "Generic", - "application/dicom": "Generic", - "application/fits": "Generic", - "application/geo+json": "Generic", - "application/mathml+xml": "Generic", - "application/netcdf": "Generic", - "application/sbml+xml": "Generic", - "application/sla": "Generic", - "application/vnd.wolfram.cdf": "Generic", - "application/vnd.wolfram.cdf.text": "Generic", - "application/wmo-grib2": "Generic", - "application/x-3ds": "Generic", - "application/x-cdf": "Generic", - "application/x-grib": "Generic", - "application/x-hdf": "Generic", - "application/x-hdf5": "Generic", - "application/x-netcdf": "Generic", - "chemical/seq-aa-fasta": "Generic", - "chemical/seq-na-fasta": "Generic", - "chemical/seq-na-fastq": "Generic", - "chemical/seq-na-genbank": "Generic", - "chemical/seq-na-sff": "Generic", - "chemical/x-cactus": "Generic", - "chemical/x-cactus-ascii": "Generic", - "chemical/x-cdx": "Generic", - "chemical/x-cdxml": "Generic", - "chemical/x-cerius": "Generic", - "chemical/x-chem3d": "Generic", - "chemical/x-cif": "Generic", - "chemical/x-cmdf": "Generic", - "chemical/x-cml": "Generic", - "chemical/x-crossfire": "Generic", - "chemical/x-cube": "Generic", - "chemical/x-daylight-smiles": "Generic", - "chemical/x-embl-dl-nucleotide": "Generic", - "chemical/x-galactic-spc": "Generic", - "chemical/x-gamess-input": "Generic", - "chemical/x-gaussian-checkpoint": "Generic", - "chemical/x-gaussian-log": "Generic", - "chemical/x-gcg8-sequence": "Generic", - "chemical/x-hin": "Generic", - "chemical/x-isostar": "Generic", - "chemical/x-jcamp-dx": "Generic", - "chemical/x-kinemage": "Generic", - "chemical/x-macmolecule": "Generic", - "chemical/x-macromodel-input": "Generic", - "chemical/x-mdl-molfile": "Generic", - "chemical/x-mdl-rdfile": "Generic", - "chemical/x-mdl-rxnfile": "Generic", - "chemical/x-mdl-sdfile": "Generic", - "chemical/x-mdl-tgf": "Generic", - "chemical/x-mmcif": "Generic", - "chemical/x-mol2": "Generic", - "chemical/x-molconn-Z": "Generic", - "chemical/x-pdb": "Generic", - "chemical/x-swissprot": "Generic", - "chemical/x-vamas-iso14976": "Generic", - "chemical/x-xtel": "Generic", - "hemical/x-alchemy": "Generic", - "image/dicom-rle": "Generic", - "image/fits": "Generic", - "image/x-3ds": "Generic", - "model/mesh": "Generic", - "model/vnd.collada+xml": "Generic", - "text/mathml": "Generic", - "text/x-bed": "Generic", - "text/x-fasta": "Generic", - "text/x-gff3": "Generic", - "text/x-nh": "Generic", - "text/x-stockholm-alignment": "Generic" -} diff --git a/fuji_server/data/software_file.json b/fuji_server/data/software_file.json deleted file mode 100644 index 4859fef5..00000000 --- a/fuji_server/data/software_file.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - "Jenkinsfile": { - "category": [ - "automation" - ], - "parse": "full", - "pattern": [ - "(\\w*/)*Jenkinsfile" - ] - }, - "README": { - "category": [ - "documentation" - ], - "parse": "full", - "pattern": [ - "(\\w*/)*README(\\.(txt|md))?" - ] - }, - "dependencies": { - "category": [ - "documentation", - "automation" - ], - "parse": "file_name", - "pattern": [ - "requirements\\.txt" - ] - }, - "docs_directory": { - "category": [ - "documentation" - ], - "parse": "file_name", - "pattern": [ - "(\\w*/)*docs(/\\w*\\.\\w*)*" - ] - }, - "github_actions": { - "category": [ - "automation" - ], - "parse": "full", - "pattern": [ - "\\.github/workflows(/\\w*\\.\\w*)*" - ] - }, - "license_file": { - "category": [ - "provenance" - ], - "parse": "full", - "pattern": [ - "(\\w*/)*LICEN(S|C)E(\\.\\w*)?", - "(\\w*/)*licen(s|c)e(\\.\\w*)?", - "(\\w*/)*COPYING" - ] - }, - "maven_pom": { - "category": [ - "documentation", - "automation" - ], - "parse": "full", - "pattern": [ - "pom\\.xml" - ] - } -} diff --git a/fuji_server/data/software_file.yaml b/fuji_server/data/software_file.yaml new file mode 100644 index 00000000..0425c53c --- /dev/null +++ b/fuji_server/data/software_file.yaml @@ -0,0 +1,46 @@ +Jenkinsfile: + category: + - automation + parse: full + pattern: + - (\w*/)*Jenkinsfile +README: + category: + - documentation + parse: full + pattern: + - (\w*/)*README(\.(txt|md))? +dependencies: + category: + - documentation + - automation + parse: file_name + pattern: + - requirements\.txt +docs_directory: + category: + - documentation + parse: file_name + pattern: + - (\w*/)*docs(/\w*\.\w*)* +github_actions: + category: + - automation + parse: full + pattern: + - \.github/workflows(/\w*\.\w*)* +license_file: + category: + - provenance + parse: full + pattern: + - (\w*/)*LICEN(S|C)E(\.\w*)? + - (\w*/)*licen(s|c)e(\.\w*)? + - (\w*/)*COPYING +maven_pom: + category: + - documentation + - automation + parse: full + pattern: + - pom\.xml diff --git a/fuji_server/data/standard_uri_protocols.json b/fuji_server/data/standard_uri_protocols.json deleted file mode 100644 index 3637fbfa..00000000 --- a/fuji_server/data/standard_uri_protocols.json +++ /dev/null @@ -1,50 +0,0 @@ -{ - "amqp": { - "name": "Advanced Message Queuing Protocol" - }, - "coap": { - "name": "Constrained Application Protocol" - }, - "coaps": { - "name": "Constrained Application Protocol Secure" - }, - "ftp": { - "name": "File Transfer Protocol" - }, - "http": { - "name": "Hyper Text Transfer Protocol" - }, - "https": { - "name": "Hyper Text Transfer Protocol Secure" - }, - "mqtt": { - "name": "Message Queuing Telemetry Transport" - }, - "rtsp": { - "name": "Real Time Streaming Protocol" - }, - "rtspu": { - "name": "Real Time Streaming Protocol" - }, - "sftp": { - "name": "Secure File Transfer Protocol" - }, - "shttp": { - "name": "Secure Hypertext Transfer Protocol" - }, - "ssh": { - "name": "Secure Shell" - }, - "svn": { - "name": "Subversion" - }, - "telnet": { - "name": "Telnet" - }, - "ws": { - "name": "WebSocket" - }, - "wss": { - "name": "WebSocket Secure" - } -} diff --git a/fuji_server/data/standard_uri_protocols.yaml b/fuji_server/data/standard_uri_protocols.yaml new file mode 100644 index 00000000..8779b93e --- /dev/null +++ b/fuji_server/data/standard_uri_protocols.yaml @@ -0,0 +1,32 @@ +amqp: + name: Advanced Message Queuing Protocol +coap: + name: Constrained Application Protocol +coaps: + name: Constrained Application Protocol Secure +ftp: + name: File Transfer Protocol +http: + name: Hyper Text Transfer Protocol +https: + name: Hyper Text Transfer Protocol Secure +mqtt: + name: Message Queuing Telemetry Transport +rtsp: + name: Real Time Streaming Protocol +rtspu: + name: Real Time Streaming Protocol +sftp: + name: Secure File Transfer Protocol +shttp: + name: Secure Hypertext Transfer Protocol +ssh: + name: Secure Shell +svn: + name: Subversion +telnet: + name: Telnet +ws: + name: WebSocket +wss: + name: WebSocket Secure diff --git a/fuji_server/harvester/github_harvester.py b/fuji_server/harvester/github_harvester.py index 80ed3e16..2d34f6fa 100644 --- a/fuji_server/harvester/github_harvester.py +++ b/fuji_server/harvester/github_harvester.py @@ -2,15 +2,17 @@ # # SPDX-License-Identifier: MIT -import json import os import re import time from configparser import ConfigParser +from pathlib import Path from github import Auth, Github from github.GithubException import UnknownObjectException +import yaml + class GithubHarvester: def __init__(self, id, logger, host="https://github.com", verbose=True): @@ -23,10 +25,10 @@ def __init__(self, id, logger, host="https://github.com", verbose=True): self.verbose = verbose self.authenticate(config) self.data = {} # dictionary with all info - fuji_server_dir = os.path.dirname(os.path.dirname(__file__)) # project_root - software_file_path = os.path.join(fuji_server_dir, "data", "software_file.json") + fuji_server_dir = Path(__file__).parent.parent # project_root + software_file_path = fuji_server_dir / "data" / "software_file.yaml" with open(software_file_path) as f: - self.files_map = json.load(f) + self.files_map = yaml.safe_load(f) def authenticate(self, config): """Runs every time a new harvesting request comes in, as the harvester is re-initialised every time. Picks a token (if available) and initialises the pyGithub handle. diff --git a/fuji_server/helper/linked_vocab_helper.py b/fuji_server/helper/linked_vocab_helper.py index 58d38081..abab1582 100644 --- a/fuji_server/helper/linked_vocab_helper.py +++ b/fuji_server/helper/linked_vocab_helper.py @@ -2,15 +2,20 @@ # # SPDX-License-Identifier: MIT -import json -import os +import logging import re +from pathlib import Path from tldextract import extract +import yaml + +logger = logging.getLogger(__name__) + class linked_vocab_helper: - fuji_server_dir = os.path.dirname(os.path.dirname(__file__)) # project_root + fuji_server_dir = Path(__file__).parent.parent # project_root + linked_vocabs_dir = fuji_server_dir / "data/linked_vocabs" def __init__(self, linked_vocab_index={}): self.linked_vocab_index = linked_vocab_index @@ -20,16 +25,13 @@ def __init__(self, linked_vocab_index={}): self.ignore_domain = ["orcid.org", "doi.org", "ror.org", "zenodo.org", "isni.org"] def set_linked_vocab_dict(self): - print("Setting up the vocab dict.........................") + logger.info("Setting up the vocab dict.........................") # a new implementation based on bioportal etc.. - for ont_reg_file in os.listdir(os.path.join(self.fuji_server_dir, "data", "linked_vocabs")): - if ont_reg_file.endswith(".json"): # and ont_reg_file not in ['fuji_ontologies.json', 'bioregistry.json']: - with open( - os.path.join(self.fuji_server_dir, "data", "linked_vocabs", ont_reg_file), encoding="utf-8" - ) as reg_file: - reg_ontologies = json.load(reg_file) - self.linked_vocab_dict.update(reg_ontologies) + for ont_reg_file in self.linked_vocabs_dir.glob("*.yaml"): + with open(ont_reg_file, encoding="utf-8") as reg_file: + reg_ontologies = yaml.safe_load(reg_file) + self.linked_vocab_dict.update(reg_ontologies) def split_iri(self, iri): ret = {} diff --git a/fuji_server/helper/preprocessor.py b/fuji_server/helper/preprocessor.py index b384fb1d..a9a5d594 100644 --- a/fuji_server/helper/preprocessor.py +++ b/fuji_server/helper/preprocessor.py @@ -2,11 +2,10 @@ # # SPDX-License-Identifier: MIT -import json import logging import mimetypes -import os import time +from pathlib import Path from urllib.parse import urlparse import requests @@ -53,8 +52,8 @@ class Preprocessor: identifiers_org_data = {} google_data_dois = [] google_data_urls = [] - # fuji_server_dir = os.path.dirname(sys.modules['__main__'].__file__) - fuji_server_dir = os.path.dirname(os.path.dirname(__file__)) # project_root + fuji_server_dir = Path(__file__).parent.parent # project_root + data_dir = fuji_server_dir / "data" header = {"Accept": "application/json"} logger = logging.getLogger(__name__) data_files_limit = 3 @@ -122,9 +121,9 @@ def get_identifiers_org_data(cls): @classmethod def retrieve_identifiers_org_data(cls): - std_uri_path = os.path.join(cls.fuji_server_dir, "data", "identifiers_org_resolver_data.json") - with open(std_uri_path, encoding="utf8") as f: - identifiers_data = json.load(f) + std_uri_path = cls.data_dir / "identifiers_org_resolver_data.yaml" + with open(std_uri_path, encoding="utf-8") as f: + identifiers_data = yaml.safe_load(f) if identifiers_data: for namespace in identifiers_data["payload"]["namespaces"]: cls.identifiers_org_data[namespace["prefix"]] = { @@ -141,7 +140,7 @@ def get_resource_types(cls): @classmethod def retrieve_resource_types(cls): ns = [] - ns_file_path = os.path.join(cls.fuji_server_dir, "data", "ResourceTypes.txt") + ns_file_path = cls.data_dir / "ResourceTypes.txt" with open(ns_file_path) as f: ns = [line.lower().rstrip() for line in f] if ns: @@ -150,9 +149,9 @@ def retrieve_resource_types(cls): @classmethod def retrieve_schema_org_context(cls): data = {} - std_uri_path = os.path.join(cls.fuji_server_dir, "data", "jsonldcontext.json") + std_uri_path = cls.data_dir / "jsonldcontext.yaml" with open(std_uri_path) as f: - data = json.load(f) + data = yaml.safe_load(f) if data: for context, schemadict in data.get("@context").items(): if isinstance(schemadict, dict): @@ -166,11 +165,11 @@ def retrieve_schema_org_context(cls): @classmethod def retrieve_schema_org_creativeworks(cls, include_bioschemas=True): data = [] - cw_path = os.path.join(cls.fuji_server_dir, "data", "creativeworktypes.txt") + cw_path = cls.data_dir / "creativeworktypes.txt" with open(cw_path) as f: data = f.read().splitlines() if include_bioschemas: - bs_path = os.path.join(cls.fuji_server_dir, "data", "bioschemastypes.txt") + bs_path = cls.data_dir / "bioschemastypes.txt" with open(bs_path) as f: bdata = f.read().splitlines() data.extend(bdata) @@ -223,8 +222,8 @@ def retrieve_metrics_yaml(cls, yaml_metric_path): def retrieve_datacite_re3repos(cls): # retrieve all client id and re3data doi from datacite isDebugMode = True - re3dict_path = os.path.join(cls.fuji_server_dir, "data", "repodois.yaml") - repolistdate = os.path.getmtime(re3dict_path) + re3dict_path = cls.data_dir / "repodois.yaml" + repolistdate = re3dict_path.stat().st_mtime try: # update once a day if time.time() - repolistdate >= 86400: @@ -250,30 +249,30 @@ def retrieve_datacite_re3repos(cls): # fix wrong entry cls.re3repositories["bl.imperial"] = "http://doi.org/10.17616/R3K64N" with open(re3dict_path, "w") as f2: - yaml.dump(cls.re3repositories, f2) + yaml.safe_dump(cls.re3repositories, f2) except requests.exceptions.RequestException as e: - os.utime(re3dict_path) + re3dict_path.touch() print("Preprocessor Error: " + str(e)) cls.logger.error(e) @classmethod def get_access_rights(cls): data = None - jsn_path = os.path.join(cls.fuji_server_dir, "data", "access_rights.json") - with open(jsn_path) as f: - data = json.load(f) + path = cls.data_dir / "access_rights.yaml" + with path.open() as f: + data = yaml.safe_load(f) return data @classmethod def retrieve_licenses(cls, isDebugMode): data = None - jsn_path = os.path.join(cls.fuji_server_dir, "data", "licenses.json") + path = cls.data_dir / "licenses.yaml" # The repository can be found at https://github.com/spdx/license-list-data # https://spdx.org/spdx-license-list/license-list-overview if isDebugMode: # use local file instead of downloading the file online - with open(jsn_path) as f: - data = json.load(f) + with open(path) as f: + data = yaml.safe_load(f) else: # cls.SPDX_URL = license_path try: @@ -284,12 +283,12 @@ def retrieve_licenses(cls, isDebugMode): data = resp["licenses"] for d in data: d["name"] = d["name"].lower() # convert license name to lowercase - with open(jsn_path, "w") as f: - json.dump(data, f) - except json.decoder.JSONDecodeError as e1: - cls.logger.error(e1) - except requests.exceptions.RequestException as e2: - cls.logger.error(e2) + with open(path, "w") as f: + yaml.safe_dump(data, f) + except yaml.YAMLError as exc1: + cls.logger.error(exc1) + except requests.exceptions.RequestException as exc2: + cls.logger.error(exc2) if data: cls.all_licenses = data for licenceitem in cls.all_licenses: @@ -314,9 +313,9 @@ def retrieve_licenses(cls, isDebugMode): @classmethod def retrieve_metadata_standards_uris(cls): data = {} - std_uri_path = os.path.join(cls.fuji_server_dir, "data", "metadata_standards_uris.json") + std_uri_path = cls.data_dir / "metadata_standards_uris.yaml" with open(std_uri_path) as f: - data = json.load(f) + data = yaml.safe_load(f) if data: cls.metadata_standards_uris = data @@ -324,11 +323,11 @@ def retrieve_metadata_standards_uris(cls): def retrieve_metadata_standards(cls): # cls.retrieve_metadata_standards_uris() data = {} - std_path = os.path.join(cls.fuji_server_dir, "data", "metadata_standards.json") + std_path = cls.data_dir / "metadata_standards.yaml" # The original repository can be retrieved via https://rdamsc.bath.ac.uk/api/m # or at https://github.com/rd-alliance/metadata-catalog-dev with open(std_path) as f: - data = json.load(f) + data = yaml.safe_load(f) """else: try: r = requests.get(catalog_url) @@ -366,9 +365,9 @@ def retrieve_metadata_standards(cls): @classmethod def retrieve_all_file_formats(cls): data = {} - sci_file_path = os.path.join(cls.fuji_server_dir, "data", "file_formats.json") + sci_file_path = cls.data_dir / "file_formats.yaml" with open(sci_file_path) as f: - data = json.load(f) + data = yaml.safe_load(f) if data: cls.all_file_formats = data @@ -384,9 +383,6 @@ def retrieve_science_file_formats(cls, isDebugMode): domain = file.get("domain")[0] for mime in file.get("mime"): data[mime] = domain - """sci_file_path = os.path.join(cls.fuji_server_dir, 'data', 'science_formats.json') - with open(sci_file_path) as f: - data = json.load(f)""" if data: cls.science_file_formats = data @@ -402,9 +398,6 @@ def retrieve_long_term_file_formats(cls, isDebugMode): domain = file.get("domain")[0] for mime in file.get("mime"): data[mime] = domain - """sci_file_path = os.path.join(cls.fuji_server_dir, 'data', 'longterm_formats.json') - with open(sci_file_path) as f: - data = json.load(f)""" if data: cls.long_term_file_formats = data @@ -420,25 +413,22 @@ def retrieve_open_file_formats(cls, isDebugMode): domain = file.get("domain")[0] for mime in file.get("mime"): data[mime] = domain - """sci_file_path = os.path.join(cls.fuji_server_dir, 'data', 'open_formats.json') - with open(sci_file_path) as f: - data = json.load(f)""" if data: cls.open_file_formats = data @classmethod def retrieve_standard_protocols(cls, isDebugMode): data = {} - protocols_path = os.path.join(cls.fuji_server_dir, "data", "standard_uri_protocols.json") + protocols_path = cls.data_dir / "standard_uri_protocols.yaml" with open(protocols_path) as f: - data = json.load(f) + data = yaml.safe_load(f) if data: cls.standard_protocols = data @classmethod def retrieve_default_namespaces(cls): ns = [] - ns_file_path = os.path.join(cls.fuji_server_dir, "data", "default_namespaces.txt") + ns_file_path = cls.data_dir / "default_namespaces.txt" with open(ns_file_path) as f: # ns = [line.split(':',1)[1].strip() for line in f] ns = [line.rstrip().rstrip("/#") for line in f] @@ -465,11 +455,11 @@ def retrieve_linkedvocabs(cls, lov_api, lodcloud_api, isDebugMode): cls.LOD_CLOUDNET = lodcloud_api # cls.BIOPORTAL_API = bioportal_api # cls.BIOPORTAL_KEY = bioportal_key - ld_path = os.path.join(cls.fuji_server_dir, "data", "linked_vocab.json") + ld_path = cls.data_dir / "linked_vocab.yaml" vocabs = [] if isDebugMode: with open(ld_path) as f: - cls.linked_vocabs = json.load(f) + cls.linked_vocabs = yaml.safe_load(f) else: # 1. retrieve records from https://lov.linkeddata.es/dataset/lov/api # 714 vocabs, of which 104 vocabs uri specified are broken (02072020) @@ -549,7 +539,7 @@ def retrieve_linkedvocabs(cls, lov_api, lodcloud_api, isDebugMode): # 3. write to a local file try: with open(ld_path, "w") as f: - json.dump(vocabs, f) + yaml.safe_dump(vocabs, f) cls.linked_vocabs = vocabs except OSError: cls.logger.error(f"Couldn't write to file {ld_path}.") diff --git a/tests/conftest.py b/tests/conftest.py index 722dbc5e..44aa5beb 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -103,6 +103,10 @@ def temporary_preprocessor(temporary_data_directory) -> Preprocessor: # point the preprocessor to a temporary directory, # to not change the fuji_server/data contents when running tests Preprocessor.fuji_server_dir = temporary_data_directory + + # hard reset these attritbutes, because sometimes when running the tests in parallel, these were still populated + Preprocessor.identifiers_org_data = {} + Preprocessor.schema_org_context = [] yield Preprocessor restore_preprocessor_state(current_state) diff --git a/tests/harvester/test_github_harvester.py b/tests/harvester/test_github_harvester.py new file mode 100644 index 00000000..384f3d92 --- /dev/null +++ b/tests/harvester/test_github_harvester.py @@ -0,0 +1,15 @@ +# SPDX-FileCopyrightText: 2020 PANGAEA (https://www.pangaea.de/) +# +# SPDX-License-Identifier: MIT + +import logging + +from fuji_server.harvester.github_harvester import GithubHarvester + + +def test_github_harvester(): + # this test just makes sure, that the GithubHarvester can read the "software_file.yaml" file + id_ = "some-id" + logger = logging.getLogger() + harvester = GithubHarvester(id_, logger) + assert harvester.files_map diff --git a/tests/helper/test_linked_vocab_helper.py b/tests/helper/test_linked_vocab_helper.py new file mode 100644 index 00000000..43cf3e0f --- /dev/null +++ b/tests/helper/test_linked_vocab_helper.py @@ -0,0 +1,15 @@ +# SPDX-FileCopyrightText: 2020 PANGAEA (https://www.pangaea.de/) +# +# SPDX-License-Identifier: MIT + +from fuji_server.helper.linked_vocab_helper import linked_vocab_helper + + +def test_linked_vocab_helper(): + linked_vocab_helper_ = linked_vocab_helper() + assert not linked_vocab_helper_.linked_vocab_dict + linked_vocab_helper_.set_linked_vocab_dict() + assert linked_vocab_helper_.linked_vocab_dict + # test entries from two different files are present + assert "bioportal.aba-amb" in linked_vocab_helper_.linked_vocab_dict + assert "bioregistry.3dmet" in linked_vocab_helper_.linked_vocab_dict diff --git a/tests/helper/test_preprocessor.py b/tests/helper/test_preprocessor.py index 192dfe38..426609e1 100644 --- a/tests/helper/test_preprocessor.py +++ b/tests/helper/test_preprocessor.py @@ -20,7 +20,6 @@ """ -import json from typing import Any import pytest @@ -32,11 +31,6 @@ isDebug = True -def load_json_from_data_directory(filename: str): - path = DATA_DIR.joinpath(filename) - return json.loads(path.read_text()) - - def load_yaml_from_data_directory(filename: str): path = DATA_DIR.joinpath(filename) return yaml.safe_load(path.read_text()) @@ -47,14 +41,19 @@ def load_txt_from_data_directory(filename: str): return path.read_text() +@pytest.fixture(scope="session") +def access_rights(): + return load_yaml_from_data_directory("access_rights.yaml") + + @pytest.fixture(scope="session") def licenses(): - return load_json_from_data_directory("licenses.json") + return load_yaml_from_data_directory("licenses.yaml") @pytest.fixture(scope="session") def metadata_standards(): - return load_json_from_data_directory("metadata_standards.json") + return load_yaml_from_data_directory("metadata_standards.yaml") @pytest.fixture(scope="session") @@ -64,42 +63,27 @@ def repodois(): @pytest.fixture(scope="session") def metadata_standards_uris(): - return load_json_from_data_directory("metadata_standards_uris.json") - - -@pytest.fixture(scope="session") -def science_formats(): - return load_json_from_data_directory("science_formats.json") + return load_yaml_from_data_directory("metadata_standards_uris.yaml") @pytest.fixture(scope="session") def linked_vocab(): - return load_json_from_data_directory("linked_vocab.json") + return load_yaml_from_data_directory("linked_vocab.yaml") @pytest.fixture(scope="session") def identifiers_org_resolver_data(): - return load_json_from_data_directory("identifiers_org_resolver_data.json") + return load_yaml_from_data_directory("identifiers_org_resolver_data.yaml") @pytest.fixture(scope="session") def jsonldcontext(): - return load_json_from_data_directory("jsonldcontext.json") - - -@pytest.fixture(scope="session") -def longterm_formats(): - return load_json_from_data_directory("longterm_formats.json") - - -@pytest.fixture(scope="session") -def open_formats(): - return load_json_from_data_directory("open_formats.json") + return load_yaml_from_data_directory("jsonldcontext.yaml") @pytest.fixture(scope="session") def standard_uri_protocols(): - return load_json_from_data_directory("standard_uri_protocols.json") + return load_yaml_from_data_directory("standard_uri_protocols.yaml") @pytest.fixture(scope="session") @@ -111,7 +95,7 @@ def default_namespaces(): @pytest.fixture(scope="session") def resource_types(): txt = load_txt_from_data_directory("ResourceTypes.txt").rstrip() - return [line.rstrip() for line in txt.split("\n")] + return [line.lower().rstrip() for line in txt.split("\n")] @pytest.fixture(scope="session") @@ -163,13 +147,6 @@ def test_retrieve_datacite_re3repos(temporary_preprocessor: Preprocessor, repodo assert len(temporary_preprocessor.re3repositories) == expected -def test_retrieve_metadata_standards(temporary_preprocessor: Preprocessor, metadata_standards) -> None: - assert not temporary_preprocessor.metadata_standards - temporary_preprocessor.retrieve_metadata_standards() - expected = len(metadata_standards) - assert len(temporary_preprocessor.metadata_standards) == expected - - def test_retrieve_linkedvocabs( temporary_preprocessor: Preprocessor, test_config: dict, linked_vocab: list[dict[str, str]] ) -> None: @@ -186,3 +163,83 @@ def test_retrieve_default_namespaces(temporary_preprocessor: Preprocessor, defau temporary_preprocessor.retrieve_default_namespaces() expected = len(default_namespaces) assert len(temporary_preprocessor.default_namespaces) == expected + + +def test_get_access_rights(temporary_preprocessor: Preprocessor, access_rights): + assert not temporary_preprocessor.access_rights + result = temporary_preprocessor.get_access_rights() + assert result == access_rights + + +def test_get_resource_types(temporary_preprocessor: Preprocessor, resource_types): + assert not temporary_preprocessor.resource_types + result = temporary_preprocessor.get_resource_types() + assert result == resource_types + assert temporary_preprocessor.resource_types == resource_types + + +def test_get_identifiers_org_data(temporary_preprocessor: Preprocessor, identifiers_org_resolver_data): + assert not temporary_preprocessor.identifiers_org_data + result = temporary_preprocessor.get_identifiers_org_data() + # check a given key in the result dictionary + expected = {"pattern": "^[a-z][a-z]/[0-9]+$", "url_pattern": "https://w3id.org/oc/corpus/{$id}"} + assert result["occ"] == expected + assert temporary_preprocessor.identifiers_org_data["occ"] == expected + + +def test_get_metadata_standards(temporary_preprocessor: Preprocessor, metadata_standards): + assert not temporary_preprocessor.metadata_standards + result = temporary_preprocessor.get_metadata_standards() + assert result == metadata_standards + assert temporary_preprocessor.metadata_standards == metadata_standards + + +def test_get_metadata_standards_uris(temporary_preprocessor: Preprocessor, metadata_standards_uris): + assert not temporary_preprocessor.metadata_standards_uris + result = temporary_preprocessor.get_metadata_standards_uris() + assert result == metadata_standards_uris + assert temporary_preprocessor.metadata_standards_uris == metadata_standards_uris + + +def test_get_schema_org_context(temporary_preprocessor: Preprocessor): + assert not temporary_preprocessor.schema_org_context + result = temporary_preprocessor.get_schema_org_context() + assert isinstance(result, list) + assert "orderpickupavailable" in result + assert result == temporary_preprocessor.schema_org_context + + +def test_get_schema_org_creativeworks(temporary_preprocessor: Preprocessor): + assert not temporary_preprocessor.schema_org_creativeworks + result = temporary_preprocessor.get_schema_org_creativeworks() + assert isinstance(result, list) + assert "3dmodel" in result + assert result == temporary_preprocessor.schema_org_creativeworks + + +def test_get_science_file_formats(temporary_preprocessor: Preprocessor): + assert not temporary_preprocessor.science_file_formats + result = temporary_preprocessor.get_science_file_formats() + assert "application/CCP4-mtz" in result + assert result == temporary_preprocessor.science_file_formats + + +def test_get_long_term_file_formats(temporary_preprocessor: Preprocessor): + assert not temporary_preprocessor.long_term_file_formats + result = temporary_preprocessor.get_long_term_file_formats() + assert "audio/mp4" in result + assert result == temporary_preprocessor.long_term_file_formats + + +def test_get_open_file_formats(temporary_preprocessor: Preprocessor): + assert not temporary_preprocessor.open_file_formats + result = temporary_preprocessor.get_open_file_formats() + assert "audio/mp4" in result + assert result == temporary_preprocessor.open_file_formats + + +def test_get_standard_protocols(temporary_preprocessor: Preprocessor, standard_uri_protocols): + assert not temporary_preprocessor.standard_protocols + result = temporary_preprocessor.get_standard_protocols() + assert result == standard_uri_protocols + assert temporary_preprocessor.standard_protocols == standard_uri_protocols From d7ff5bce75d1601e24a66c42da05729a1edc0aab Mon Sep 17 00:00:00 2001 From: Heinz-Alexander Fuetterer Date: Fri, 9 Aug 2024 10:21:20 +0200 Subject: [PATCH 2/6] chore: remove obsolete commented code --- fuji_server/helper/preprocessor.py | 31 ------------------------------ 1 file changed, 31 deletions(-) diff --git a/fuji_server/helper/preprocessor.py b/fuji_server/helper/preprocessor.py index a9a5d594..53e476d4 100644 --- a/fuji_server/helper/preprocessor.py +++ b/fuji_server/helper/preprocessor.py @@ -328,37 +328,6 @@ def retrieve_metadata_standards(cls): # or at https://github.com/rd-alliance/metadata-catalog-dev with open(std_path) as f: data = yaml.safe_load(f) - """else: - try: - r = requests.get(catalog_url) - try: - if r.status_code == 200: - resp = r.json() - schemes = resp['metadata-schemes'] - for s in schemes: - r2 = requests.get(catalog_url + str(s['id']), headers=cls.header) - if r2.status_code == 200: - std = r2.json() - urls = None - keywords = std.get('keywords') - standard_title = std.get('title') - locations = std.get('locations') - if locations: - urls = [d['url'] for d in std.get('locations') if 'url' in d] - # if keywords: - # for k in keywords: - # data.setdefault(k.lower(), []).append(standard_title) - # else: - # data.setdefault('other', []).append(standard_title) - if standard_title: - data[standard_title] = {'subject_areas': keywords, 'urls': urls} - - with open(std_path, 'w') as f: - json.dump(data, f) - except json.decoder.JSONDecodeError as e1: - cls.logger.error(e1) - except requests.exceptions.RequestException as e2: - cls.logger.error(e2)""" if data: cls.metadata_standards = data From 875ff7edcb21098cdcad7b4f769bbdafccc871f7 Mon Sep 17 00:00:00 2001 From: huberrob Date: Wed, 25 Sep 2024 12:50:18 +0200 Subject: [PATCH 3/6] updated +- to pr480 --- fuji_server/helper/preprocessor.py | 130 ++++++++++++----------------- 1 file changed, 52 insertions(+), 78 deletions(-) diff --git a/fuji_server/helper/preprocessor.py b/fuji_server/helper/preprocessor.py index 7ca4c834..f51e9f79 100644 --- a/fuji_server/helper/preprocessor.py +++ b/fuji_server/helper/preprocessor.py @@ -2,11 +2,10 @@ # # SPDX-License-Identifier: MIT -import json import logging import mimetypes -import os import time +from pathlib import Path from urllib.parse import urlparse import requests @@ -53,8 +52,8 @@ class Preprocessor: identifiers_org_data = {} google_data_dois = [] google_data_urls = [] - # fuji_server_dir = os.path.dirname(sys.modules['__main__'].__file__) - fuji_server_dir = os.path.dirname(os.path.dirname(__file__)) # project_root + fuji_server_dir = Path(__file__).parent.parent # project_root + data_dir = fuji_server_dir / "data" header = {"Accept": "application/json"} logger = logging.getLogger(__name__) data_files_limit = 3 @@ -122,9 +121,9 @@ def get_identifiers_org_data(cls): @classmethod def retrieve_identifiers_org_data(cls): - std_uri_path = os.path.join(cls.fuji_server_dir, "data", "identifiers_org_resolver_data.json") - with open(std_uri_path, encoding="utf8") as f: - identifiers_data = json.load(f) + std_uri_path = cls.data_dir / "identifiers_org_resolver_data.yaml" + with open(std_uri_path, encoding="utf-8") as f: + identifiers_data = yaml.safe_load(f) if identifiers_data: for namespace in identifiers_data["payload"]["namespaces"]: cls.identifiers_org_data[namespace["prefix"]] = { @@ -141,7 +140,7 @@ def get_resource_types(cls): @classmethod def retrieve_resource_types(cls): ns = [] - ns_file_path = os.path.join(cls.fuji_server_dir, "data", "ResourceTypes.txt") + ns_file_path = cls.data_dir / "ResourceTypes.txt" with open(ns_file_path) as f: ns = [line.lower().rstrip() for line in f] if ns: @@ -150,9 +149,9 @@ def retrieve_resource_types(cls): @classmethod def retrieve_schema_org_context(cls): data = {} - std_uri_path = os.path.join(cls.fuji_server_dir, "data", "jsonldcontext.json") + std_uri_path = cls.data_dir / "jsonldcontext.yaml" with open(std_uri_path) as f: - data = json.load(f) + data = yaml.safe_load(f) if data: for context, schemadict in data.get("@context").items(): if isinstance(schemadict, dict): @@ -166,11 +165,11 @@ def retrieve_schema_org_context(cls): @classmethod def retrieve_schema_org_creativeworks(cls, include_bioschemas=True): data = [] - cw_path = os.path.join(cls.fuji_server_dir, "data", "creativeworktypes.txt") + cw_path = cls.data_dir / "creativeworktypes.txt" with open(cw_path) as f: data = f.read().splitlines() if include_bioschemas: - bs_path = os.path.join(cls.fuji_server_dir, "data", "bioschemastypes.txt") + bs_path = cls.data_dir / "bioschemastypes.txt" with open(bs_path) as f: bdata = f.read().splitlines() data.extend(bdata) @@ -223,8 +222,8 @@ def retrieve_metrics_yaml(cls, yaml_metric_path): def retrieve_datacite_re3repos(cls): # retrieve all client id and re3data doi from datacite isDebugMode = True - re3dict_path = os.path.join(cls.fuji_server_dir, "data", "repodois.yaml") - repolistdate = os.path.getmtime(re3dict_path) + re3dict_path = cls.data_dir / "repodois.yaml" + repolistdate = re3dict_path.stat().st_mtime try: # update once a day if time.time() - repolistdate >= 86400: @@ -250,30 +249,30 @@ def retrieve_datacite_re3repos(cls): # fix wrong entry cls.re3repositories["bl.imperial"] = "http://doi.org/10.17616/R3K64N" with open(re3dict_path, "w") as f2: - yaml.dump(cls.re3repositories, f2) + yaml.safe_dump(cls.re3repositories, f2) except requests.exceptions.RequestException as e: - os.utime(re3dict_path) + re3dict_path.touch() print("Preprocessor Error: " + str(e)) cls.logger.error(e) @classmethod def get_access_rights(cls): data = None - jsn_path = os.path.join(cls.fuji_server_dir, "data", "access_rights.json") - with open(jsn_path) as f: - data = json.load(f) + path = cls.data_dir / "access_rights.yaml" + with path.open() as f: + data = yaml.safe_load(f) return data @classmethod def retrieve_licenses(cls, isDebugMode): data = None - jsn_path = os.path.join(cls.fuji_server_dir, "data", "licenses.json") + path = cls.data_dir / "licenses.yaml" # The repository can be found at https://github.com/spdx/license-list-data # https://spdx.org/spdx-license-list/license-list-overview if isDebugMode: # use local file instead of downloading the file online - with open(jsn_path) as f: - data = json.load(f) + with open(path) as f: + data = yaml.safe_load(f) else: # cls.SPDX_URL = license_path try: @@ -284,12 +283,12 @@ def retrieve_licenses(cls, isDebugMode): data = resp["licenses"] for d in data: d["name"] = d["name"].lower() # convert license name to lowercase - with open(jsn_path, "w") as f: - json.dump(data, f) - except json.decoder.JSONDecodeError as e1: - cls.logger.error(e1) - except requests.exceptions.RequestException as e2: - cls.logger.error(e2) + with open(path, "w") as f: + yaml.safe_dump(data, f) + except yaml.YAMLError as exc1: + cls.logger.error(exc1) + except requests.exceptions.RequestException as exc2: + cls.logger.error(exc2) if data: cls.all_licenses = data for licenceitem in cls.all_licenses: @@ -311,55 +310,33 @@ def retrieve_licenses(cls, isDebugMode): # seeAlso = [s['seeAlso'] for s in data if 'seeAlso' in s] # cls.license_urls = dict(zip(referenceNumber, seeAlso)) + @classmethod + def retrieve_metadata_standards_uris(cls): + data = {} + std_uri_path = cls.data_dir / "metadata_standards_uris.yaml" + with open(std_uri_path) as f: + data = yaml.safe_load(f) + if data: + cls.metadata_standards_uris = data + @classmethod def retrieve_metadata_standards(cls): # cls.retrieve_metadata_standards_uris() data = {} - std_path = os.path.join(cls.fuji_server_dir, "data", "metadata_standards.json") + std_path = cls.data_dir / "metadata_standards.yaml" # The original repository can be retrieved via https://rdamsc.bath.ac.uk/api/m # or at https://github.com/rd-alliance/metadata-catalog-dev with open(std_path) as f: - data = json.load(f) - """else: - try: - r = requests.get(catalog_url) - try: - if r.status_code == 200: - resp = r.json() - schemes = resp['metadata-schemes'] - for s in schemes: - r2 = requests.get(catalog_url + str(s['id']), headers=cls.header) - if r2.status_code == 200: - std = r2.json() - urls = None - keywords = std.get('keywords') - standard_title = std.get('title') - locations = std.get('locations') - if locations: - urls = [d['url'] for d in std.get('locations') if 'url' in d] - # if keywords: - # for k in keywords: - # data.setdefault(k.lower(), []).append(standard_title) - # else: - # data.setdefault('other', []).append(standard_title) - if standard_title: - data[standard_title] = {'subject_areas': keywords, 'urls': urls} - - with open(std_path, 'w') as f: - json.dump(data, f) - except json.decoder.JSONDecodeError as e1: - cls.logger.error(e1) - except requests.exceptions.RequestException as e2: - cls.logger.error(e2)""" + data = yaml.safe_load(f) if data: cls.metadata_standards = data @classmethod def retrieve_all_file_formats(cls): data = {} - sci_file_path = os.path.join(cls.fuji_server_dir, "data", "file_formats.json") + sci_file_path = cls.data_dir / "file_formats.yaml" with open(sci_file_path) as f: - data = json.load(f) + data = yaml.safe_load(f) if data: cls.all_file_formats = data @@ -375,9 +352,6 @@ def retrieve_science_file_formats(cls, isDebugMode): domain = file.get("domain")[0] for mime in file.get("mime"): data[mime] = domain - """sci_file_path = os.path.join(cls.fuji_server_dir, 'data', 'science_formats.json') - with open(sci_file_path) as f: - data = json.load(f)""" if data: cls.science_file_formats = data @@ -393,9 +367,6 @@ def retrieve_long_term_file_formats(cls, isDebugMode): domain = file.get("domain")[0] for mime in file.get("mime"): data[mime] = domain - """sci_file_path = os.path.join(cls.fuji_server_dir, 'data', 'longterm_formats.json') - with open(sci_file_path) as f: - data = json.load(f)""" if data: cls.long_term_file_formats = data @@ -411,25 +382,22 @@ def retrieve_open_file_formats(cls, isDebugMode): domain = file.get("domain")[0] for mime in file.get("mime"): data[mime] = domain - """sci_file_path = os.path.join(cls.fuji_server_dir, 'data', 'open_formats.json') - with open(sci_file_path) as f: - data = json.load(f)""" if data: cls.open_file_formats = data @classmethod def retrieve_standard_protocols(cls, isDebugMode): data = {} - protocols_path = os.path.join(cls.fuji_server_dir, "data", "standard_uri_protocols.json") + protocols_path = cls.data_dir / "standard_uri_protocols.yaml" with open(protocols_path) as f: - data = json.load(f) + data = yaml.safe_load(f) if data: cls.standard_protocols = data @classmethod def retrieve_default_namespaces(cls): ns = [] - ns_file_path = os.path.join(cls.fuji_server_dir, "data", "default_namespaces.txt") + ns_file_path = cls.data_dir / "default_namespaces.txt" with open(ns_file_path) as f: # ns = [line.split(':',1)[1].strip() for line in f] ns = [line.rstrip().rstrip("/#") for line in f] @@ -456,11 +424,11 @@ def retrieve_linkedvocabs(cls, lov_api, lodcloud_api, isDebugMode): cls.LOD_CLOUDNET = lodcloud_api # cls.BIOPORTAL_API = bioportal_api # cls.BIOPORTAL_KEY = bioportal_key - ld_path = os.path.join(cls.fuji_server_dir, "data", "linked_vocab.json") + ld_path = cls.data_dir / "linked_vocab.yaml" vocabs = [] if isDebugMode: with open(ld_path) as f: - cls.linked_vocabs = json.load(f) + cls.linked_vocabs = yaml.safe_load(f) else: # 1. retrieve records from https://lov.linkeddata.es/dataset/lov/api # 714 vocabs, of which 104 vocabs uri specified are broken (02072020) @@ -540,7 +508,7 @@ def retrieve_linkedvocabs(cls, lov_api, lodcloud_api, isDebugMode): # 3. write to a local file try: with open(ld_path, "w") as f: - json.dump(vocabs, f) + yaml.safe_dump(vocabs, f) cls.linked_vocabs = vocabs except OSError: cls.logger.error(f"Couldn't write to file {ld_path}.") @@ -614,6 +582,12 @@ def get_custom_metrics(cls, wanted_fields): new_dict[dictm["metric_identifier"]] = {k: v for k, v in dictm.items() if k in wanted_fields} return new_dict + @classmethod + def get_metadata_standards_uris(cls) -> object: + if not cls.metadata_standards_uris: + cls.retrieve_metadata_standards_uris() + return cls.metadata_standards_uris + @classmethod def get_metadata_standards(cls) -> object: if not cls.metadata_standards: From 0db401db623ce96c36cb12f8602e7a61c0fb9c1d Mon Sep 17 00:00:00 2001 From: huberrob Date: Wed, 25 Sep 2024 13:30:43 +0200 Subject: [PATCH 4/6] updated +- to pr480 --- fuji_server/controllers/fair_check.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/fuji_server/controllers/fair_check.py b/fuji_server/controllers/fair_check.py index 3a2fd7c2..ff35906d 100644 --- a/fuji_server/controllers/fair_check.py +++ b/fuji_server/controllers/fair_check.py @@ -71,7 +71,7 @@ class FAIRCheck: LONG_TERM_FILE_FORMATS = None OPEN_FILE_FORMATS = None DEFAULT_NAMESPACES = None - VOCAB_NAMESPACES = None + # VOCAB_NAMESPACES = None ARCHIVE_MIMETYPES = Mapper.ARCHIVE_COMPRESS_MIMETYPES.value STANDARD_PROTOCOLS = None SCHEMA_ORG_CONTEXT = [] @@ -242,8 +242,8 @@ def load_predata(cls): cls.OPEN_FILE_FORMATS = Preprocessor.get_open_file_formats() if not cls.DEFAULT_NAMESPACES: cls.DEFAULT_NAMESPACES = Preprocessor.getDefaultNamespaces() - if not cls.VOCAB_NAMESPACES: - cls.VOCAB_NAMESPACES = Preprocessor.getLinkedVocabs() + # if not cls.VOCAB_NAMESPACES: + # cls.VOCAB_NAMESPACES = Preprocessor.getLinkedVocabs() if not cls.STANDARD_PROTOCOLS: cls.STANDARD_PROTOCOLS = Preprocessor.get_standard_protocols() if not cls.SCHEMA_ORG_CONTEXT: From 3ca81abb2db7f4041134d23362b2d25df91245f0 Mon Sep 17 00:00:00 2001 From: huberrob Date: Wed, 25 Sep 2024 13:44:56 +0200 Subject: [PATCH 5/6] updated +- to pr480 --- fuji_server/data/README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/fuji_server/data/README.md b/fuji_server/data/README.md index 60c2ccea..373ec61d 100644 --- a/fuji_server/data/README.md +++ b/fuji_server/data/README.md @@ -13,7 +13,6 @@ - [`licenses.json`](./licenses.json): Used to populate `Preprocessor.license_names`, a list of SPDX licences. Used in evaluation of licenses, FsF-R1.1-01M. - [`linked_vocab.json`](./linked_vocab.json) - [`longterm_formats.json`](./longterm_formats.json): This isn't used any more (code is commented out). Instead, the info should be pulled from [`file_formats.json`](./file_formats.json). -- [`metadata_standards_uris.json`](./metadata_standards_uris.json) - [`metadata_standards.json`](./metadata_standards.json): Used in evaluation of community metadata, FsF-R1.3-01M. - [`open_formats.json`](./open_formats.json): This isn't used any more (code is commented out). Instead, the info should be pulled from [`file_formats.json`](./file_formats.json). - [`repodois.yaml`](./repodois.yaml): DOIs from re3data (Datacite). From f4e5df0d7f042437cf34552b1c8badbf8855b394 Mon Sep 17 00:00:00 2001 From: huberrob Date: Wed, 25 Sep 2024 13:47:45 +0200 Subject: [PATCH 6/6] updated +- to pr480 --- fuji_server/data/repodois.yaml | 21 +- fuji_server/helper/fuji_vocab_builder.py | 415 ++++++++++++++ fuji_server/helper/fuji_vocab_helper.py | 9 + fuji_server/yaml/metrics_v0.4.yaml | 2 +- fuji_server/yaml/metrics_v0.6.yaml | 674 +++++++++++++++++++++++ 5 files changed, 1117 insertions(+), 4 deletions(-) create mode 100644 fuji_server/helper/fuji_vocab_builder.py create mode 100644 fuji_server/helper/fuji_vocab_helper.py create mode 100644 fuji_server/yaml/metrics_v0.6.yaml diff --git a/fuji_server/data/repodois.yaml b/fuji_server/data/repodois.yaml index db9707e2..35eb04f9 100644 --- a/fuji_server/data/repodois.yaml +++ b/fuji_server/data/repodois.yaml @@ -4,6 +4,7 @@ ardcx.curtin: https://doi.org/10.17616/R3WM02 ardcx.griffith: https://doi.org/10.17616/R3FG92 ardcx.usq: https://doi.org/10.17616/R36Q18 arfm.ufzdrp: https://doi.org/10.17616/R31NJN1M +awsod.roda: https://doi.org/10.17616/R3M91V awzy.fednnv: https://doi.org/10.17616/R3PM1K bamf.bamf: https://doi.org/10.17616/R31NJMZ5 bf.discover: https://doi.org/10.17616/R31NJMN0 @@ -48,6 +49,7 @@ bl.ukda: https://doi.org/10.17616/R3088K bmbf.hirzqt: https://doi.org/10.17616/R3CK9G brown.bdr: https://doi.org/10.17616/R3193B brvz.rdr: https://doi.org/10.17616/R31NJN5S +bvbw.dhbqgy: https://doi.org/10.17616/R3H35C caltech.data: https://doi.org/10.17616/R3SW99 carl.frdr: https://doi.org/10.17616/R3X50W cbg.datasets: https://doi.org/10.17616/R3PP7J @@ -90,6 +92,7 @@ dkrz.wdcc: https://doi.org/10.17616/R3989R dryad.dryad: https://doi.org/10.17616/R34S33 dzhw.fdz-dzhw: https://doi.org/10.17616/R3BR0G elsevier.md: https://doi.org/10.17616/R3DD11 +epua.rdcrki: https://doi.org/10.17616/R3K31G esdis.ornl: https://doi.org/10.17616/R3SG61 estdoi.keel: https://doi.org/10.17616/R3P636 estdoi.qdb: https://doi.org/10.17616/R31NJMVF @@ -131,8 +134,8 @@ gesis.dezim: https://doi.org/10.17616/R31NJMNK gesis.gesis: https://doi.org/10.17616/R3BB70 gesis.icpsr: https://doi.org/10.17616/R3BC8Q gesis.indepth: https://doi.org/10.17616/R3432T +gesis.iqb: https://doi.org/10.17616/R3M30D gesis.neps: https://doi.org/10.17616/R35P7W -gesis.rki: https://doi.org/10.17616/R3K31G gesis.share: https://doi.org/10.17616/R3BK5N gesis.sodanet: https://doi.org/10.17616/R38G7R gesis.srda: https://doi.org/10.17616/R31NJMLA @@ -141,6 +144,7 @@ gesis.zpid: https://doi.org/10.17616/R3FS48 hain.njltcl: https://doi.org/10.17616/R31NJNAM heliophy.spdf: https://doi.org/10.17616/R3P301 hlqc.znxeli: https://doi.org/10.17616/R31NJMJP +hyfx.gqlzxo: https://doi.org/10.17616/R31NJNDH ieee.dataport: https://doi.org/10.17616/R3H77H iiasa.dare: https://doi.org/10.17616/R31NJMH0 illinois.databank: https://doi.org/10.17616/R3C93F @@ -150,7 +154,7 @@ inist.humanum: https://doi.org/10.17616/R3JM1B inist.ifremer: https://doi.org/10.17616/R31NJMHX inist.ifsttar: https://doi.org/10.17616/R31NJMKM inist.ill: https://doi.org/10.17616/R33H18 -inist.inra: https://doi.org/10.17616/R3DJ4J +inist.osuna: https://doi.org/10.17616/R31NJNKA inist.otelo: https://doi.org/10.17616/R3F19K inist.resif: https://doi.org/10.17616/R37Q06 iris.iris: https://doi.org/10.17616/R3X607 @@ -161,6 +165,7 @@ jbru.bbees: https://doi.org/10.17616/R31NJNEN jcvi.eivbwb: https://doi.org/10.17616/R30P93 jcvi.gxpwaq: https://doi.org/10.17616/R3S634 kaggle.kaggle: https://doi.org/10.17616/R32N5V +kim.colabfit: https://doi.org/10.17616/R31NJNJL kim.openkim: https://doi.org/10.17616/R3SK8T kmot.rdr: https://doi.org/10.17616/R31NJMN6 ktsw.aezvvv: https://doi.org/10.17616/R31NJMVX @@ -173,6 +178,7 @@ mdw.repository: https://doi.org/10.17616/R30M00 mit.physio: https://doi.org/10.17616/R3D06S mlbs.skuxgs: https://doi.org/10.17616/R3ZP8D nasapds.nasapds: https://doi.org/10.17616/R37593 +nbqj.daks: https://doi.org/10.17616/R31NJMZS nkn.nkn: https://doi.org/10.17616/R3JK91 nlqq.xoncsf: https://doi.org/10.17616/R31NJMYB noaa.ncei: https://doi.org/10.17616/R3362J @@ -192,8 +198,15 @@ psu.datacom: https://doi.org/10.17616/R31NJMGV psu.scholar: https://doi.org/10.17616/R34W4H pu.dataspace: https://doi.org/10.17616/R33B6F purdue.purduelib: https://doi.org/10.17616/R3V90N +rdg.prod: https://doi.org/10.17616/R31NJN8R +repod.dbuw: https://doi.org/10.17616/R31NJNHR +repod.mxrdr: https://doi.org/10.17616/R31NJMYU +repod.rds: https://doi.org/10.17616/R31NJMYP rg.rg: https://doi.org/10.17616/R36H16 rice.kinder: https://doi.org/10.17616/R3GB90 +rpak.jpbpto: https://doi.org/10.17616/R31NJNLU +rpak.tjjamp: https://doi.org/10.17616/R31NJNLW +rpak.zvrzin: https://doi.org/10.17616/R31NJNLV sagebio.synapse: https://doi.org/10.17616/R3B934 si.cda: https://doi.org/10.17616/R3201S si.si: https://doi.org/10.17616/R3W49N @@ -224,9 +237,11 @@ tib.kit4radar: https://doi.org/10.17616/R31NJMVU tib.ldeo: https://doi.org/10.17616/R3PV10 tib.luis: https://doi.org/10.17616/R3C519 tib.radar: https://doi.org/10.17616/R3ZX96 +tib.repod: https://doi.org/10.17616/R3JS93 tib.tuhh: https://doi.org/10.17616/R31NJML0 tib.ub-hro: https://doi.org/10.17616/R31NJMQH tib.ubbs: https://doi.org/10.17616/R31NJMTU +tib.ubmr: https://doi.org/10.17616/R31NJMTD tib.ukon: https://doi.org/10.17616/R3M024 tib.zih: https://doi.org/10.17616/R31NJMHY tuw.tethys: https://doi.org/10.17616/R31NJMU0 @@ -237,7 +252,7 @@ umn.drum: https://doi.org/10.17616/R30D19 umn.ipums: https://doi.org/10.17616/R3ZS59 undr.undr: https://doi.org/10.17616/R31NJN9K unimelb.repo1: https://doi.org/10.17616/R3HH10 -unm.dataone: https://doi.org/10.17616/R3101G +unisalzb.anc: https://doi.org/10.17616/R31NJNKJ usda.usda: https://doi.org/10.17616/R3G051 usgs.prod: https://doi.org/10.17616/R33S3S uva.libra: https://doi.org/10.17616/R3TS86 diff --git a/fuji_server/helper/fuji_vocab_builder.py b/fuji_server/helper/fuji_vocab_builder.py new file mode 100644 index 00000000..b4b689aa --- /dev/null +++ b/fuji_server/helper/fuji_vocab_builder.py @@ -0,0 +1,415 @@ +# SPDX-FileCopyrightText: 2020 PANGAEA (https://www.pangaea.de/) +# +# SPDX-License-Identifier: MIT + +import json +import os + +from fuji_server.helper.identifier_helper import IdentifierHelper +from fuji_server.helper.linked_vocab_helper import LinkedVocabHelper +from fuji_server.helper.metadata_collector import ( + MetadataFormats, + MetadataOfferingMethods, + metadata_mapper, +) + + +class fuji_knowledge_base: + def __init__(self, root=""): + self.namespace = "https://f-uji.net/vocab" + self.vocabdict = { + self.namespace + "/metadata": { + "uri": self.namespace + "/metadata", + "label": "Metadata", + "description": "Everything about metadata", + "source": "f-uji.net", + }, + self.namespace + "/data": { + "uri": self.namespace + "/data", + "label": "Data", + "description": "Everything about data, usually the item(s) which is/are described by metadata", + "source": "f-uji.net", + }, + self.namespace + "/identifier": { + "uri": self.namespace + "/identifier", + "label": "Digital Identifier", + "description": "A name or identifier which identifies a digital object", + "source": "f-uji.net", + }, + self.namespace + "/access_condition": { + "uri": self.namespace + "/access_condition", + "label": "Access Conditions", + "description": "Information concerning the accessibility of resources, especially about existing restrictions.", + "source": "f-uji.net", + }, + } + self.root = root + base_path = os.path.abspath(os.path.dirname(__file__)) + self.fuji_data_path = os.path.join(base_path, "..", "data") + + def get_vocab_dict(self): + self.add_transport_protocol() + self.add_identifiers() + self.add_metadata_properties() + self.add_metadata_methods() + self.add_metadata_formats() + self.add_metadata_exchange_method() + self.add_metadata_standards() + self.add_semantic_resources() + self.add_licenses() + self.add_file_types() + self.add_data_properties() + self.add_access_rights() + return self.vocabdict + # self.add_metadata_methods('metadata/method') + + def add_transport_protocol(self): + parentkey = "transport_protocol" + prdict = {} + with open(os.path.join(self.fuji_data_path, "standard_uri_protocols.json"), encoding="utf-8") as acf: + protocol_dict = json.load(acf) + for protocolid, protocol in protocol_dict.items(): + prdict[self.namespace + "/" + parentkey + "/" + protocolid] = { + "label": protocol.get("name"), + "uri": self.namespace + "/" + parentkey + "/" + protocolid, + "broader": self.namespace + "/" + parentkey, + } + + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/transport_protocol", + "label": "Transport Protocol", + "description": "Transport protocols used to handle data or metadata ideally via the internet.", + "source": "f-uji.net", + } + self.vocabdict.update(prdict) + return prdict + + def add_access_rights(self): + parentkey = "access_condition" + ac_dict = {} + with open(os.path.join(self.fuji_data_path, "access_rights.json"), encoding="utf-8") as acf: + access_rights_dict = json.load(acf) + for access_source in access_rights_dict.values(): + ac_dict[self.namespace + "/" + parentkey + "/" + access_source.get("id")] = { + "label": access_source.get("label"), + "uri": self.namespace + "/" + parentkey + "/" + access_source.get("id"), + "identifier": access_source.get("identifier"), + "broader": self.namespace + "/" + parentkey, + "source": access_source.get("source"), + } + for access_info in access_source.get("members"): + ac_dict[ + self.namespace + "/" + parentkey + "/" + access_source.get("id") + "/" + access_info.get("id") + ] = { + "label": access_info.get("label"), + "uri": self.namespace + + "/" + + parentkey + + "/" + + access_source.get("id") + + "/" + + access_info.get("id"), + "identifier": {"value": access_info.get("uri"), "type": "homepage"}, + "broader": self.namespace + "/" + parentkey + "/" + access_source.get("id"), + "source": access_info.get("source"), + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Access Conditions", + "description": "Information concerning the accessibility of resources, especially about existing restrictions.", + "source": "f-uji.net", + } + self.vocabdict.update(ac_dict) + return ac_dict + + # serialisation: html, json, json-ld, rdf (ttl, n3), xml + def add_identifiers(self): + parentkey = "identifier/persistent" + id_dict = {} + identifiers = IdentifierHelper.VALID_PIDS + for idk, idv in identifiers.items(): + id_dict[self.namespace + "/" + parentkey + "/" + idk] = { + "label": idv.get("label"), + "uri": self.namespace + "/" + parentkey + "/" + idk, + "broader": self.namespace + "/" + parentkey, + "source": idv.get("source"), + } + + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Persistent Identifier", + "broader": self.namespace + "/identifier", + "source": "f-uji.net", + } + self.vocabdict.update(id_dict) + + def add_data_properties(self): + parentkey = "data/property/" + self.vocabdict[self.namespace + "/" + parentkey + "/size"] = { + "uri": self.namespace + "/" + parentkey, + "label": "Data (File) Size", + "broader": self.namespace + "/" + parentkey, + "source": "f-uji.net", + } + self.vocabdict[self.namespace + "/" + parentkey + "/url"] = { + "uri": self.namespace + "/" + parentkey, + "label": "Data (File) Identifier (URI)", + "broader": self.namespace + "/" + parentkey, + "source": "f-uji.net", + } + self.vocabdict[self.namespace + "/" + parentkey + "/type"] = { + "uri": self.namespace + "/" + "/data", + "alias": "url", + "label": "Data Type (Mime Type)", + "broader": self.namespace + "/data", + "narrower": self.namespace + "/data/format", + "source": "f-uji.net", + } + + def add_metadata_properties(self): + parentkey = "metadata/property" + properties_dict = {} + properties = metadata_mapper.Mapper.REFERENCE_METADATA_LIST.value + if properties: + for propkey, propvalue in properties.items(): + propvalue["source"] = "f-uji.net" + propvalue["uri"] = str(self.namespace) + "/" + parentkey + "/" + str(propkey) + propvalue["broader"] = self.namespace + "/" + parentkey + properties_dict[self.namespace + "/" + parentkey + "/" + propkey] = propvalue + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Metadata Property", + "description": "", + "broader": self.namespace + "/metadata", + "source": "f-uji.net", + } + self.vocabdict.update(properties_dict) + + def add_relation_types(self): + reltype_dict = {} + parentkey = "relation_type" + for rel in metadata_mapper.Mapper.DC_MAPPING.value.get("related_resources"): + reltype_dict[self.namespace + "/" + parentkey + "/" + rel] = { + "label": rel, + "broader": self.namespace + "/" + parentkey, + "uri": self.namespace + "/" + parentkey + "/" + rel, + "sameAs": "http://purl.org/dc/terms/" + rel, + "source": "dublincore.org", + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Relation Types", + "description": "Terms describing the type of relation between digital entities. This list is based on but not restricted to those defined by dublin core. Internally, relation types other than DC terms are mappred to dc terms", + "broader": self.namespace, + "source": "f-uji.net", + } + self.vocabdict.update(reltype_dict) + + def add_metadata_formats(self): + parentkey = "metadata/format" + metamethod_dict = {} + for method in MetadataFormats: + metamethod_dict[self.namespace + "/" + parentkey + "/" + method.acronym()] = { + "label": method.value.get("label"), + "broader": self.namespace + "/" + parentkey, + "uri": self.namespace + "/" + parentkey + "/" + method.acronym(), + "source": "f-uji.net", + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Metadata Format", + "description": "Formats in which metadata van be serialised such as XML, RDF etc.", + "broader": self.namespace + "/metadata", + "source": "f-uji.net", + } + self.vocabdict.update(metamethod_dict) + + def add_metadata_methods(self): + parentkey = "metadata/offering_method" + metamethod_dict = {} + for method in MetadataOfferingMethods: + metamethod_dict[self.namespace + "/" + parentkey + "/" + method.acronym()] = { + "label": method.value.get("label"), + "broader": self.namespace + "/" + parentkey, + "uri": self.namespace + "/" + parentkey + "/" + method.acronym(), + "source": "f-uji.net", + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Metadata Offering Method", + "description": "", + "broader": self.namespace + "/metadata", + "source": "f-uji.net", + } + self.vocabdict.update(metamethod_dict) + + def add_metadata_standards(self): + parentkey = "metadata/standard" + metastandards_dict = {} + with open(os.path.join(self.fuji_data_path, "metadata_standards.json")) as mdf: + mddict = json.load(mdf) + for mk, mv in mddict.items(): + mk = mk.replace(".yml", "") + sources = [] + identifiers = [] + for ident in mv.get("identifier"): + if ident.get("type") in ["namespace", "schema", "homepage"]: + identifiers.append(ident) + if ident.get("value"): + if "msc:" in ident.get("value"): + sources.append("rd-alliance.org") + elif "fairsharing.org" in ident.get("value"): + sources.append("fairsharing.org") + elif "www.dcc.ac" in ident.get("value"): + sources.append("dcc.ac") + metastandards_dict[self.namespace + "/" + parentkey + "/" + mk] = { + "label": mv.get("title"), + "uri": self.namespace + "/" + parentkey + "/" + mk, + "broader": self.namespace + "/" + parentkey, + "identifier": identifiers, + "field_of_science": mv.get("field_of_science"), + "source": sources, + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Metadata Standard", + "description": "", + "broader": self.namespace + "/metadata", + "source": "f-uji.net", + } + self.vocabdict.update(metastandards_dict) + + def add_semantic_resources(self): + parentkey = "semantic_resource" + semanticdict = {} + lov_helper = LinkedVocabHelper() + lov_helper.set_linked_vocab_dict() + linked_vocab_index = lov_helper.linked_vocab_dict + for lovk, lovv in linked_vocab_index.items(): + identifiers = [] + if lovv.get("uri_format"): + namespace = str(lovv.get("uri_format")).replace("$1", "") + identifiers.append({"type": "namespace", "value": namespace}) + if lovv.get("homepage"): + homepage = str(lovv.get("homepage")) + identifiers.append({"type": "homepage", "value": homepage}) + semanticdict[self.namespace + "/" + parentkey + "/" + lovk] = { + "uri": self.namespace + "/" + parentkey + "/" + lovk, + "broader": self.namespace + "/" + parentkey, + "label": lovv.get("name"), + "identifier": identifiers, + "source": lovv.get("source"), + "field_of_science": lovv.get("subjects"), + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Semantic Resource", + "description": "", + "source": "f-uji.net", + } + self.vocabdict.update(semanticdict) + + def add_licenses(self): + parentkey = "license" + license_dict = {} + with open(os.path.join(self.fuji_data_path, "licenses.json")) as lcd: + license_list = json.load(lcd) + for lic in license_list: + license_dict[self.namespace + "/" + parentkey + "/" + lic.get("licenseId")] = { + "uri": self.namespace + "/" + parentkey + "/" + lic.get("licenseId"), + "broader": self.namespace + "/" + parentkey, + "label": lic.get("name"), + "identifier": [ + { + "type": "homepage", + "value": str(lic.get("reference")).replace("./", "https://spdx.org/licenses/"), + }, + {"type": "schema", "value": lic.get("detailsUrl")}, + ], + "source": "spdx.org", + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "label": "Licenses", + "description": "", + "source": "f-uji.net", + } + self.vocabdict.update(license_dict) + + def add_metadata_exchange_method(self): + service_dict = { + self.namespace + "/metadata/exchange_service": { + "uri": self.namespace + "/metadata/exchange_service", + "label": "Metadata Exchange Service", + "description": "Standardised services which are used to exchange metadata between machines", + "source": "f-uji.net", + }, + self.namespace + "/metadata/exchange_service/oai_pmh": { + "uri": self.namespace + "/metadata/exchange_service/oai_pmh", + "label": "OAI-PMH", + "broader": self.namespace + "/metadata/exchange_service", + "description": "Open Archives Initiative Protocol for Metadata Harvesting", + "source": "f-uji.net", + }, + self.namespace + "/metadata/exchange_service/ogc_csw": { + "uri": self.namespace + "/metadata/exchange_service/ogc_csw", + "label": "OGC CSW", + "broader": self.namespace + "/metadata/exchange_service", + "description": "Catalogue Service for the Web", + "source": "f-uji.net", + }, + self.namespace + "/metadata/exchange_service/sparql": { + "uri": self.namespace + "/metadata/exchange_service/sparql", + "label": "SPARQL", + "broader": self.namespace + "/metadata/exchange_service", + "description": "SPARQL Protocol and RDF Query Language", + "source": "f-uji.net", + }, + } + self.vocabdict.update(service_dict) + + def add_file_types(self): + parentkey = "data/format" + filedict = {} + with open(os.path.join(self.fuji_data_path, "file_formats.json")) as lcd: + file_format_list = json.load(lcd) + for ffk, ffv in file_format_list.items(): + identifiers = [] + for mime in ffv.get("mime"): + identifiers.append({"type": "mime", "value": mime}) + filedict[self.namespace + "/" + parentkey + "/" + ffk] = { + "uri": self.namespace + "/" + parentkey + "/" + ffk, + "label": ffv.get("name"), + "broader": self.namespace + "/" + parentkey, + "identifier": identifiers, + "source": ffv.get("source"), + "type": ffv.get("reason"), + } + self.vocabdict[self.namespace + "/" + parentkey] = { + "uri": self.namespace + "/" + parentkey, + "broader": self.namespace + "/data", + "label": "Data Format", + "description": "", + "source": "f-uji.net", + } + self.vocabdict.update(filedict) + + +fb = fuji_knowledge_base() +vocabdir = "C:\\xampp\\htdocs\\fuji\\.vocab" +for tk, tv in fb.get_vocab_dict().items(): + print(tk.replace(fb.namespace, "")) + # if tv.get('broader'): + termid = tk.split("/")[-1] + termdir = vocabdir + "/".join(tk.split("/")[:-1]).replace(fb.namespace, "").replace("/", "\\") + print(termdir) + # termdir = vocabdir+tv.get('broader').replace(fb.namespace,'').replace('/','\\') + os.makedirs(termdir, exist_ok=True) + with open(termdir + "\\" + termid + ".json", "w") as termfile: + json.dump(tv, termfile) +# add_metadata_properties('metadata/property') +# fb.add_relation_types() +# print(fuji_vocab_dict) + +# print(add_licenses('metadata/licenses')) +# print(add_semantic_resources('metadata/licenses')) diff --git a/fuji_server/helper/fuji_vocab_helper.py b/fuji_server/helper/fuji_vocab_helper.py new file mode 100644 index 00000000..27e0d125 --- /dev/null +++ b/fuji_server/helper/fuji_vocab_helper.py @@ -0,0 +1,9 @@ +# SPDX-FileCopyrightText: 2020 PANGAEA (https://www.pangaea.de/) +# +# SPDX-License-Identifier: MIT + + +class fuji_term: + def __init__(self, term=None): + if term: + self.term = term diff --git a/fuji_server/yaml/metrics_v0.4.yaml b/fuji_server/yaml/metrics_v0.4.yaml index 08693071..98c2c1ca 100644 --- a/fuji_server/yaml/metrics_v0.4.yaml +++ b/fuji_server/yaml/metrics_v0.4.yaml @@ -125,7 +125,7 @@ metrics: evaluation_mechanism: The metric is evaluated using the given metadata standards known to support major search engines such as JSON-LD and Dublin Core. Presence of metadata in research data registries is further evaluated. metric_tests: - metric_test_identifier: FsF-F4-01M-1 - metric_test_name: Metadata is given in a way major search engines can ingest it for their catalogues (JSON-LD, Dublin Core, RDFa) + metric_test_name: Metadata is given in a way major search engines can ingest it for their catalogues (embedded JSON-LD, Dublin Core or RDFa) metric_test_score: 1 metric_test_maturity: 3 - metric_test_identifier: FsF-F4-01M-2 diff --git a/fuji_server/yaml/metrics_v0.6.yaml b/fuji_server/yaml/metrics_v0.6.yaml new file mode 100644 index 00000000..ed4eea80 --- /dev/null +++ b/fuji_server/yaml/metrics_v0.6.yaml @@ -0,0 +1,674 @@ +# LIST OF FAIRSFAIR METRICS AND THEIR RESPONSE OUTPUT FORMATS +config: + metric_specification: https://doi.org/10.5281/zenodo.4081213 + metric_status: draft +metrics: + ## ---------------- FINDABILITY ---------------- ## +- metric_identifier: FsF-F1-01M + metric_number: 1 + metric_short_name: Unique Identifier Metadata + metric_name: Metadata is assigned a globally unique identifier. + description: A globally unique identifier may be assigned to a landing page containing metadata or a metadata file such that it can be referenced unambiguously by humans or machines. Globally unique means an identifier should be associated with only one resource at any time. Examples of unique identifiers are Internationalized Resource Identifier (IRI), Uniform Resource Identifier (URI) such as URL and URN, Digital Object Identifier (DOI), the Handle System, identifiers.org, w3id.org and Archival Resource Key (ARK). A data repository may assign a globally unique identifier to your metadata when you publish and make it available through their services. + fair_principle: F1 + target: Metadata or Landingpage + evaluation_mechanism: Identifier is considered unique if it is successfully validated through https://pythonhosted.org/IDUtils/. Supported schemes are ISBN10, ISBN13, ISSN, ISTC, DOI, Handle, EAN8, EAN13, ISNI ORCID, ARK, PURL, LSID, URN, Bibcode, arXiv, PubMed ID, PubMed Central ID, GND. + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-F1-01M-1 + metric_test_name: Identifier is resolvable and follows a defined unique identifier syntax (IRI, URL) + metric_test_score: 1 + metric_test_maturity: 3 + metric_test_requirements: + - target: https://f-uji.net/vocab/identifier + tested_on: https://f-uji.net/vocab/metadata/property/object_identifier + modality: any + comment: identifier can be given as user input + - metric_test_identifier: FsF-F1-01M-2 + metric_test_name: Identifier is not resolvable but follows an UUID or HASH type syntax + metric_test_score: 0.5 + metric_test_maturity: 1 + metric_test_requirements: + - target: https://f-uji.net/vocab/identifier/unique + tested_on: https://f-uji.net/vocab/metadata/property/object_identifier + modality: any + required: + name: + - uuid + - hash + comment: identifier can be given as user input + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-11-25 + version: 0.6 + total_score: 1 + +- metric_identifier: FsF-F1-02M + metric_number: 2 + metric_short_name: Persistent Identifier Metadata + metric_name: Data is assigned a persistent identifier. + description: We make a distinction between the uniqueness and persistence of an identifier. An HTTP URL (the address of a given unique resource on the web) is globally unique, but may not be persistent as the URL of data may be not accessible (link rot problem) or the data available under the original URL may be changed (content drift problem). Identifiers based on the Handle System, DOI, ARK are both globally unique and persistent. They are maintained and governed such that they remain stable and resolvable for the long term. The persistent identifier (PID) of a data object may be resolved (point) to a landing page with metadata containing further information on how to access the data content, in some cases a downloadable artefact, or none if the data or repository is no longer maintained. Therefore, ensuring persistence is a shared responsibility between a PID service provider (e.g., datacite) and its clients (e.g., data repositories). For example, the DOI system guarantees the persistence of its identifiers through its social (e.g., policy) and technical infrastructures, whereas a data provider ensures the availability of the resource (e.g., landing page, downloadable artefact) associated with the identifier. + fair_principle: F1 + target: Data + evaluation_mechanism: A persistent identifier is considered to be valid if the given identifier complies with a valid PID synthax. To be valid, the PID further has to be resolvable. + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-F1-02M-1 + metric_test_name: Identifier follows a defined persistent identifier syntax + metric_test_score: 0.5 + metric_test_maturity: 1 + metric_test_requirements: + - target: https://f-uji.net/vocab/identifier/persistent + tested_on: https://f-uji.net/vocab/metadata/property/object_identifier + modality: any + comment: identifier can be given as user input + - metric_test_identifier: FsF-F1-02M-2 + metric_test_name: Persistent identifier is resolvable + metric_test_requirements: + - target: https://f-uji.net/vocab/identifier/persistent + tested_on: https://f-uji.net/vocab/metadata/property/object_identifier + comment: identifier has to resolve to a valid URI + metric_test_score: 0.25 + metric_test_maturity: 2 + - metric_test_identifier: FsF-F1-02M-3 + metric_test_name: Persistent identifier resolves to a page which belongs to the issuer's domain + metric_test_requirements: + - target: https://f-uji.net/vocab/identifier/persistent + tested_on: https://f-uji.net/vocab/metadata/property/object_identifier + comment: identifier has to resolve to a domain owned by the issuer, e.g. PIDs listed in a landing page metadata record should point back to that landing page + metric_test_score: 0.25 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-11-25 + version: 0.6 + total_score: 1 + +- metric_identifier: FsF-F1-01DD + metric_number: 1 + metric_short_name: Unique Identifier Data + metric_name: Data is assigned a globally unique identifier. + description: A globally unique identifier may be assigned to data such as a data file such that it can be referenced unambiguously by humans or machines. Globally unique means an identifier should be associated with only one resource at any time. Examples of unique identifiers are Internationalized Resource Identifier (IRI), Uniform Resource Identifier (URI) such as URL and URN, Digital Object Identifier (DOI), the Handle System, identifiers.org, w3id.org and Archival Resource Key (ARK). A data repository may assign a globally unique identifier to your data files when you publish and make it available through their services. + fair_principle: F1 + target: Data + evaluation_mechanism: Data identifier is considered unique if it is successfully validated through https://pythonhosted.org/IDUtils/. Supported schemes are ISBN10, ISBN13, ISSN, ISTC, DOI, Handle, EAN8, EAN13, ISNI ORCID, ARK, PURL, LSID, URN, Bibcode, arXiv, PubMed ID, PubMed Central ID, GND. + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-F1-01DD-1 + metric_test_name: Data identifier is resolvable and follows a defined unique identifier syntax (IRI, URL) + metric_test_score: 1 + metric_test_maturity: 3 + - metric_test_identifier: FsF-F1-01DD-2 + metric_test_name: Data identifier is not resolvable but follows an UUID or HASH type syntax + metric_test_score: 0.5 + metric_test_maturity: 1 + created_by: FAIRsFAIR + date_created: 2023-05-15 + date_updated: 2023-05-15 + version: 0.6 + total_score: 1 + +- metric_identifier: FsF-F1-02DD + metric_number: 4 + metric_short_name: Persistent Identifier Data + metric_name: Data is assigned a persistent identifier. + description: We make a distinction between data and metadata as well as the uniqueness and persistence of an identifier as explained in FsF-F1-02M. The persistent identifier (PID) of a data may point to a file or streaming object or a service providing that data. + fair_principle: F1 + target: Data + evaluation_mechanism: A persistent identifier is considered to be valid if the given identifier complies with a valid PID synthax. To be valid, the PID further has to be resolvable. + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-F1-02DD-1 + metric_test_name: A data identifier follows a defined persistent identifier syntax + metric_test_score: 0.5 + metric_test_maturity: 1 + metric_test_requirements: + - target: https://f-uji.net/vocab/identifier/persistent + tested_on: https://f-uji.net/vocab/metadata/property/object_identifier + modality: any + - metric_test_identifier: FsF-F1-02DD-2 + metric_test_name: A persistent identifier of data is resolvable + metric_test_score: 1 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2023-05-15 + date_updated: 2023-05-15 + version: 0.6 + total_score: 1 + +- metric_identifier: FsF-F2-01M + metric_number: 3 + metric_short_name: Descriptive Core Metadata + metric_name: Metadata includes descriptive core elements (creator, title, data identifier, publisher, publication date, summary and keywords) to support data findability. + description: Metadata is descriptive information about a data object. Since the metadata required differs depending on the users and their applications, this metric focuses on core metadata. The core metadata is the minimum descriptive information required to enable data finding, including citation which makes it easier to find data. We determine the required metadata based on common data citation guidelines (e.g., DataCite, ESIP, and IASSIST), and metadata recommendations for data discovery (e.g., EOSC Datasets Minimum Information (EDMI), DataCite Metadata Schema, W3C Recommendation Data on the Web Best Practices and Data Catalog Vocabulary). This metric focuses on domain-agnostic core metadata. Domain or discipline-specific metadata specifications are covered under metric FsF-R1.3-01M. A repository should adopt a schema that includes properties of core metadata, whereas data authors should take the responsibility of providing core metadata. + fair_principle: F2 + target: Metadata + evaluation_mechanism: Metadata can be offered in different ways. here we focus on common web based strategies. These include 1) embedding metadata within the landing page such as JSON-LD, OpenGraph, Microdata, Dublin Core, 2) offering typed links which lead to metadata within the HTML code of the metadata or signposting links. 3) enable content negotiation and deliver e.g. RDF, JSON-LD or XML on demand. The metric evaluates the completeness of metadata in case metadata has been retrieved. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-F2-01M-1 + metric_test_name: Metadata has been made available via common web methods + metric_test_score: 0.5 + metric_test_maturity: 1 + metric_test_requirements: + - target: https://f-uji.net/vocab/metadata/offering_method + modality: any + - metric_test_identifier: FsF-F2-01M-2 + metric_test_name: Core data citation metadata is available + metric_test_score: 0.5 + metric_test_maturity: 2 + metric_test_requirements: + - target: https://f-uji.net/vocab/metadata/property + modality: all + tested_on: https://f-uji.net/vocab/metadata/property + required: + name: + - creator + - title + - object_identifier + - publication_date + - publisher + - object_type + - metric_test_identifier: FsF-F2-01M-3 + metric_test_name: Core descriptive metadata is available + metric_test_score: 1 + metric_test_maturity: 3 + metric_test_requirements: + - target: https://f-uji.net/vocab/metadata/property + modality: all + tested_on: https://f-uji.net/vocab/metadata/property + required: + name: + - creator + - title + - object_identifier + - publication_date + - publisher + - object_type + - summary + - keywords + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2022-05-30 + version: 0.5 + total_score: 2 + +- metric_identifier: FsF-F3-01M + metric_number: 4 + metric_short_name: Inclusion of Data Identifier in Metadata + metric_name: Metadata includes the identifier of the data it describes. + description: The metadata should explicitly specify the identifier of the data such that users can discover and access the data through the metadata. If the identifier specified is persistent and points to a landing page, the data identifier and links to download the data content should be taken into account in the assessment. + fair_principle: F3 + target: Metadata + evaluation_mechanism: Several metadata standards provide the possibility to include links to the actual data content. The presence of such links is evaluated here. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-F3-01M-1 + metric_test_name: Metadata contains data content related information (file name, size, type) + metric_test_score: 0.5 + metric_test_maturity: 1 + metric_test_requirements: + - target: https://f-uji.net/vocab/data/property + tested_on: https://f-uji.net/vocab/metadata/property/object_content_identifier + modality: all + required: + - type + - size + - metric_test_identifier: FsF-F3-01M-2 + metric_test_name: Metadata contains a PID or URL which indicates the location of the downloadable data content + metric_test_score: 0.5 + metric_test_maturity: 3 + metric_test_requirements: + - target: https://f-uji.net/vocab/data/property/url + tested_on: https://f-uji.net/vocab/metadata/property/object_content_identifier + modality: any + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2022-05-30 + version: 0.5 + total_score: 1 + +- metric_identifier: FsF-F4-01M + metric_number: 5 + metric_short_name: Searchable Metadata + metric_name: Metadata is offered in such a way that it can be retrieved programmatically. + description: This metric refers to ways through which the metadata of data is exposed or provided in a standard and machine-readable format. Assessing this metric will require an understanding of the capabilities offered by the data repository used to host the data. Metadata may be available through multiple endpoints. For example, if data is hosted by a repository, the repository may disseminate its metadata through a metadata harvesting protocol (e.g., via OAI-PMH) and/or a web service. Metadata may also be embedded as structured data on a data page for use by web search engines such as Google and Bing or be available as linked (open) data. + fair_principle: F4 + target: Metadata + evaluation_mechanism: The metric is evaluated using the given metadata standards known to support major search engines such as JSON-LD and Dublin Core. Presence of metadata in research data registries is further evaluated. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-F4-01M-1 + metric_test_name: Metadata is given in a way major search engines can ingest it for their catalogues (embedded JSON-LD, Dublin Core or RDFa) + metric_test_score: 1 + metric_test_maturity: 3 + metric_test_requirements: + - target: http://f-uji.net/vocab/metadata/standard + modality: any + required: + name: + - dublin-core + - schemaorg + - dcat-data-catalog-vocabulary + - target: http://f-uji.net/vocab/metadata/offering_method + modality: any + required: + name: + - rdfa + - microdata + - meta_tag + - json_in_html + - metric_test_identifier: FsF-F4-01M-2 + metric_test_name: Metadata is registered in major research data registries (DataCite) + metric_test_score: 1 + metric_test_maturity: 2 + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2022-05-30 + version: 0.5 + total_score: 2 + +- metric_identifier: FsF-A1-01M + metric_number: 6 + metric_short_name: Data Access Information + metric_name: Metadata contains access level and access conditions of the data. + description: This metric determines if the metadata includes the level of access to the data such as public, embargoed, restricted, or metadata-only access and its access conditions. Both access level and conditions are necessary information to potentially gain access to the data. It is recommended that data should be as open as possible and as closed as necessary. There are no access conditions for public data. Datasets should be released into the public domain (e.g., with an appropriate public-domain-equivalent license such as Creative Commons CC0 licence) and openly accessible without restrictions when possible. Embargoed access refers to data that will be made publicly accessible at a specific date which should be specified in the metadata. For example, a data author may release their data after having published their findings from the data. Therefore, access conditions such as the date the data will be released publically is essential. Restricted access refers to data that can be accessed under certain conditions (e.g. because of commercial, sensitive, or other confidentiality reasons or the data is only accessible via a subscription or a fee). Restricted data may be available to a particular group of users or after permission is granted. For restricted data, the metadata should include the conditions of access to the data such as point of contact or instructions to access the data. Metadata-only access refers to data that is not made publicly available and for which only metadata is publicly available. + fair_principle: A1 + target: Metadata + evaluation_mechanism: Metric evaluation is based on the presence of access information in an appropriate metadata element/field. + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-A1-01M-1 + metric_test_name: Information about access restrictions or rights can be identified in metadata + metric_test_score: 0.5 + metric_test_maturity: 1 + metric_test_requirements: + - target: http://f-uji.net/vocab/metadata/property/access_level + modality: any + - metric_test_identifier: FsF-A1-01M-3 + metric_test_name: Data access information is indicated by (not machine readable) standard terms + metric_test_score: 1 + metric_test_maturity: 2 + metric_test_requirements: + - target: http://f-uji.net/vocab/access_condition + modality: any + tested_on: http://f-uji.net/vocab/metadata/property/access_level + comment: label and id + - metric_test_identifier: FsF-A1-01M-2 + metric_test_name: Data access information is machine readable + metric_test_score: 1 + metric_test_maturity: 3 + metric_test_requirements: + - target: http://f-uji.net/vocab/access_condition + modality: any + tested_on: http://f-uji.net/vocab/metadata/property/access_level + comment: identifier (namespace) + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-12-03 + version: 0.5 + total_score: 1 + +- metric_identifier: FsF-A1-03D + metric_number: 8 + metric_short_name: Standardized Communication Protocol of Data + metric_name: Data is accessible through a standardized communication protocol. + description: Given an identifier of a dataset, the dataset should be retrievable using a standard communication protocol such as HTTP, HTTPS, FTP, TFTP, SFTP, FTAM and AtomPub. Avoid disseminating data using a proprietary protocol. + fair_principle: A1 + target: Data + evaluation_mechanism: The data link which is given in the metadata is tested for an standard communication protocol + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-A1-03D-1 + metric_test_name: Metadata includes a resolvable link to data based on standardized web communication protocols. + metric_test_score: 1 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-10-23 + date_updated: 2020-12-05 + version: 0.5 + total_score: 1 + +- metric_identifier: FsF-A1-02M + metric_number: 7 + metric_short_name: Standardized Communication Protocol of Metadata + metric_name: Metadata is accessible through a standardized communication protocol. + description: Given an identifier of a dataset, the metadata of the dataset should be retrievable using a standard communication protocol such as HTTP, HTTPS, FTP, TFTP, SFTP, FTAM and AtomPub. Avoid disseminating data using a proprietary protocol. + fair_principle: A1 + target: Metadata + evaluation_mechanism: The URI scheme of the landing page is tested for a standard communication protocol + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-A1-02M-1 + metric_test_name: Landing page link is based on standardized web communication protocols. + metric_test_score: 1 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-10-23 + date_updated: 2020-12-05 + version: 0.5 + total_score: 1 + +#- metric_identifier: FsF-A2-01M +# metric_number: 9 +# metric_short_name: Metadata Preservation +# metric_name: Metadata remains available, even if the data is no longer available. +# description: This metric determines if the metadata will be preserved even when the data they represent are no longer available, replaced or lost. +# fair_principle: A2 +# target: Metadata +# evaluation_mechanism: Currently this metric can only be assessed using the persistent identifier as an indicator. DOI metadata is preserved by DataCite. +# metric_tests: +# - metric_test_identifier: FsF-A2-01M-1 +# metric_test_name: The persistent identifier system used guarantees the preservation of associated metadata +# metric_test_score: 1 +# metric_test_maturity: 3 +# created_by: FAIRsFAIR +# date_created: 2020-07-08 +# date_updated: 2020-12-05 +# version: 0.5 +# total_score: 1 + +- metric_identifier: FsF-I1-01M + metric_number: 10 + metric_short_name: Formal Representation of Metadata + metric_name: Metadata is represented using a formal knowledge representation language. + description: Knowledge representation is vital for machine-processing of the knowledge of a domain. Expressing the metadata of a data object using a formal knowledge representation will enable machines to process it in a meaningful way and enable more data exchange possibilities. Examples of knowledge representation languages are RDF, RDFS, and OWL. These languages may be serialized (written) in different formats. For instance, RDF/XML, RDFa, Notation3, Turtle, N-Triples and N-Quads, and JSON-LD are RDF serialization formats. + fair_principle: I1 + target: Metadata + evaluation_mechanism: Metadata has to be serialised in a common formal knowledge representation language. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-I1-01M-1 + metric_test_name: Parsable, structured metadata (JSON-LD, RDFa) is embedded in the landing page XHTML/HTML code + metric_test_score: 1 + metric_test_maturity: 2 + metric_test_requirements: + - target: http://f-uji.net/vocab/metadata/format + modality: any + required: + name: + - RDF + - JSON-LD + - RDFa + - target: http://f-uji.net/vocab/metadata/offering_method + modality: any + required: + name: + - meta_tag + - microdata + - rdfa + - json_in_html + - metric_test_identifier: FsF-I1-01M-2 + metric_test_name: Parsable, graph data (RDF, JSON-LD) is accessible through content negotiation, typed links or sparql endpoint + metric_test_score: 1 + metric_test_maturity: 3 + metric_test_requirements: + - target: http://f-uji.net/vocab/metadata/format + modality: any + required: + name: + - RDF + - JSON-LD + - RDFa + - target: http://f-uji.net/vocab/metadata/offering_method + modality: any + required: + name: + - content_negotiation + - target: http://f-uji.net/vocab/metadata/exchange_service + modality: any + required: + name: + - sparql + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2023-06-01 + version: 0.5 + total_score: 2 + +- metric_identifier: FsF-I2-01M + metric_number: 11 + metric_short_name: Metadata with Semantic Resources + metric_name: Metadata uses semantic resources + description: A metadata document or selected parts of the document may incorporate additional terms from semantic resources (also referred as semantic artefacts) so that the contents are unambiguous and can be processed automatically by machines. This enrichment facilitates enhanced data search and interoperability of data from different sources. Ontology, thesaurus, and taxonomy are kinds of semantic resources, and they come with varying degrees of expressiveness and computational complexity. Knowledge organization schemes such as thesaurus and taxonomy are semantically less formal than ontologies. + fair_principle: I2 + target: Metadata + evaluation_mechanism: Used namespaces are identified in given graph or XML metadata and verified using a controlled list. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-I2-01M-1 + metric_test_name: Vocabulary namespace URIs can be identified in metadata + metric_test_score: 0 + metric_test_maturity: 1 + metric_test_requirements: + - comment: The sheer existence of namespaces declared in XML or RDF files is checked here. This test is not scored + - metric_test_identifier: FsF-I2-01M-2 + metric_test_name: Namespaces of known semantic resources can be identified in metadata + metric_test_score: 1 + metric_test_maturity: 3 + metric_test_requirements: + - target: http://f-uji.net/vocab/semantic_resource + modality: any + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-12-03 + version: 0.5 + total_score: 1 + +- metric_identifier: FsF-I3-01M + metric_number: 12 + metric_short_name: Links to related entities + metric_name: Metadata includes links between the data and its related entities. + description: Linking data to its related entities will increase its potential for reuse. The linking information should be captured as part of the metadata. A dataset may be linked to its prior version, related datasets or resources (e.g. publication, physical sample, funder, repository, platform, site, or observing network registries). Links between data and its related entities should be expressed through relation types (e.g., DataCite Metadata Schema specifies relation types between research objects through the fields ‘RelatedIdentifier’ and ‘RelationType’), and preferably use persistent Identifiers for related entities (e.g., ORCID for contributors, DOI for publications, and ROR for institutions). + fair_principle: I3 + target: Metadata + evaluation_mechanism: Metadata is checked for existing relations to related entities which can be e.g. citations or other related resources + metric_tests: + - metric_test_identifier: FsF-I3-01M-1 + metric_test_name: Related resources are explicitly mentioned in metadata + metric_test_score: 1 + metric_test_maturity: 2 + metric_test_requirements: + - target: http://f-uji.net/vocab/relation_type + modality: any + tested_on: http://f-uji.net/vocab/metadata/property/related_resources + comment: The presence of a (typed, default = related) related resource is checked, can be a string or URI + - metric_test_identifier: FsF-I3-01M-2 + metric_test_name: Related resources are indicated by machine readable links or identifiers + metric_test_requirements: + - comment: same as above but relations have to be machine readable/actionable + metric_test_score: 1 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-12-03 + version: 0.5 + total_score: 1 + +- metric_identifier: FsF-R1-01MD + metric_number: 13 + metric_short_name: Metadata of Data Content + metric_name: Metadata specifies the content of the data. + description: This metric evaluates if a description (properties) of the content of the data is specified in the metadata. The description should be an accurate reflection of the actual data deposited. Data content descriptors include but are not limited to resource type (e.g., data or a collection of data), variable(s) measured or observed, method, data format and size. Ideally, ontological vocabularies should be used to describe data content to support interdisciplinary reuse. + fair_principle: R1 + target: Metadata, Data + evaluation_mechanism: Metric is evaluated using the resource type given in the metadata as well as data object specific properties file size and file type. Further presence of measured variables is tested. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-R1-01MD-1_ss + metric_test_name: Minimal information about available data content is given in metadata + metric_test_score: 1 + metric_test_maturity: 1 + - metric_test_identifier: FsF-R1-01MD-1a + metric_test_name: Resource type (e.g. dataset) is given in metadata + metric_test_score: 0 + - metric_test_identifier: FsF-R1-01MD-1b + metric_test_name: Information about data content (e.g. links) is given in metadata + metric_test_score: 0 + - metric_test_identifier: FsF-R1-01MD-2 + metric_test_name: Verifiable data descriptors (file info, measured variables or observation types) are specified in metadata + metric_test_score: 1 + metric_test_maturity: 2 + - metric_test_identifier: FsF-R1-01MD-2a + metric_test_name: File size and type information are specified in metadata + metric_test_score: 0 + - metric_test_identifier: FsF-R1-01MD-2b + metric_test_name: Measured variables or observation types are specified in metadata + metric_test_score: 0 + - metric_test_identifier: FsF-R1-01MD-3 + metric_test_name: Data content matches file type and size specified in metadata + metric_test_score: 1 + metric_test_maturity: 3 + - metric_test_identifier: FsF-R1-01MD-4 + metric_test_name: Data content matches measured variables or observation types specified in metadata + metric_test_score: 1 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-07-08 + version: 0.5 + total_score: 4 + +- metric_identifier: FsF-R1.1-01M + metric_number: 14 + metric_short_name: Data Usage License + metric_name: Metadata includes license information under which data can be reused. + description: This metric evaluates if data is associated with a license because otherwise users cannot reuse it in a clear legal context. We encourage the application of licenses for all kinds of data whether public, restricted or for specific users. Without an explicit license, users do not have a clear idea of what can be done with your data. Licenses can be of standard type (Creative Commons, Open Data Commons Open Database License) or bespoke licenses, and rights statements which indicate the conditions under which data can be reused. It is highly recommended to use a standard, machine-readable license such that it can be interpreted by machines and humans. In order to inform users about what rights they have to use a dataset, the license information should be specified as part of the dataset’s metadata. + fair_principle: R1.1 + target: Metadata + evaluation_mechanism: Metric evaluation is based on the presence of a machine readable license information in an appropriate metadata element/field. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-R1.1-01M-1 + metric_test_name: Licence information is given in an appropriate metadata element + metric_test_score: 1 + metric_test_maturity: 1 + - metric_test_identifier: FsF-R1.1-01M-2 + metric_test_name: Recognized licence is valid (community specific or registered at SPDX) + metric_test_score: 1 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2023-06-02 + version: 0.5 + total_score: 2 + +- metric_identifier: FsF-R1.2-01M + metric_number: 15 + metric_short_name: Data Provenance + metric_name: Metadata includes provenance information about data creation or generation. + description: >- + Data provenance (also known as lineage) represents a dataset’s history, including the people, entities, and processes involved in its creation, management and longer-term curation. It is essential to provide provenance information about your data to provide valuable context and to enable informed use and reuse. The levels of provenance information needed can vary depending on the data type (e.g., measurement, observation, derived data, or data product) and research domains. For that reason, it is difficult to define a set of finite provenance properties that will be adequate for all domains. Based on existing work, we suggest that the following provenance properties of data generation or collection are included in the metadata record as a minimum. + (a) Sources of data, e.g., datasets the data is derived from and instruments + (b) Data creation or collection date + (c) Contributors involved in data creation and their roles + (d) Data publication, modification and versioning information + There are various ways through which provenance information may be included in a metadata record. Some of the provenance properties (e.g., instrument, contributor) may be best represented using PIDs (such as DOIs for data, ORCIDs for researchers). + This way, humans and systems can retrieve more information about each of the properties by resolving the PIDs. Alternatively, the provenance information can be given in a linked provenance record expressed explicitly in e.g., PROV-O or PAV or Vocabulary of Interlinked Datasets (VoID). + fair_principle: R1.2 + target: Metadata + evaluation_mechanism: Metrics are assessed using provenance related information contained in metadata which can either be specific elements which can be mapped e.g. to PROV-O or the use of provenance related namespaces and associated terms. + test_scoring_mechanism: cumulative + metric_tests: + - metric_test_identifier: FsF-R1.2-01M-1 + metric_test_name: Metadata contains elements which hold provenance information and can be mapped to PROV + metric_test_score: 1 + metric_test_maturity: 2 + - metric_test_identifier: FsF-R1.2-01M-2 + metric_test_name: Metadata contains provenance information using formal provenance ontologies (PROV-O) + metric_test_score: 1 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2023-06-01 + version: 0.5 + total_score: 2 + +- metric_identifier: FsF-R1.3-01M + metric_number: 16 + metric_short_name: Community-Endorsed Metadata Standard + metric_name: Metadata follows a standard recommended by the target research community of the data. + description: In addition to core metadata required to support data discovery (covered under metric FsF-F2-01M), metadata to support data reusability should be made available following community-endorsed metadata standards. Some communities have well-established metadata standards (e.g., geospatial [ISO19115], biodiversity [DarwinCore, ABCD, EML], social science [DDI], astronomy [International Virtual Observatory Alliance Technical Specifications]) while others have limited standards or standards that are under development (e.g., engineering and linguistics). The use of community-endorsed metadata standards is usually encouraged and supported by domain and discipline-specific repositories. + fair_principle: R1.3 + target: Metadata + evaluation_mechanism: Metadata encodings can be verified using community specific namespaces and schemas listed by the RDA metadata standards WG or fairsharing.org + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-R1.3-01M-1 + metric_test_name: Community specific metadata standard is detected using namespaces or schemas found in provided metadata or metadata services outputs + metric_test_score: 1 + metric_test_maturity: 3 + metric_test_requirements: + - modality: any except + target: https://f-uji.net/vocab/metadata/standards + required: + field_of_science: + - science + - generic + comment: test performed on namespaces or schemas found in exposed metadata + - metric_test_identifier: FsF-R1.3-01M-2 + metric_test_name: Community specific metadata standard is listed in the re3data record of the responsible repository + metric_test_score: 1 + metric_test_maturity: 2 + metric_test_requirements: + - modality: any except + target: https://f-uji.net/vocab/metadata/standards + required: + field_of_science: + - science + - generic + comment: test is performed using information collected from re3data + - metric_test_identifier: FsF-R1.3-01M-3 + metric_test_name: Multidisciplinary but community endorsed metadata (RDA Metadata Standards Catalog, fairsharing) standard is listed in the re3data record or detected by namespace + metric_test_score: 1 + metric_test_maturity: 1 + metric_test_requirements: + - modality: any + target: https://f-uji.net/vocab/metadata/standards + required: + field_of_science: + - science + - generic + source: + - rd-alliance.org + - fairsharing.org + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-12-03 + version: 0.5 + total_score: 1 + +- metric_identifier: FsF-R1.3-02D + metric_number: 17 + metric_short_name: Data File format + metric_name: Data is available in a file format recommended by the target research community. + description: >- + File formats refer to methods for encoding digital information. For example, CSV for tabular data, NetCDF for multidimensional data and GeoTIFF for raster imagery. Data should be made available in a file format that is backed by the research community to enable data sharing and reuse. Consider for example, file formats that are widely used and supported by the most commonly used software and tools. These formats also should be suitable for long-term storage and archiving, which are usually recommended by a data repository. The formats not only give a higher certainty that your data can be read in the future, but they will also help to increase the reusability and interoperability. Using community-endorsed formats enables data to be loaded directly into the software and tools used for data analysis. It makes it possible to easily integrate your data with other data using the same preferred format. The use of preferred formats will also help to transform the format to a newer one, in case a preferred format gets outdated. + Similar to metric FsF-F4-01M, answering this metric will require an understanding of the capabilities offered, data preservation plan and policies implemented by the data repository and data services (e.g., Datacite PID service). + Continued access to metadata depends on a data repository’s preservation practice which is usually documented in the repository’s service policies or statements. + A trustworthy data repository offering DOIs and implementing a PID Policy should guarantee that metadata will remain accessible even when data is no longer available for any reason (e.g., by providing a tombstone page). + fair_principle: R1.3 + target: Data + evaluation_mechanism: Data file format given in metadata is compared to a controlled list of known scientific formats. + test_scoring_mechanism: alternative + metric_tests: + - metric_test_identifier: FsF-R1.3-02D-1 + metric_test_name: The format of a data file given in the metadata is listed in the long term file formats, open file formats or scientific file formats controlled list + metric_test_score: 1 + - metric_test_identifier: FsF-R1.3-02D-1a + metric_test_name: The format of the data file is an open format + metric_test_score: 0 + metric_test_maturity: 1 + - metric_test_identifier: FsF-R1.3-02D-1b + metric_test_name: The format of the data file is a long term format + metric_test_score: 0 + metric_test_maturity: 2 + - metric_test_identifier: FsF-R1.3-02D-1c + metric_test_name: The format of the data file is a scientific format + metric_test_score: 0 + metric_test_maturity: 3 + created_by: FAIRsFAIR + date_created: 2020-07-08 + date_updated: 2020-12-03 + version: 0.5 + total_score: 1 + metric_specification: 10.5281/zenodo.6461229